diff --git a/DESCRIPTION b/DESCRIPTION index 682699d..cdf6c35 100755 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -71,6 +71,7 @@ Imports: gtable (>= 0.3.1), digest (>= 0.6.29), png, + ggExtra, httr, jsonlite, plyr, diff --git a/NAMESPACE b/NAMESPACE index 5168a76..ce7814a 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -30,6 +30,7 @@ import(cowplot) import(data.table) import(dplyr) import(gdata) +import(ggExtra) import(ggplot2) import(ggpubr) import(ggrepel) @@ -49,6 +50,7 @@ import(tools) import(utils) importFrom(ComplexHeatmap,pheatmap) importFrom(RColorBrewer,brewer.pal) +importFrom(RColorBrewer,brewer.pal.info) importFrom(Seurat,AddMetaData) importFrom(Seurat,CreateAssayObject) importFrom(Seurat,DotPlot) @@ -66,10 +68,14 @@ importFrom(dplyr,across) importFrom(dplyr,all_of) importFrom(dplyr,arrange) importFrom(dplyr,case_when) +importFrom(dplyr,desc) importFrom(dplyr,filter) +importFrom(dplyr,if_else) importFrom(dplyr,mutate) importFrom(dplyr,mutate_if) importFrom(dplyr,pull) +importFrom(dplyr,relocate) +importFrom(dplyr,row_number) importFrom(dplyr,select) importFrom(dplyr,summarise) importFrom(ggplot2,aes) diff --git a/R/Combine_and_Normalize.R b/R/Combine_and_Normalize.R index c684849..3e60a74 100755 --- a/R/Combine_and_Normalize.R +++ b/R/Combine_and_Normalize.R @@ -32,9 +32,6 @@ #' Options: vst, mean.var.plot, dispersion. (Default: 'vst') #' @param draw.umap If TRUE, draw UMAP plot. (Default: TRUE) #' @param draw.tsne If TRUE, draw TSNE plot. (Default: TRUE) -#' @param only.var.genes If dataset is larger than ~40k filtered cells, -#' set to TRUE. If TRUE, only variable genes will be available for -#' downstream analysis. (Default: FALSE) #' @param seed.for.pca Set a random seed for PCA calculation. (Default: 42) #' @param seed.for.tsne Set a random seed for TSNE calculation. (Default: 1) #' @param seed.for.umap Set a random seed for UMAP calculation. (Default: 42) @@ -51,27 +48,44 @@ #' @param methods.pca Methods available: Marchenko-Pastur: use eigenvalue #' null upper bound from URD, Elbow: Find threshold where percent change #' in variation between consecutive PCs is less than X% (set in var.threshold). -#' (Default: c('Elbow','Marchenko-Pastur')) +#' If none is selected (regardless of other selections) the plot will not be +#' generated. (Default: 'none') #' @param var.threshold For Elbow method, set percent change threshold #' in variation between consecutive PCs. (Default: 0.1) #' @param jackstraw Opt to visualize your data in a Jackstraw plot. Jackstraw #' plot can add more description than an elbow plot but is compute intensive #' process and may not be suitable for larger datasets. (Default: FALSE) #' @param jackstraw.dims Recommended max 10.(Default: 5) +#' @param pca.reg.plot Opt to visualize the effect of your regression variables +#' on in a PCA plot. This plot will create PCA plots with and without +#' regression variables applied and can be used to help determine if +#' regression is necessary to properly normalize your data. (Default: FALSE) #' @param exclude.sample Exclude unwanted samples from the merge step. #' Include sample names to be removed. If you want to exclude several samples, #' separate each sample number by comma (e.g. sample1,sample2,sample3,sample4). +#' (Default: NULL) #' @param project.name Add project name to the Seurat object metadata. #' (Default: 'scRNAProject') #' @param cell.hashing.data Set to "TRUE" if you are using cell-hashed data. #' (Default: FALSE) +#' @param only.var.genes If dataset is larger than ~40k filtered cells, +#' set to TRUE. If TRUE, only variable genes will be available for +#' downstream analysis. If dataset is larger than the number of cells set in +#' "Conserve Memory Max Cell Limit" "Only Variable Genes" is automatically +#' set to TRUE. (Default: FALSE) +#' @param cell.count.limit If total number of cell exceeds this limit conserve +#' memory option of SCTransform will be used and return only Variable Genes. +#' (Default: 35000) +#' @param reduce.so Remove any additional assays from input Seurat Objects +#' except for the original RNA Assay. This option should be used if input +#' Seurat Object was created outside of the NIDAP pipeline. (Default: FALSE) #' #' #' @importFrom Seurat CreateAssayObject Idents as.SingleCellExperiment AddMetaData #' @importFrom reshape2 melt #' @importFrom magrittr %>% #' @importFrom ggplot2 ggplot -#' @importFrom RColorBrewer brewer.pal +#' @importFrom RColorBrewer brewer.pal brewer.pal.info #' @importFrom ggpubr annotate_figure get_legend ggarrange #' #' @export @@ -83,43 +97,46 @@ combineNormalize <- function(object, # Nomralization variables - npcs = 30, - SCT.level="Merged", - vars.to.regress = NULL, + npcs = 30, + SCT.level="Merged", + vars.to.regress = NULL, # FindVariableFeatures - nfeatures = 2000, - low.cut = 0.1, - high.cut = 8, - low.cut.disp = 1, - high.cut.disp = 100000, - selection.method = 'vst', + nfeatures = 2000, + low.cut = 0.1, + high.cut = 8, + low.cut.disp = 1, + high.cut.disp = 100000, + selection.method = 'vst', # Dim Reduction - only.var.genes = FALSE, - draw.umap = TRUE, - draw.tsne = TRUE, - - seed.for.pca = 42, - seed.for.tsne = 1, - seed.for.umap = 42, - + only.var.genes = FALSE, + draw.umap = TRUE, + draw.tsne = TRUE, + + seed.for.pca = 42, + seed.for.tsne = 1, + seed.for.umap = 42, + # Clustering Varables - clust.res.low = 0.2, - clust.res.high = 1.2, - clust.res.bin = 0.2, + clust.res.low = 0.2, + clust.res.high = 1.2, + clust.res.bin = 0.2, - # Select PCA - methods.pca = c('Elbow','Marchenko-Pastur'), - var.threshold = 0.1, - jackstraw = FALSE, - jackstraw.dims=5, + # Select PCs + methods.pca = NULL, + var.threshold = 0.1, + pca.reg.plot = FALSE, + jackstraw = FALSE, + jackstraw.dims=5, + + exclude.sample = NULL, + cell.count.limit= 35000, + reduce.so = FALSE, + project.name = 'scRNAProject', + cell.hashing.data = FALSE - exclude.sample = "", - project.name = 'scRNAProject', - cell.hashing.data = FALSE - ){ @@ -127,7 +144,7 @@ combineNormalize <- function(object, ##--------------- ## ## Error Messages ## ## -------------- ## - + ## --------- ## ## Functions #### @@ -221,9 +238,6 @@ combineNormalize <- function(object, } } - - - .plotElbow <- function(so,sample){ @@ -292,7 +306,7 @@ combineNormalize <- function(object, } ## --------------- ## - ## Main Code Block #### + # Main Code Block ==== ## --------------- ## @@ -311,15 +325,27 @@ combineNormalize <- function(object, object <- object[!names(object)%in%exclude.sample] } + # Remove all assays except RNA + if(reduce.so==T){ + smpls=names(object) + object2=sapply(smpls,function(x){ + so=object[[x]] + DefaultAssay(so)='RNA' + so=DietSeurat(object = so, + assays = c('RNA','Protein') + ) + return(so) + }) + } - ### Auto detect number of cells and turn on Conserve memory #### + ## Auto detect number of cells and turn on Conserve memory ==== ## Calculate total number of cells in input SO. cell.count <- sum(unlist((lapply(object, function(x) dim(x)[2])))) ## Setting a limit for cell numbers - # if (dim(object)[2] < 35000) { - if (cell.count < 35000) { + # if (dim(object)[2] < cell.count.limit) { + if (cell.count < cell.count.limit) { too.many.cells <- FALSE } else { too.many.cells <- TRUE @@ -333,11 +359,14 @@ combineNormalize <- function(object, } - ### Normalize Data #### + ## Normalize Data ==== if (SCT.level=="Merged") { - #### Merge and SCTransform #### - ### Merge Samples ==== + # samples -> merge -> SCTransform -> + # PrepSCTFindMarkers -> Find Variable Features + + ### Merge and SCTransform ==== + #### Merge Samples ==== dat = vector() if (length(object) > 1) { for(i in 2:length(object)){dat=c(dat,object[[i]]) } @@ -354,23 +383,17 @@ combineNormalize <- function(object, allgenes <- rownames(object.merge) } - #### SCTransform #### + #### SCTransform ==== object.merge <-SCTransform(object.merge, do.correct.umi = TRUE, vars.to.regress=vars.to.regress, conserve.memory = conserve.memory, return.only.var.genes = only.var.genes) - if(is.null(vars.to.regress)==F){ - object.merge.nr <-SCTransform(object.merge, - do.correct.umi = TRUE, - conserve.memory = conserve.memory, - return.only.var.genes = only.var.genes) - } - #### rescaling to lowest median SCT score accross samples ==== + #### rescaling to lowest median SCT score across samples ==== object.merge=PrepSCTFindMarkers(object.merge) - + #### FindVariableFeatures using options ==== object.merge<-FindVariableFeatures( object = object.merge, nfeatures = nfeatures, @@ -379,9 +402,36 @@ combineNormalize <- function(object, selection.method = selection.method, verbose = FALSE) + + if(is.null(vars.to.regress)==F& pca.reg.plot==T){ + + object.merge.nr <-SCTransform(object.merge, + do.correct.umi = TRUE, + vars.to.regress=vars.to.regress, + conserve.memory = conserve.memory, + return.only.var.genes = only.var.genes) + + #### rescaling to lowest median SCT score across samples ==== + object.merge.nr=PrepSCTFindMarkers(object.merge.nr) + + #### FindVariableFeatures using options ==== + object.merge.nr<-FindVariableFeatures( + object = object.merge.nr, + nfeatures = nfeatures, + mean.cutoff = c(low.cut, high.cut), + dispersion.cutoff=c(low.cut.disp,high.cut.disp), + selection.method = selection.method, + verbose = FALSE) + + } + + } else if (SCT.level=="Sample"){ - #### SCTransform and merge #### - #### SCTransform #### + # Samples -> SCTransform -> + # SelectIntegrationFeatures(set as Variable Features) -> + # merge -> PrepSCTFindMarkers -> Set Variable Features + ### SCTransform and merge ==== + #### SCTransform ==== object.merge <- lapply(object,function(x){ SCTransform(x, do.correct.umi = TRUE, @@ -391,7 +441,7 @@ combineNormalize <- function(object, }) - #### Integration features to set as Varable Features #### + #### Integration features to set as Variable Features #### integ.features <- SelectIntegrationFeatures( object.list = object.merge, nfeatures = nfeatures, @@ -416,17 +466,17 @@ combineNormalize <- function(object, allgenes <- rownames(object.merge) } - #### rescaling to lowest median SCT score accross samples #### + #### rescaling to lowest median SCT score across samples ==== object.merge=PrepSCTFindMarkers(object.merge) - #### Set Variable Features #### + #### Set Variable Features ==== VariableFeatures(object.merge) = integ.features ### non-Regression Test - if(is.null(vars.to.regress)==F){ + if(is.null(vars.to.regress)==F& pca.reg.plot==T){ #### Merge object.merge.nr <- lapply(object,function(x){ SCTransform(x, @@ -435,7 +485,7 @@ combineNormalize <- function(object, return.only.var.genes = only.var.genes) }) - #### Integration Features + #### Integration Features integ.features.nr <- SelectIntegrationFeatures( object.list = object.merge.nr, nfeatures = nfeatures, @@ -444,7 +494,7 @@ combineNormalize <- function(object, normalization.method="SCT", verbose = FALSE) - #### Merge Samples + #### Merge Samples dat = vector() if (length(object) > 1) { for(i in 2:length(object.merge.nr)){dat=c(dat,object.merge.nr[[i]]) } @@ -458,38 +508,44 @@ combineNormalize <- function(object, allgenes.nr <- rownames(object.merge.nr) } - #### rescaling to lowest median SCT score accross samples #### + #### rescaling to lowest median SCT score accross samples ==== object.merge.nr=PrepSCTFindMarkers(object.merge.nr) - #### Set Variable Features ==== + #### Set Variable Features ==== VariableFeatures(object.merge.nr) = integ.features.nr } - - } else {stop("SCT method should be either Merged or Sample")} + ### QC plots ==== + grobsList = list() - ### QC samples #### - grobsList = list() - + ## Internal Error Check + ## Turn off pca.reg.plot if no regression variables selected. + if(is.null(vars.to.regress)&pca.reg.plot==T){ + pca.reg.plot==F + print('pca.reg.plot set to false because no + Regression Variables were selected') + } - #### PCA on individual samples #### - object.merge.split=SplitObject(object.merge, split.by = "orig.ident") + if ('none'%in%methods.pca==F|pca.reg.plot==T|jackstraw==T) { + + #### PCA on individual samples ==== + object.merge.split=SplitObject(object.merge, split.by = "orig.ident") n=names(object.merge.split) - object.merge.split=lapply(n,function(x){ - RunPCA(object = object.merge.split[[x]], - npcs = (npcs+10), verbose = FALSE, - seed.use = seed.for.pca)}) - names(object.merge.split)=n - - + object.merge.split=lapply(n,function(x){ + RunPCA(object = object.merge.split[[x]], + npcs = (npcs+10), verbose = FALSE, + seed.use = seed.for.pca)}) + names(object.merge.split)=n + + } else {"No PCA plots created"} - #### Create PCA regression plots #### - if (is.null(vars.to.regress)==F) { + #### Create PCA regression plots ==== + if (pca.reg.plot==T) { object.merge.nr.split=SplitObject(object.merge.nr, split.by = "orig.ident") nr=names(object.merge.nr.split) @@ -502,73 +558,74 @@ combineNormalize <- function(object, k <- 1 pca.grob=list() - for (i in 1:length(vars.to.regress)){ - v=vars.to.regress[i] - print(v) - r <- lapply(names(object.merge.split), - function(x){.plotPCA(object.merge.split[[x]],v,x)}) - nr <- lapply(names(object.merge.nr.split), - function(x){.plotPCA(object.merge.nr.split[[x]],v,x)}) - - grob = ggarrange(plotlist=r,ncol=1, - common.legend = F, - legend = 'right')%>% - annotate_figure(top=text_grob(paste0(v,' Regression'), - face = "bold", size = 20), - fig.lab.size = 20, - fig.lab.face = 'bold', - fig.lab.pos='top') - grob.nr = ggarrange(plotlist=nr - ,ncol=1, - common.legend = F, - legend = 'right')%>% - annotate_figure(top=text_grob('No Regression', - face = "bold", size = 20), - fig.lab.size = 20, - fig.lab.face ='bold', - fig.lab.pos='top') - - pca.grob=ggarrange(grob,grob.nr) - - grobsList[['Regression Plots']][[v]] =pca.grob + for (i in 1:length(vars.to.regress)){ + v=vars.to.regress[i] + print(v) + r <- lapply(names(object.merge.split), + function(x){.plotPCA(object.merge.split[[x]],v,x)}) + nr <- lapply(names(object.merge.nr.split), + function(x){.plotPCA(object.merge.nr.split[[x]],v,x)}) + + grob = ggarrange(plotlist=r,ncol=1, + common.legend = F, + legend = 'right')%>% + annotate_figure(top=text_grob(paste0(v,' Regression'), + face = "bold", size = 20), + fig.lab.size = 20, + fig.lab.face = 'bold', + fig.lab.pos='top') + grob.nr = ggarrange(plotlist=nr + ,ncol=1, + common.legend = F, + legend = 'right')%>% + annotate_figure(top=text_grob('No Regression', + face = "bold", size = 20), + fig.lab.size = 20, + fig.lab.face ='bold', + fig.lab.pos='top') + + pca.grob=ggarrange(grob,grob.nr) + + grobsList[['Regression Plots']][[v]] =pca.grob + + } - } } else { - print("Regression not prefomred") + print("PCA regression plots not created") } + ### Determin # of PCs ==== + #### create Elbow plot ==== + if (is.null(methods.pca) == FALSE) { + + elbow.grob=lapply(names(object.merge.split),function(x){ + gg= + .plotElbow(object.merge.split[[x]],sample=x) + return(gg+ylab("")+xlab("")) + } + ) + elbow.comb=ggarrange(plotlist=elbow.grob,ncol =1) %>% + annotate_figure(left=text_grob("Standard deviation",size=16,rot=90), + bottom=text_grob("PC",size=16)) + + grobsList[["Elbow Plot"]]=elbow.comb + grobsList[["Elbow Plot Individual"]]=elbow.grob + + } - - #### create Elbow plot #### - - elbow.grob=lapply(names(object.merge.split),function(x){ - gg= - .plotElbow(object.merge.split[[x]],sample=x) - return(gg+ylab("")+xlab("")) - } - ) - elbow.comb=ggarrange(plotlist=elbow.grob,ncol =1) %>% - annotate_figure(left=text_grob("Standard deviation",size=16,rot=90), - bottom=text_grob("PC",size=16)) - - grobsList[["Elbow Plot"]]=elbow.comb - grobsList[["Elbow Plot Individual"]]=elbow.grob - - - - #### Create Jackstraw plot #### - ## Jackstraw does not work with SCT data so create ScaleData - if (jackstraw) { + #### Create Jackstraw plot ==== + ## Jackstraw does not work with SCT data so create ScaleData + if (jackstraw==T) { # jackstraw.dims = (npcs+10) js <-lapply(names(object.merge.split), function(x){ jso=object.merge.split[[x]] DefaultAssay(jso)="RNA" jso=ScaleData(jso)%>% - FindVariableFeatures(nfeatures = nfeatures, - mean.cutoff = c(low.cut, high.cut), - dispersion.cutoff=c(low.cut.disp,high.cut.disp), - selection.method = selection.method, - verbose = F)%>% + FindVariableFeatures(nfeatures = nfeatures, + mean.cutoff = c(low.cut, high.cut), + dispersion.cutoff=c(low.cut.disp,high.cut.disp), + selection.method = selection.method, + verbose = F)%>% RunPCA(npcs = (npcs+10), verbose = FALSE, seed.use = seed.for.pca)%>% @@ -578,19 +635,19 @@ combineNormalize <- function(object, prop.freq = 0.01, verbose = F, maxit = 1000)%>%suppressWarnings() - }) + }) names(js)=names(object.merge.split) js <- lapply(names(js), function(x) ScoreJackStraw(js[[x]], - dims = 1:jackstraw.dims)) + dims = 1:jackstraw.dims)) names(js )=names(object.merge.split) grob4 <- lapply(names(js), function(x) {JackStrawPlot(js[[x]], - dims = 1:jackstraw.dims)+ + dims = 1:jackstraw.dims)+ ggtitle(x)+ ylab("")+xlab("")+ theme(plot.title = element_text(size=16,face='bold'), axis.title=element_text(size=16)) - }) + }) names(grob4 )=names(object.merge.split) js.comb=ggarrange(plotlist=grob4,ncol =1) %>% @@ -602,37 +659,11 @@ combineNormalize <- function(object, } - - #### Detect Citeseq #### - - #initialize Citeseq functionality as false, - #later the template will check for a Protein assay and run if it finds it - - do.cite.seq <- FALSE - - if ("Protein" %in% names(object.merge@assays)){ - do.cite.seq <-TRUE - } - - - ### HTO #### - if(cell.hashing.data){ - object.merge <- ScaleData(object.merge, assay = "HTO") - } - - - - ### Dimension reduction #### + ## Dimension reduction ==== object.merge <- RunPCA(object = object.merge, npcs = npcs, verbose = FALSE, seed.use = seed.for.pca) - if(is.null(vars.to.regress)==F){ - object.merge.nr <- RunPCA(object = object.merge.nr, - npcs = npcs, verbose = FALSE, - seed.use = seed.for.pca) - } - object.merge <- RunUMAP(object = object.merge, reduction = "pca", dims = 1:npcs, @@ -644,46 +675,87 @@ combineNormalize <- function(object, seed.use = seed.for.tsne) object.merge <- FindNeighbors(object.merge, dims = 1:npcs) + ### non-Regression Test + if(is.null(vars.to.regress)==F& pca.reg.plot==T){ + object.merge.nr <- RunPCA(object = object.merge.nr, + npcs = npcs, verbose = FALSE, + seed.use = seed.for.pca) + } + + ### HTO scale merged ==== + if(cell.hashing.data){ + object.merge <- ScaleData(object.merge, assay = "HTO") + } - ### Citeseq #### - - #check for CITE-seq data and if so, run reductions + ## Process Citeseq ==== + # Original Workflow + # https://satijalab.org/seurat/archive/v3.2/multimodal_vignette.html + # from SeuratV4 workflow is the same + # https://satijalab.org/seurat/archive/v4.3/weighted_nearest_neighbor_analysis + + ### Detect Citeseq + #initialize Citeseq functionality as false, + #later the template will check for a Protein assay and run if it finds it + + do.cite.seq <- FALSE + if ("Protein" %in% names(object.merge@assays)){ + do.cite.seq <-TRUE + } + if(do.cite.seq) { - object.merge <- ScaleData(object.merge, assay = "Protein") + print("finding Protein variable features...") + + #### Normalize -> scale -> PCA - Citeseq ==== - print("finding protein variable features...") - VariableFeatures(object.merge,assay="Protein") <- + VariableFeatures(object.merge,assay="Protein") <- rownames(object.merge$Protein) - #Support for partial - if(all(sapply(seq.along(object), + if(all(sapply(seq_along(object), function(i) "Protein" %in% names(object[[i]]@assays)))){ - print("running protein pca...") + object.merge = NormalizeData(object.merge, + assay = "Protein", + normalization.method = "CLR") + object.merge = ScaleData(object.merge, assay = 'Protein', verbose = FALSE) + print("running Protein pca...") + + p.npcs=min(nrow(object.merge$Protein),npcs) object.merge <- RunPCA(object = object.merge, assay="Protein", - npcs = npcs, - reduction.name="protein.pca", - seed.use = seed.for.pca, - verbose = FALSE) + npcs = p.npcs, + reduction.name="protein_pca", + reduction.key ="proteinPC_" + ) + + ### FindMultiModalNeighbors - Citeseq ==== + + object.merge <- FindMultiModalNeighbors( + object.merge, + reduction.list = list("pca", "protein_pca"), + dims.list = list(1:npcs, 1:(p.npcs-1)), + modality.weight.name = "RNA.weight" + ) + ### Dimension Reduction - Citeseq ==== + object.merge <- RunUMAP(object = object.merge, assay="Protein", + nn.name = "weighted.nn", + reduction.name = "protein_umap", + reduction.key = "ProteinUMAP_", features=rownames(object.merge$Protein), - reduction.name="protein.umap", seed.use=seed.for.umap) object.merge <- RunTSNE(object = object.merge, assay="Protein", + nn.name = "weighted.nn", + reduction.name="protein_tsne", + reduction.key ="ProteinTSNE_", features=rownames(object.merge$Protein), seed.use = seed.for.tsne, - reduction.name="protein.tsne", check.duplicates=F) - object.merge <- FindNeighbors(object.merge, assay="Protein", - graph.name="Protein.snn", - features=rownames(object.merge$Protein)) }else{ - do.cite.seq <- FALSE #set to false so we don't cluster protein + do.cite.seq <- FALSE #set to false so we don't cluster Protein } } else { @@ -691,20 +763,26 @@ combineNormalize <- function(object, } - ## Cluster #### + ## Cluster ==== for (i in seq(clust.res.low,clust.res.high,clust.res.bin)){ - object.merge <- FindClusters(object.merge, resolution = i, algorithm = 1) + ## Clustr RNAseq + object.merge <- FindClusters(object.merge, + resolution = i, + algorithm = 1) if(do.cite.seq==TRUE){ object.merge <- FindClusters(object.merge, - graph.name="Protein_snn", + graph.name="wsnn", resolution = i, - algorithm = 1) + algorithm = 1, + verbose = FALSE) } } print("Clustering successful!") + + ## create plots #### n <- 60 @@ -794,10 +872,8 @@ combineNormalize <- function(object, } - - - return(list(object=object.merge, - plots=grobsList)) + return(list(object=object.merge, + plots=grobsList)) } diff --git a/R/Dual_Labeling.R b/R/Dual_Labeling.R index 864e9eb..2c5f0e2 100755 --- a/R/Dual_Labeling.R +++ b/R/Dual_Labeling.R @@ -15,7 +15,7 @@ #' @param marker.2.type Slot to use for second marker. Choices are "SCT", #' "protein","HTO" (default is "SCT") #' @param data.reduction Dimension Reduction method to use for image. Options -#' are "umap" or "tsne" (default is "umap") +#' are umap, tsne, or both (default is "umap") #' @param point.size Point size for image (default is 0.5) #' @param point.shape Point shape for image (default is 16) #' @param point.transparency Point transparency for image (default is 0.5) @@ -24,10 +24,10 @@ #' @param marker.2.threshold Threshold set for second marker (default is 0.5) #' @param filter.data Add new parameter column to metadata annotating where #' marker thresholds are applied (default is TRUE) -#' @param M1.filter.direction Annotate cells that have gene expression levels +#' @param marker.1.filter.direction Annotate cells that have gene expression levels #' for marker 1 using the marker 1 threshold. Choices are "greater than" #' or "less than" (default is "greater than") -#' @param M2.filter.direction Annotate cells that have gene expression levels +#' @param marker.2.filter.direction Annotate cells that have gene expression levels #' for marker 2 using the marker 2 threshold. Choices are "greater than" #' or "less than" (default is "greater than") #' @param apply.filter.1 If TRUE, apply the first filter (default is TRUE) @@ -35,20 +35,19 @@ #' @param filter.condition If TRUE, apply both filters 1 and 2 and take #' intersection. If FALSE, apply both filters and take the union. #' @param parameter.name Name for metadata column for new marker filters -#' (Default is "Marker") +#' (Default is "My_CoExp") #' @param trim.marker.1 Trim top and bottom percentile of marker 1 signal to #' pre-scale trim values (below) to remove extremely low and high values -#' (Default is TRUE) +#' (Default is FALSE) #' @param trim.marker.2 Trim top and bottom percentile of marker 2 signal to #' pre-scale trim values (below) to remove extremely low and high values -#' (Default is TRUE) +#' (Default is FALSE) #' @param pre.scale.trim Set trimming percentile values (Defalut is 0.99) -#' @param density.heatmap Creates a additional heatmap showing the density -#' distribution of cells. (Default is FALSE) #' @param display.unscaled.values Set to TRUE if you want to view the unscaled #' gene/protein expression values (Default is FALSE) -#' @importFrom Seurat +#' @import Seurat +#' @import ggExtra #' @importFrom scales rescale #' @importFrom gridExtra arrangeGrob #' @importFrom grid grid.draw @@ -64,430 +63,529 @@ #' positive or negative for gene markers, a coexpression plot and contingency #' table showing sum of cells filtered. -dualLabeling <- function(object, - samples, - marker.1, - marker.2, - marker.1.type = "SCT", - marker.2.type = "SCT", - data.reduction = "umap", - point.size = 0.5, - point.shape = 16, - point.transparency = 0.5, - add.marker.thresholds = FALSE, - marker.1.threshold = 0.5, - marker.2.threshold = 0.5, - filter.data = FALSE, - M1.filter.direction = "greater than", - M2.filter.direction = "greater than", - apply.filter.1 = TRUE, - apply.filter.2 = TRUE, - filter.condition = TRUE, - parameter.name = "Marker", - trim.marker.1 = TRUE, - trim.marker.2 = TRUE, - pre.scale.trim = 0.99, - density.heatmap = FALSE, - display.unscaled.values = FALSE) { - - +dualLabeling <- function (object, + samples, + marker.1, + marker.2, + marker.1.type = "SCT", + marker.2.type = "SCT", + data.reduction = "both", + point.size = 0.5, + point.shape = 16, + point.transparency = 0.5, + add.marker.thresholds = TRUE, + marker.1.threshold = 0.5, + marker.2.threshold = 0.5, + filter.data = TRUE, + marker.1.filter.direction = "greater than", + marker.2.filter.direction = "greater than", + apply.filter.1 = TRUE, + apply.filter.2 = TRUE, + filter.condition = TRUE, + parameter.name = "My_CoExp", + trim.marker.1 = FALSE, + trim.marker.2 = FALSE, + pre.scale.trim = 0.99, + display.unscaled.values = FALSE) +{ + #### Error Messages #### #Errors for genes not available in dataset/slot - if (!(marker.1 %in% rownames(object))) { - stop(sprintf("%s is not found in dataset", marker.1)) - } - if (!(marker.2 %in% rownames(object))) { - stop(sprintf("%s is not found in dataset", marker.2)) - } - if (!(marker.1.type %in% names(object@assays))) { - stop(sprintf("%s slot is not found in dataset", marker.1.type)) - } - if (!(marker.2.type %in% names(object@assays))) { - stop(sprintf("%s slot is not found in dataset", marker.2.type)) - } - + if (!(marker.1 %in% rownames(object))) { + stop(sprintf("%s is not found in dataset", marker.1)) + } + if (!(marker.2 %in% rownames(object))) { + stop(sprintf("%s is not found in dataset", marker.2)) + } + if (!(marker.1.type %in% names(object@assays))) { + stop(sprintf("%s slot is not found in dataset", marker.1.type)) + } + if (!(marker.2.type %in% names(object@assays))) { + stop(sprintf("%s slot is not found in dataset", marker.2.type)) + } + if (data.reduction=='both') { + if(sum(c('tsne','umap')%in%names(object@reductions))<2){ + rdctns=names(object@reductions)[names(object@reductions)%in%c('umap','tsne')] + stop(sprintf("Object does not contain both umap and tsne reductions. + Change Data Reduction parameter to %s", + paste(rdctns,collapse=' or ') + ) + ) + } + }else{ + if (data.reduction%in%names(object@reductions)==F){ + stop(sprintf("Object does not contain %s reduction. \n ", + data.reduction), + sprintf("Change Data Reduction parameter to %s", + c('tsne','umap')[c('tsne','umap')%in%names(object@reductions)]) + ) + } + } #### Functions #### #Function for drawing overlay images for umap/tsne: - .ggOverlay <- function(so.sub, df, marker.1, marker.2) { - df <- df %>% arrange(mark1.scale) - - xmin <- min(df$dr1) - 0.1 * min(df$dr1) - xmax <- max(df$dr1) + 0.1 * min(df$dr1) - - #ggplot for umap/tsne (marker 1) - gg.z1 <- ggplot(df, aes(dr1, dr2)) + - geom_point( - color = rgb( - red = df$mark1.scale, - green = 0, - blue = 0 - ), - shape = point.shape, - size = point.size, - alpha = point.transparency - ) + - theme_classic() + - xlab(paste0(data.reduction, "-1")) + - ylab(paste0(data.reduction, "-2")) + - ggtitle(marker.1) + - coord_fixed() - - df <- df %>% arrange(mark2.scale) - - #ggplot for umap/tsne (marker 2) - gg.z2 <- ggplot(df, aes(dr1, dr2)) + - geom_point( - color = rgb( - red = 0, - green = df$mark2.scale, - blue = 0 - ), - shape = point.shape, - size = point.size, - alpha = point.transparency - ) + - theme_classic() + - xlab(paste0(data.reduction, "-1")) + - ylab(paste0(data.reduction, "-2")) + - ggtitle(marker.2) + - coord_fixed() - - df <- df %>% - mutate(avg = mark2.scale + mark1.scale) %>% - arrange(avg) + .ggOverlay <- function(so.sub, df, marker.1, marker.2,reduction) { + df <- df %>% arrange(mark1.scale) + + xmin <- min(df$dr1) - 0.1 * min(df$dr1) + xmax <- max(df$dr1) + 0.1 * min(df$dr1) + + #ggplot for umap/tsne (marker 1) + gg.z1 <- ggplot(df, aes(dr1, dr2)) + + geom_point( + color = rgb( + red = df$mark1.scale, + green = 0, + blue = 0 + ), + shape = point.shape, + size = point.size, + alpha = point.transparency + ) + + theme_classic() + + xlab(paste0(reduction, "-1")) + + ylab(paste0(reduction, "-2")) + + ggtitle(marker.1) + + coord_fixed() + + df <- df %>% arrange(mark2.scale) + + #ggplot for umap/tsne (marker 2) + gg.z2 <- ggplot(df, aes(dr1, dr2)) + + geom_point( + color = rgb( + red = 0, + green = df$mark2.scale, + blue = 0 + ), + shape = point.shape, + size = point.size, + alpha = point.transparency + ) + + theme_classic() + + xlab(paste0(reduction, "-1")) + + ylab(paste0(reduction, "-2")) + + ggtitle(marker.2) + + coord_fixed() + + df <- df %>% + mutate(avg = mark2.scale + mark1.scale) %>% + arrange(avg) + + #ggplot for umap/tsne (marker 1 & marker 2) + gg <- ggplot(df, aes(dr1, dr2)) + + geom_point( + color = rgb( + red = df$mark1.scale, + green = df$mark2.scale, + blue = 0 + ), + shape = point.shape, + size = point.size, + alpha = point.transparency + ) + + theme_classic() + + xlab(paste0(reduction, "-1")) + + ylab(paste0(reduction, "-2")) + + ggtitle("Combined") + + coord_fixed() + + return(list(gg.z1, gg.z2, gg)) + } + + #Function for plotting expression data in xy overlay format: + .ggOverlay2 <- function(so.sub, df, marker.1, marker.2) { + df <- df %>% arrange(mark1.scale) + # Create unscaled axis labels + + if (display.unscaled.values == TRUE) { + label1.min <- + paste("unscaled min:", round(min(mark1),digits = 2)) + label1.max <- paste("unscaled max:", round(max(mark1), digits = 2)) + label1 <- + paste(as.character(marker.1), label1.min, label1.max, sep = "\n") + + label2.min <- + paste("unscaled min:", round(min(mark2), digits = 2)) + label2.max <- + paste("unscaled max:", round(max(mark2), digits = 2)) + label2 <- + paste(as.character(marker.2), label2.min, label2.max, sep = "\n") + } else { + label1 <- as.character(marker.1) + label2 <- as.character(marker.2) + } + + #ggplot for scatter plot (marker 1) + gg.z1 <- ggplot(df, aes(mark1.scale, mark2.scale)) + + geom_point( + color = rgb( + red = df$mark1.scale, + green = 0, + blue = 0 + ), + shape = 20, + size = point.size + ) + + theme_classic() + + xlab(label1) + + ylab(label2) + + coord_fixed() + + df <- df %>% arrange(mark2.scale) + + #ggplot for scatter plot (marker 2) + gg.z2 <- ggplot(df, aes(mark1.scale, mark2.scale)) + + geom_point( + color = rgb( + red = 0, + green = df$mark2.scale, + blue = 0 + ), + shape = 20, + size = point.size + ) + + theme_classic() + + xlab(label1) + + ylab(label2) + + coord_fixed() + + df <- df %>% + mutate(avg = mark2.scale + mark1.scale) %>% + arrange(avg) + + #ggplot for scatter plot (marker 1 & marker.2) + gg <- ggplot(df, aes(mark1.scale, mark2.scale)) + + geom_point( + color = rgb( + red = df$mark1.scale, + green = df$mark2.scale, + blue = 0 + ), + shape = 20, + size = point.size + ) + + theme_classic() + + xlab(label1) + + ylab(label2) + + coord_fixed() + + if (add.marker.thresholds == TRUE) { + gg.z1 <- gg.z1 + + geom_vline(xintercept = t1, linetype = "dashed") + + geom_hline(yintercept = t2, linetype = "dashed") + gg.z2 <- gg.z2 + + geom_vline(xintercept = t1, linetype = "dashed") + + geom_hline(yintercept = t2, linetype = "dashed") + gg <- gg + + geom_vline(xintercept = t1, linetype = "dashed") + + geom_hline(yintercept = t2, linetype = "dashed") + } + + return(list(gg.z1, gg.z2, gg)) + } - #ggplot for umap/tsne (marker 1 & marker 2) - gg <- ggplot(df, aes(dr1, dr2)) + - geom_point( - color = rgb( - red = df$mark1.scale, - green = df$mark2.scale, - blue = 0 - ), - shape = point.shape, - size = point.size, - alpha = point.transparency - ) + - theme_classic() + - xlab(paste0(data.reduction, "-1")) + - ylab(paste0(data.reduction, "-2")) + - ggtitle("Combined") + - coord_fixed() + ## --------------- ## + ## Main Code Block ## + ## --------------- ## - return(list(gg.z1, gg.z2, gg)) - } - - #Function for plotting expression data in xy overlay format: - .ggOverlay2 <- function(so.sub, df, marker.1, marker.2) { - df %>% arrange(mark1.scale) -> df - # Create unscaled axis labels + # Load and subset data using sample names - if (display.unscaled.values == TRUE) { - label1.min <- paste("unscaled min:", round(min(mark1), digits = 2)) - label1.max <- - paste("unscaled max:", round(max(mark1), digits = 2)) - label1 <- - paste(as.character(marker.1), label1.min, label1.max, sep = "\n") - - label2.min <- - paste("unscaled min:", round(min(mark2), digits = 2)) - label2.max <- - paste("unscaled max:", round(max(mark2), digits = 2)) - label2 <- - paste(as.character(marker.2), label2.min, label2.max, sep = "\n") + if ("active.ident" %in% slotNames(object)) { + sample.name <- as.factor(object@meta.data$orig.ident) + names(sample.name) <- names(object@active.ident) + object@active.ident <- as.factor(vector()) + object@active.ident <- sample.name + so.sub <- subset(object, ident = samples) } else { - label1 <- as.character(marker.1) - label2 <- as.character(marker.2) + sample.name <- as.factor(object@meta.data$orig.ident) + names(sample.name) <- names(object@active.ident) + object@active.ident <- as.factor(vector()) + object@active.ident <- sample.name + so.sub <- subset(object, ident = samples) } + t1 <- marker.1.threshold + t2 <- marker.2.threshold - #ggplot for scatter plot (marker 1) - gg.z1 <- ggplot(df, aes(mark1.scale, mark2.scale)) + - geom_point( - color = rgb( - red = df$mark1.scale, - green = 0, - blue = 0 - ), - shape = 20, - size = point.size - ) + - theme_classic() + - xlab(label1) + - ylab(label2) + - coord_fixed() - - df <- df %>% arrange(mark2.scale) - - #ggplot for scatter plot (marker 2) - gg.z2 <- ggplot(df, aes(mark1.scale, mark2.scale)) + - geom_point( - color = rgb( - red = 0, - green = df$mark2.scale, - blue = 0 - ), - shape = 20, - size = point.size - ) + - theme_classic() + - xlab(label1) + - ylab(label2) + - coord_fixed() - - df <- df %>% - mutate(avg = mark2.scale + mark1.scale) %>% - arrange(avg) - #ggplot for scatter plot (marker 1 & marker.2) - gg <- ggplot(df, aes(mark1.scale, mark2.scale)) + - geom_point( - color = rgb( - red = df$mark1.scale, - green = df$mark2.scale, - blue = 0 - ), - shape = 20, - size = point.size - ) + - theme_classic() + - xlab(label1) + - ylab(label2) + - coord_fixed() - - if (add.marker.thresholds == TRUE) { - gg.z1 <- gg.z1 + - geom_vline(xintercept = t1, linetype = "dashed") + - geom_hline(yintercept = t2, linetype = "dashed") - gg.z2 <- gg.z2 + - geom_vline(xintercept = t1, linetype = "dashed") + - geom_hline(yintercept = t2, linetype = "dashed") - gg <- gg + - geom_vline(xintercept = t1, linetype = "dashed") + - geom_hline(yintercept = t2, linetype = "dashed") + #Select marker 1 values and scale: + # use data slot for Spatial assay + if(marker.1.type == "Spatial"){ + mark1 <- so.sub@assays[[marker.1.type]]@data[marker.1,] + } else { + mark1 <- so.sub@assays[[marker.1.type]]@scale.data[marker.1,] } + if (trim.marker.1 == TRUE) { + q1 <- quantile(mark1, pre.scale.trim) + q0 <- quantile(mark1, 1 - pre.scale.trim) + mark1[mark1 < q0] <- q0 + mark1[mark1 > q1] <- q1 + } + mark1.scale <- rescale(mark1, to = c(0, 1)) - return(list(gg.z1, gg.z2, gg)) - } - - ## --------------- ## - ## Main Code Block ## - ## --------------- ## - - # Load and subset data using sample names - - if ("active.ident" %in% slotNames(object)) { - sample.name <- as.factor(object@meta.data$orig.ident) - names(sample.name) <- names(object@active.ident) - object@active.ident <- as.factor(vector()) - object@active.ident <- sample.name - so.sub <- subset(object, ident = samples) - } else { - sample.name <- as.factor(object@meta.data$orig.ident) - names(sample.name) <- names(object@active.ident) - object@active.ident <- as.factor(vector()) - object@active.ident <- sample.name - so.sub <- subset(object, ident = samples) - } - - t1 <- marker.1.threshold - t2 <- marker.2.threshold - - #Select marker 1 values and scale: - mark1 <- so.sub@assays[[marker.1.type]]@scale.data[marker.1,] - if (trim.marker.1 == TRUE) { - q1 <- quantile(mark1, pre.scale.trim) - q0 <- quantile(mark1, 1 - pre.scale.trim) - mark1[mark1 < q0] <- q0 - mark1[mark1 > q1] <- q1 - } - mark1.scale <- rescale(mark1, to = c(0, 1)) - - #Select marker 2 values and scale: - mark2 <- so.sub@assays[[marker.2.type]]@scale.data[marker.2,] - if (trim.marker.2 == TRUE) { - q1 <- quantile(mark2, pre.scale.trim) - q0 <- quantile(mark2, 1 - pre.scale.trim) - mark2[mark2 < q0] <- q0 - mark2[mark2 > q1] <- q1 - } - mark2.scale <- rescale(mark2, to = c(0, 1)) - - #Draw Plots: - df <- data.frame( - cbind( - dr1 = so.sub@reductions[[data.reduction]]@cell.embeddings[, 1], - dr2 = so.sub@reductions[[data.reduction]]@cell.embeddings[, 2], - mark1.scale, - mark2.scale - ) - ) - gg.list <- .ggOverlay(so.sub, df, marker.1, marker.2) - gg.list2 <- .ggOverlay2(so.sub, df, marker.1, marker.2) - - if (density.heatmap == TRUE) { - x = df$mark1.scale - y = df$mark2.scale - - df_heatmap <- data.frame( - x = x, - y = y, - d <- densCols( - x, - y, - nbin = 1000, - bandwidth = 1, - colramp <- - colorRampPalette(rev(rainbow(10, end = 4 / 6))) - ) - ) - - p <- ggplot(df_heatmap) + - geom_point(aes(x, y, col = d), size = 1) + - scale_color_identity() + xlab(marker.1) + ylab(marker.2) + - theme_bw() + - geom_vline(xintercept = t1, linetype = "dashed") + - geom_hline(yintercept = t2, linetype = "dashed") - - - grob <- - arrangeGrob(gg.list[[1]], - gg.list[[2]], - gg.list[[3]], - gg.list2[[1]], - gg.list2[[2]], - gg.list2[[3]], - p, - ncol = 3) - } else { - grob <- - arrangeGrob(gg.list[[1]], - gg.list[[2]], - gg.list[[3]], - gg.list2[[1]], - gg.list2[[2]], - gg.list2[[3]], - ncol = 3) - } - - #Applying Filters to Data using Thresholds: - if (filter.data == TRUE && (apply.filter.1 == TRUE | apply.filter.2 == TRUE)) { - df <- df %>% mutate(sample = so.sub@meta.data$orig.ident) %>% - mutate(cellbarcode = rownames(so.sub@meta.data)) - - if (M1.filter.direction == "greater than") { - ind1 <- df$`mark1.scale` > t1 + #Select marker 2 values and scale: + if(marker.2.type == "Spatial"){ + mark2 <- so.sub@assays[[marker.2.type]]@data[marker.2, ] } else { - ind1 <- df$`mark1.scale` < t1 + mark2 <- so.sub@assays[[marker.2.type]]@scale.data[marker.2, ] } + + if (trim.marker.2 == TRUE) { + q1 <- quantile(mark2, pre.scale.trim) + q0 <- quantile(mark2, 1 - pre.scale.trim) + mark2[mark2 < q0] <- q0 + mark2[mark2 > q1] <- q1 + } + mark2.scale <- rescale(mark2, to = c(0, 1)) - cat("\n") - print("Marker 1 filter:") - print(sum(ind1)) + - if (M2.filter.direction == "greater than") { - ind2 <- df$`mark2.scale` > t2 + if (data.reduction=='tsne'|data.reduction=='umap') { + + #Draw Plots: + df <- data.frame( + cbind( + dr1 = so.sub@reductions[[data.reduction]]@cell.embeddings[,1], + dr2 = so.sub@reductions[[data.reduction]]@cell.embeddings[,2], + mark1.scale, + mark2.scale + ) + ) + + gg.list <- .ggOverlay(so.sub, df, marker.1, marker.2,data.reduction) + gg.list2 <- .ggOverlay2(so.sub, df, marker.1, marker.2) + + grob <- + arrangeGrob(gg.list[[1]], + gg.list[[2]], + gg.list[[3]], + gg.list2[[1]], + gg.list2[[2]], + gg.list2[[3]], + ncol = 3) + + + } else if (data.reduction=='both'){ + + #Draw Plots: + df.u <- data.frame( + cbind( + dr1 = so.sub@reductions[['umap']]@cell.embeddings[,1], + dr2 = so.sub@reductions[['umap']]@cell.embeddings[,2], + mark1.scale, + mark2.scale + ) + ) + gg.list.u <- .ggOverlay(so.sub, df.u, marker.1, marker.2,'umap') + + + #Draw Plots: + df.t <- data.frame( + cbind( + dr1 = so.sub@reductions[['tsne']]@cell.embeddings[,1], + dr2 = so.sub@reductions[['tsne']]@cell.embeddings[,2], + mark1.scale, + mark2.scale + ) + ) + gg.list.t <- .ggOverlay(so.sub, df.t, marker.1, marker.2,'tsne') + + + ## df.u being used is arbitrary. only difference between df.u and df.t is + ## reduction columns which are not being used by ggOverlay2 + df=df.u[,colnames(df.u)%in%c('dr1','dr2')==F] + + gg.list2 <- .ggOverlay2(so.sub, df, marker.1, marker.2) + + + grob.u <- + arrangeGrob(gg.list.u[[1]], + gg.list.u[[2]], + gg.list.u[[3]], + gg.list2[[1]], + gg.list2[[2]], + gg.list2[[3]], + ncol = 3) + grob.t <- + arrangeGrob(gg.list.t[[1]], + gg.list.t[[2]], + gg.list.t[[3]], + gg.list2[[1]], + gg.list2[[2]], + gg.list2[[3]], + ncol = 3) + } else { - ind2 <- df$`mark2.scale` < t2 + stop("Incorrect selection for data.reduction: use either umap,tsne or both") } - cat("\n") - print("Marker 2 filter:") - print(sum(ind2)) + x = df$mark1.scale + y = df$mark2.scale + + df_heatmap <- data.frame( + x = x, + y = y, + d <- densCols( + x, + y, + nbin = 1000, + bandwidth = 1, + colramp <- + colorRampPalette(rev(rainbow(10, end = 4/6))) + ) + ) + + p <- ggplot(df_heatmap) + + geom_point(aes(x, y, col = d), size = 1) + + scale_color_identity() + xlab(marker.1) + ylab(marker.2) + + theme_bw() + + geom_vline(xintercept = t1, linetype = "dashed") + + geom_hline(yintercept = t2, linetype = "dashed") + + p2 <- ggMarginal(p, df_heatmap, x = marker.1, y = marker.2, type = "density") + + + grobHM <- + arrangeGrob(p2,ncol=1,nrow=1) + - if (apply.filter.1 == TRUE) { - if (apply.filter.2 == TRUE) { + #Applying Filters to Data using Thresholds: + if (filter.data == TRUE && + (apply.filter.1 == TRUE | apply.filter.2 == TRUE) + ){ + df <- df %>% mutate(sample = so.sub@meta.data$orig.ident) %>% + mutate(cellbarcode = rownames(so.sub@meta.data)) + + if (marker.1.filter.direction == "greater than") { + ind1 <- df$mark1.scale > t1 + } else { + ind1 <- df$mark1.scale < t1 + } + + cat("\n") + print("Marker 1 filter:") + print(sum(ind1)) + + if (marker.2.filter.direction == "greater than") { + ind2 <- df$mark2.scale > t2 + } else { + ind2 <- df$mark2.scale < t2 + } + + cat("\n") + print("Marker 2 filter:") + print(sum(ind2)) + + if (apply.filter.1 == TRUE) { + if (apply.filter.2 == TRUE) { + if (filter.condition == TRUE) { + df <- df[c(ind1 & ind2), ] + } else { + df <- df[c(ind1 | ind2), ] + } + } else { + df <- df[ind1, ] + } + } else { + if (apply.filter.2) { + df <- df[ind2, ] + } + } + + + # Print out numbers of cells that meet threshold cutoffs for marker 1, + # marker 2 and for either intersection or union of 2 thresholds: + + colnames(df)[3:4] <- c(marker.1, marker.2) + so.sub.df <- so.sub@meta.data %>% + mutate(x = case_when( + rownames(so.sub@meta.data) %in% df$cellbarcode ~ TRUE, + TRUE ~ FALSE + )) + + colnames(so.sub.df) <- sub("x", parameter.name, + colnames(so.sub.df)) + + data.filt <- + as.data.frame.matrix(table(so.sub.df[[parameter.name]], + so.sub.df$orig.ident)) + data.filt$Total <- rowSums(data.filt) + data.filt <- data.filt %>% rownames_to_column("Passed Filter") + + # Add a title: if (filter.condition == TRUE) { - df <- df[c(ind1 & ind2),] + cond = "and" } else { - df <- df[c(ind1 | ind2),] + cond = "or" } - } else { - df <- df[ind1,] - } + + if (apply.filter.1 == TRUE) { + if (apply.filter.2 == TRUE) { + titlename <- paste( + "Number of cells that pass filters:\n", + marker.1, + marker.1.filter.direction, + marker.1.threshold, + cond, + marker.2, + marker.2.filter.direction, + marker.2.threshold + ) + } else { + titlename <- paste( + "Number of cells that pass filter:\n", + marker.1, + marker.1.filter.direction, + marker.1.threshold + ) + } + } else { + titlename <- paste( + "Number of cells that pass filter:\n", + marker.2, + marker.2.filter.direction, + marker.2.threshold + ) + } + + title <- + textGrob( + titlename, + y = 1, + vjust = 1, + gp = gpar(fontsize = 15) + ) + grid.table <- tableGrob(data.filt, rows = NULL) + g <- arrangeGrob(grid.table, top = title) + g$heights[[2]] <- unit(0.5, "npc") - max(g$grobs[[1]]$heights) + + rownames(so.sub.df) <- rownames(so.sub@meta.data) + so.sub@meta.data <- so.sub.df } else { - if (apply.filter.2) { - df <- df[ind2,] - } + g <- textGrob("No filtering thresholds applied") } - # Print out numbers of cells that meet threshold cutoffs for marker 1, - # marker 2 and for either intersection or union of 2 thresholds: - - colnames(df)[3:4] <- c(marker.1, marker.2) - so.sub.df <- so.sub@meta.data %>% - mutate(x = case_when( - rownames(so.sub@meta.data) %in% df$cellbarcode ~ TRUE, - TRUE ~ FALSE - )) - - colnames(so.sub.df) <- sub("x", parameter.name, - colnames(so.sub.df)) - - data.filt <- - as.data.frame.matrix(table(so.sub.df[[parameter.name]], - so.sub.df$orig.ident)) - data.filt$Total <- rowSums(data.filt) - data.filt <- data.filt %>% rownames_to_column("Passed Filter") - - # Add a title: - if (filter.condition == TRUE) { - cond = "and" - } else { - cond = "or" - } - - if (apply.filter.1 == TRUE) { - if (apply.filter.2 == TRUE) { - titlename <- paste( - "Number of cells that pass filters:\n", - marker.1, - M1.filter.direction, - marker.1.threshold, - cond, - marker.2, - M2.filter.direction, - marker.2.threshold - ) - } else { - titlename <- paste( - "Number of cells that pass filter:\n", - marker.1, - M1.filter.direction, - marker.1.threshold - ) - } - } else { - titlename <- paste( - "Number of cells that pass filter:\n", - marker.2, - M2.filter.direction, - marker.2.threshold - ) + if (data.reduction=='tsne'|data.reduction=='umap') { + + result.list <- list(object = so.sub, + plot = grob, + plot_densityHM = grobHM, + plot_table = g) + + + } else if (data.reduction=='both'){ + + result.list <- list(object = so.sub, + plot_tsne = grob.t, + plot_umap = grob.u, + plot_densityHM = grobHM, + plot_table = g) } + - title <- - textGrob( - titlename, - y = 1, - vjust = 1, - gp = gpar(fontsize = 15) - ) - grid.table <- tableGrob(data.filt, rows = NULL) - g <- arrangeGrob(grid.table, top = title) - g$heights[[2]] <- unit(0.5, "npc") - max(g$grobs[[1]]$heights) - - rownames(so.sub.df) <- rownames(so.sub@meta.data) - so.sub@meta.data <- so.sub.df - } else { - g <- textGrob("No filtering thresholds applied") - } - - result.list <- list("object" = so.sub, - "plot" = grob, - "plot2" = g) - - return(result.list) + return(result.list) } + + diff --git a/man/combineNormalize.Rd b/man/combineNormalize.Rd index dc24ccd..cebc1d5 100644 --- a/man/combineNormalize.Rd +++ b/man/combineNormalize.Rd @@ -24,11 +24,14 @@ combineNormalize( clust.res.low = 0.2, clust.res.high = 1.2, clust.res.bin = 0.2, - methods.pca = c("Elbow", "Marchenko-Pastur"), + methods.pca = "none", var.threshold = 0.1, + pca.reg.plot = FALSE, jackstraw = FALSE, jackstraw.dims = 5, - exclude.sample = "", + exclude.sample = NULL, + cell.count.limit = 35000, + reduce.so = FALSE, project.name = "scRNAProject", cell.hashing.data = FALSE ) @@ -71,7 +74,9 @@ Options: vst, mean.var.plot, dispersion. (Default: 'vst')} \item{only.var.genes}{If dataset is larger than ~40k filtered cells, set to TRUE. If TRUE, only variable genes will be available for -downstream analysis. (Default: FALSE)} +downstream analysis. If dataset is larger than the number of cells set in +"Conserve Memory Max Cell Limit" "Only Variable Genes" is automatically +set to TRUE. (Default: FALSE)} \item{draw.umap}{If TRUE, draw UMAP plot. (Default: TRUE)} @@ -99,11 +104,17 @@ at resolutions of 0.2, 0.4 and 0.6. (Default: 0.2)} \item{methods.pca}{Methods available: Marchenko-Pastur: use eigenvalue null upper bound from URD, Elbow: Find threshold where percent change in variation between consecutive PCs is less than X\% (set in var.threshold). -(Default: c('Elbow','Marchenko-Pastur'))} +If none is selected (regardless of other selections) the plot will not be +generated. (Default: 'none')} \item{var.threshold}{For Elbow method, set percent change threshold in variation between consecutive PCs. (Default: 0.1)} +\item{pca.reg.plot}{Opt to visualize the effect of your regression variables +on in a PCA plot. This plot will create PCA plots with and without +regression variables applied and can be used to help determine if +regression is necessary to properly normalize your data. (Default: FALSE)} + \item{jackstraw}{Opt to visualize your data in a Jackstraw plot. Jackstraw plot can add more description than an elbow plot but is compute intensive process and may not be suitable for larger datasets. (Default: FALSE)} @@ -112,7 +123,16 @@ process and may not be suitable for larger datasets. (Default: FALSE)} \item{exclude.sample}{Exclude unwanted samples from the merge step. Include sample names to be removed. If you want to exclude several samples, -separate each sample number by comma (e.g. sample1,sample2,sample3,sample4).} +separate each sample number by comma (e.g. sample1,sample2,sample3,sample4). +(Default: NULL)} + +\item{cell.count.limit}{If total number of cell exceeds this limit conserve +memory option of SCTransform will be used and return only Variable Genes. +(Default: 35000)} + +\item{reduce.so}{Remove any additional assays from input Seurat Objects +except for the original RNA Assay. This option should be used if input +Seurat Object was created outside of the NIDAP pipeline. (Default: FALSE)} \item{project.name}{Add project name to the Seurat object metadata. (Default: 'scRNAProject')} diff --git a/man/dualLabeling.Rd b/man/dualLabeling.Rd index 2aaa317..5e7eebc 100755 --- a/man/dualLabeling.Rd +++ b/man/dualLabeling.Rd @@ -12,24 +12,23 @@ dualLabeling( marker.2, marker.1.type = "SCT", marker.2.type = "SCT", - data.reduction = "umap", + data.reduction = "both", point.size = 0.5, point.shape = 16, point.transparency = 0.5, - add.marker.thresholds = FALSE, + add.marker.thresholds = TRUE, marker.1.threshold = 0.5, marker.2.threshold = 0.5, - filter.data = FALSE, - M1.filter.direction = "greater than", - M2.filter.direction = "greater than", + filter.data = TRUE, + marker.1.filter.direction = "greater than", + marker.2.filter.direction = "greater than", apply.filter.1 = TRUE, apply.filter.2 = TRUE, filter.condition = TRUE, - parameter.name = "Marker", - trim.marker.1 = TRUE, - trim.marker.2 = TRUE, + parameter.name = "My_CoExp", + trim.marker.1 = FALSE, + trim.marker.2 = FALSE, pre.scale.trim = 0.99, - density.heatmap = FALSE, display.unscaled.values = FALSE ) } @@ -49,7 +48,7 @@ dualLabeling( "protein","HTO" (default is "SCT")} \item{data.reduction}{Dimension Reduction method to use for image. Options -are "umap" or "tsne" (default is "umap")} +are umap, tsne, or both (default is "umap")} \item{point.size}{Point size for image (default is 0.5)} @@ -66,11 +65,11 @@ are "umap" or "tsne" (default is "umap")} \item{filter.data}{Add new parameter column to metadata annotating where marker thresholds are applied (default is TRUE)} -\item{M1.filter.direction}{Annotate cells that have gene expression levels +\item{marker.1.filter.direction}{Annotate cells that have gene expression levels for marker 1 using the marker 1 threshold. Choices are "greater than" or "less than" (default is "greater than")} -\item{M2.filter.direction}{Annotate cells that have gene expression levels +\item{marker.2.filter.direction}{Annotate cells that have gene expression levels for marker 2 using the marker 2 threshold. Choices are "greater than" or "less than" (default is "greater than")} @@ -82,21 +81,18 @@ or "less than" (default is "greater than")} intersection. If FALSE, apply both filters and take the union.} \item{parameter.name}{Name for metadata column for new marker filters -(Default is "Marker")} +(Default is "My_CoExp")} \item{trim.marker.1}{Trim top and bottom percentile of marker 1 signal to pre-scale trim values (below) to remove extremely low and high values -(Default is TRUE)} +(Default is FALSE)} \item{trim.marker.2}{Trim top and bottom percentile of marker 2 signal to pre-scale trim values (below) to remove extremely low and high values -(Default is TRUE)} +(Default is FALSE)} \item{pre.scale.trim}{Set trimming percentile values (Defalut is 0.99)} -\item{density.heatmap}{Creates a additional heatmap showing the density -distribution of cells. (Default is FALSE)} - \item{display.unscaled.values}{Set to TRUE if you want to view the unscaled gene/protein expression values (Default is FALSE)} } diff --git a/man/processRawData.Rd b/man/processRawData.Rd index a31d4af..efaa7db 100644 --- a/man/processRawData.Rd +++ b/man/processRawData.Rd @@ -19,7 +19,9 @@ processRawData( } \arguments{ \item{input}{Input can be a vector of scRNA-Seq .h5 files, or a list of -seurat objects for each sample. vector should include file path.} +seurat objects for each sample. TCRseq Metadata .csv files can also be +included and will be added to the corrisponding sample seurat object. +Vector of files should include entire file path.} \item{sample.metadata.table}{A table of sample metadata that you want to append to the already-existing metadata within the input Seurat Object(s). @@ -39,10 +41,9 @@ samples name (optional).} If FALSE, remove files when pattern is found in sample name. The pattern is set in the file.filter.regex parameter (below).} -\item{file.filter.regex}{Pattern or regular expression in file -name. Use the keep parameter (above) to keep or remove files -that contain pattern. If samples have been renamed set -regular expression based on new names} +\item{file.filter.regex}{Pattern or regular expression in sample +name. Use the 'keep' parameter to keep or remove files that contain pattern. +If samples have been renamed set regular expression based on new names} \item{split.h5}{If TRUE, split H5 into individual files. (Default: FALSE)} diff --git a/tests/testthat/_snaps/Filter_QC/Chariou_Standard.rds b/tests/testthat/_snaps/Filter_QC/Chariou_Standard.rds new file mode 100644 index 0000000..5d6d885 Binary files /dev/null and b/tests/testthat/_snaps/Filter_QC/Chariou_Standard.rds differ diff --git a/tests/testthat/_snaps/Filter_QC/NSCLC_Multi_Standard.rds b/tests/testthat/_snaps/Filter_QC/NSCLC_Multi_Standard.rds new file mode 100644 index 0000000..d3fd8c1 Binary files /dev/null and b/tests/testthat/_snaps/Filter_QC/NSCLC_Multi_Standard.rds differ diff --git a/tests/testthat/fixtures/PBMC_Single/PBMC_Single_Filtered_SO_downsample.rds b/tests/testthat/_snaps/Filter_QC/PBMC_Single_Standard.rds old mode 100755 new mode 100644 similarity index 100% rename from tests/testthat/fixtures/PBMC_Single/PBMC_Single_Filtered_SO_downsample.rds rename to tests/testthat/_snaps/Filter_QC/PBMC_Single_Standard.rds diff --git a/tests/testthat/_snaps/Filter_QC/TEC_Standard.rds b/tests/testthat/_snaps/Filter_QC/TEC_Standard.rds new file mode 100644 index 0000000..9fea9a8 Binary files /dev/null and b/tests/testthat/_snaps/Filter_QC/TEC_Standard.rds differ diff --git a/tests/testthat/_snaps/Filter_QC/TEC_filter.vdj.genes.rds b/tests/testthat/_snaps/Filter_QC/TEC_filter.vdj.genes.rds new file mode 100644 index 0000000..9fea9a8 Binary files /dev/null and b/tests/testthat/_snaps/Filter_QC/TEC_filter.vdj.genes.rds differ diff --git a/tests/testthat/fixtures/Chariou/Chariou_Cell_Types_SingleR_SO_downsample.rds b/tests/testthat/fixtures/Chariou/Chariou_Cell_Types_SingleR_SO_downsample.rds deleted file mode 100644 index 2efcefa..0000000 Binary files a/tests/testthat/fixtures/Chariou/Chariou_Cell_Types_SingleR_SO_downsample.rds and /dev/null differ diff --git a/tests/testthat/fixtures/Chariou/Chariou_Filtered_PCA_Norm_SO_downsample.rds b/tests/testthat/fixtures/Chariou/Chariou_Filtered_PCA_Norm_SO_downsample.rds deleted file mode 100755 index f71844a..0000000 Binary files a/tests/testthat/fixtures/Chariou/Chariou_Filtered_PCA_Norm_SO_downsample.rds and /dev/null differ diff --git a/tests/testthat/fixtures/Chariou/h5files/SCAF1713_1_1_filtered_contig_annotations.csv b/tests/testthat/fixtures/Chariou/h5files/SCAF1713_1_1_filtered_contig_annotations.csv deleted file mode 100644 index fc84fc7..0000000 --- a/tests/testthat/fixtures/Chariou/h5files/SCAF1713_1_1_filtered_contig_annotations.csv +++ /dev/null @@ -1,235 +0,0 @@ -barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id -AAAGATGTCACCTTAT-1,True,AAAGATGTCACCTTAT-1_contig_1,True,545,TRB,TRBV29,None,TRBJ2-1,TRBC2,True,True,CASSFGRTNYAEQFF,TGTGCTAGCAGTTTCGGACGGACTAACTATGCTGAGCAGTTCTTC,50816,10,clonotype2,clonotype2_consensus_2 -AAAGATGTCACCTTAT-1,True,AAAGATGTCACCTTAT-1_contig_2,True,498,TRA,TRAV1,None,TRAJ30,TRAC,True,True,CAVRAPTNAYKVIF,TGTGCTGTGAGGGCCCCCACAAATGCTTACAAAGTCATCTTT,20474,7,clonotype2,clonotype2_consensus_1 -AAAGTAGGTATCGCAT-1,True,AAAGTAGGTATCGCAT-1_contig_1,True,721,TRB,TRBV19,TRBD1,TRBJ2-2,TRBC2,True,True,CASSRGTGGSGQLYF,TGTGCCAGCAGCCGCGGGACAGGGGGCTCCGGGCAGCTCTACTTT,36634,13,clonotype3,clonotype3_consensus_2 -AAAGTAGGTATCGCAT-1,True,AAAGTAGGTATCGCAT-1_contig_2,True,606,TRA,TRAV14D-3-DV8,None,TRAJ53,TRAC,True,True,CAARNSGGSNYKLTF,TGTGCAGCAAGGAACAGTGGAGGCAGCAATTACAAACTGACATTT,3906,4,clonotype3,clonotype3_consensus_1 -AAAGTAGGTATCGCAT-1,True,AAAGTAGGTATCGCAT-1_contig_3,True,512,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,22936,4,clonotype3,None -AAAGTAGGTATCGCAT-1,True,AAAGTAGGTATCGCAT-1_contig_4,True,303,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,12480,2,clonotype3,None -AAATGCCAGTAGCGGT-1,True,AAATGCCAGTAGCGGT-1_contig_1,True,597,TRA,TRAV7-4,None,TRAJ26,TRAC,True,True,CAASDLNNYAQGLTF,TGTGCAGCTAGTGATTTAAATAACTATGCCCAGGGATTAACCTTC,21054,4,clonotype4,clonotype4_consensus_2 -AAATGCCAGTAGCGGT-1,True,AAATGCCAGTAGCGGT-1_contig_2,True,570,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-4,TRBC1,True,True,CASGDQGGSNERLFF,TGTGCCAGCGGTGACCAGGGTGGGTCCAACGAAAGATTATTTTTC,57128,10,clonotype4,clonotype4_consensus_1 -AACCGCGTCCAACCAA-1,True,AACCGCGTCCAACCAA-1_contig_1,True,499,TRA,TRAV6-5,None,TRAJ17,TRAC,True,True,CALSGHSAGNKLTF,TGTGCTCTGAGTGGACACAGTGCAGGGAACAAGCTAACTTTT,27610,2,clonotype5,clonotype5_consensus_1 -AACCGCGTCCAACCAA-1,True,AACCGCGTCCAACCAA-1_contig_2,True,589,TRA,TRAV7-4,None,TRAJ43,TRAC,True,False,None,None,16652,4,clonotype5,None -AACTGGTCAAGCGTAG-1,True,AACTGGTCAAGCGTAG-1_contig_1,True,562,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGDEWVQDTQYF,TGTGCCAGCGGTGATGAGTGGGTCCAAGACACCCAGTACTTT,61644,6,clonotype6,clonotype6_consensus_2 -AACTGGTCAAGCGTAG-1,True,AACTGGTCAAGCGTAG-1_contig_2,True,528,TRA,TRAV7D-2,None,TRAJ21,TRAC,True,True,CAASRGYNVLYF,TGTGCAGCAAGCAGAGGATACAACGTGCTTTACTTC,16798,2,clonotype6,clonotype6_consensus_1 -AAGGAGCGTTGCTCCT-1,True,AAGGAGCGTTGCTCCT-1_contig_1,True,514,TRB,TRBV14,None,TRBJ2-7,TRBC2,True,True,CASRQTGYEQYF,TGTGCCAGCAGACAGACAGGCTATGAACAGTACTTC,60078,7,clonotype7,clonotype7_consensus_2 -AAGGAGCGTTGCTCCT-1,True,AAGGAGCGTTGCTCCT-1_contig_2,True,538,TRA,TRAV8D-1,None,TRAJ44,TRAC,True,True,CATGSGGKLTL,TGTGCTACTGGCAGTGGTGGAAAACTCACTTTG,7086,2,clonotype7,clonotype7_consensus_1 -AAGTCTGAGTGGTAGC-1,True,AAGTCTGAGTGGTAGC-1_contig_1,True,530,TRA,TRAV16N,None,TRAJ45,TRAC,True,True,CAMREANTGGADRLTF,TGTGCTATGAGAGAGGCTAATACAGGAGGTGCAGATAGACTCACCTTT,818,5,clonotype8,clonotype8_consensus_1 -AAGTCTGAGTGGTAGC-1,True,AAGTCTGAGTGGTAGC-1_contig_2,True,645,TRB,TRBV2,None,TRBJ1-6,TRBC1,True,True,CASSQDGGYNSPLYF,TGTGCCAGCAGCCAAGATGGGGGCTATAATTCGCCCCTCTACTTT,440,6,clonotype8,clonotype8_consensus_2 -AAGTCTGAGTGGTAGC-1,True,AAGTCTGAGTGGTAGC-1_contig_3,True,328,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,3136,11,clonotype8,None -ACACTGAAGTTCGCAT-1,True,ACACTGAAGTTCGCAT-1_contig_1,True,713,TRA,TRAV9N-4,None,TRAJ15,TRAC,True,True,CAVSAYQGGRALIF,TGTGCTGTGAGCGCGTACCAGGGAGGCAGAGCTCTGATATTT,38776,3,clonotype9,clonotype9_consensus_1 -ACACTGAAGTTCGCAT-1,True,ACACTGAAGTTCGCAT-1_contig_2,True,558,TRB,TRBV20,None,TRBJ1-2,TRBC1,True,True,CGAKQTNSDYTF,TGTGGTGCTAAACAAACAAACTCCGACTACACCTTC,38630,3,clonotype9,clonotype9_consensus_2 -ACAGCCGCAGACAGGT-1,True,ACAGCCGCAGACAGGT-1_contig_1,True,560,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,516,11,clonotype10,clonotype10_consensus_1 -ACATCAGAGAGGGATA-1,True,ACATCAGAGAGGGATA-1_contig_1,True,571,TRB,TRBV1,None,TRBJ2-5,TRBC2,True,True,CTCSARDRVKDTQYF,TGCACCTGCAGTGCCCGGGACAGGGTTAAAGACACCCAGTACTTT,43510,8,clonotype11,clonotype11_consensus_1 -ACATCAGAGAGGGATA-1,True,ACATCAGAGAGGGATA-1_contig_2,True,422,TRA,None,None,TRAJ32,TRAC,False,False,None,None,6166,1,clonotype11,None -ACATCAGAGAGGGATA-1,True,ACATCAGAGAGGGATA-1_contig_3,True,574,Multi,TRDV1,None,TRAJ50,TRAC,True,False,CGGKAFASSSFSKLVF,TGTGGAGGGAAAGCTTTCGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,25906,8,clonotype11,None -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_1,True,557,TRA,TRAV6-2,None,TRAJ9,TRAC,True,True,CVRGNMGYKLTF,TGTGTTAGAGGGAACATGGGCTACAAACTTACCTTC,1040,8,clonotype12,clonotype12_consensus_2 -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_2,True,701,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASRDRSYNYAEQFF,TGTGCCAGCAGGGACAGGTCCTATAACTATGCTGAGCAGTTCTTC,1798,12,clonotype12,clonotype12_consensus_3 -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_3,True,570,TRA,TRAV2,None,TRAJ15,TRAC,True,True,CIVTVPYQGGRALIF,TGCATTGTGACTGTCCCCTACCAGGGAGGCAGAGCTCTGATATTT,538,7,clonotype12,clonotype12_consensus_1 -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_4,True,506,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,1846,13,clonotype12,None -ACGCCGATCCTTTCGG-1,True,ACGCCGATCCTTTCGG-1_contig_1,True,556,TRA,TRAV4-3,None,TRAJ21,TRAC,True,True,CAAERPNYNVLYF,TGTGCTGCTGAGAGGCCTAATTACAACGTGCTTTACTTC,21204,9,clonotype13,clonotype13_consensus_2 -ACGCCGATCCTTTCGG-1,True,ACGCCGATCCTTTCGG-1_contig_2,True,494,TRB,TRBV31,None,TRBJ2-4,TRBC2,True,True,CAWRRTGGDQNTLYF,TGTGCCTGGAGAAGGACAGGGGGCGATCAAAACACCTTGTACTTT,23502,6,clonotype13,clonotype13_consensus_1 -ACGCCGATCCTTTCGG-1,True,ACGCCGATCCTTTCGG-1_contig_3,True,635,TRB,None,None,TRBJ1-1,TRBC1,False,False,None,None,18264,5,clonotype13,None -ACGCCGATCCTTTCGG-1,True,ACGCCGATCCTTTCGG-1_contig_4,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,16144,5,clonotype13,None -AGGCCACGTTACGCGC-1,True,AGGCCACGTTACGCGC-1_contig_1,True,555,TRB,TRBV16,None,TRBJ2-7,TRBC2,True,True,CASSFRDWGASYEQYF,TGTGCAAGCAGCTTCCGGGACTGGGGGGCCTCCTATGAACAGTACTTC,31338,9,clonotype1,clonotype1_consensus_1 -AGGCCACGTTACGCGC-1,True,AGGCCACGTTACGCGC-1_contig_2,True,665,TRA,TRAV14D-1,None,TRAJ48,TRAC,True,True,CAASNYGNEKITF,TGTGCAGCAAGTAACTATGGAAATGAGAAAATAACTTTT,28520,7,clonotype1,clonotype1_consensus_2 -AGGCCACGTTACGCGC-1,True,AGGCCACGTTACGCGC-1_contig_3,True,413,TRA,None,None,TRAJ26,TRAC,False,False,None,None,14590,3,clonotype1,None -AGGGATGCAATTCCTT-1,True,AGGGATGCAATTCCTT-1_contig_1,True,505,TRB,TRBV13-1,None,TRBJ2-5,TRBC2,True,True,CASRGQKDTQYF,TGTGCCAGCAGGGGACAGAAAGACACCCAGTACTTT,69062,17,clonotype14,clonotype14_consensus_1 -AGTGAGGTCATCATTC-1,True,AGTGAGGTCATCATTC-1_contig_1,True,721,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSIAPVSNERLFF,TGTGCCAGCAGTATAGCTCCAGTTTCCAACGAAAGATTATTTTTC,3760,22,clonotype15,clonotype15_consensus_1 -AGTGAGGTCATCATTC-1,True,AGTGAGGTCATCATTC-1_contig_2,True,488,TRB,TRBV31,None,TRBJ1-6,TRBC1,True,False,None,None,2546,11,clonotype15,None -AGTGAGGTCATCATTC-1,True,AGTGAGGTCATCATTC-1_contig_3,True,365,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,12828,42,clonotype15,None -ATAGACCGTTAAAGTG-1,True,ATAGACCGTTAAAGTG-1_contig_1,True,523,TRB,TRBV31,None,TRBJ2-7,TRBC2,True,True,CAWSIPRQGAWEQYF,TGTGCCTGGAGCATTCCTCGACAGGGGGCGTGGGAACAGTACTTC,66062,5,clonotype16,clonotype16_consensus_2 -ATAGACCGTTAAAGTG-1,True,ATAGACCGTTAAAGTG-1_contig_2,True,623,TRA,TRAV12-3,None,TRAJ32,TRAC,True,True,CALSYYGGSGNKLIF,TGTGCTTTGAGTTATTATGGGGGCAGTGGCAACAAGCTCATCTTT,10612,2,clonotype16,clonotype16_consensus_1 -ATCACGACATAACCTG-1,True,ATCACGACATAACCTG-1_contig_1,True,571,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGDDRGGTQYF,TGTGCCAGCGGTGATGACAGGGGAGGCACCCAGTACTTT,36714,4,clonotype17,clonotype17_consensus_2 -ATCACGACATAACCTG-1,True,ATCACGACATAACCTG-1_contig_2,True,571,TRA,TRAV13-1,None,TRAJ31,TRAC,True,True,CAMNNNNRIFF,TGTGCTATGAATAACAATAACAGAATCTTCTTT,10690,2,clonotype17,clonotype17_consensus_1 -ATCACGACATAACCTG-1,True,ATCACGACATAACCTG-1_contig_3,True,651,TRA,TRAV7-1,None,TRAJ21,TRAC,True,True,CAVSMMPNYNVLYF,TGTGCAGTGAGCATGATGCCTAATTACAACGTGCTTTACTTC,11156,4,clonotype17,clonotype17_consensus_3 -ATCACGACATAACCTG-1,True,ATCACGACATAACCTG-1_contig_4,True,437,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,19478,2,clonotype17,None -ATTACTCCATGCCCGA-1,True,ATTACTCCATGCCCGA-1_contig_1,True,643,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,True,CTCSAQGAQGTEVFF,TGCACCTGCAGTGCGCAGGGGGCGCAGGGCACAGAAGTCTTCTTT,738,7,clonotype18,clonotype18_consensus_1 -ATTACTCCATGCCCGA-1,True,ATTACTCCATGCCCGA-1_contig_2,True,355,TRA,TRAV6-6,None,TRAJ15,TRAC,True,False,CALGDPQGGRALIF,TGTGCTCTGGGTGATCCCCAGGGAGGCAGAGCTCTGATATTT,246,1,clonotype18,None -ATTACTCCATGCCCGA-1,True,ATTACTCCATGCCCGA-1_contig_3,True,393,TRA,TRAV6-6,None,TRAJ15,TRAC,True,False,CALGDPQGGRALIF,TGTGCTCTGGGTGATCCCCAGGGAGGCAGAGCTCTGATATTT,106,2,clonotype18,None -ATTATCCGTCCTAGCG-1,True,ATTATCCGTCCTAGCG-1_contig_1,True,544,TRA,TRAV13-2,None,TRAJ30,TRAC,True,True,CAIDRDTNAYKVIF,TGTGCTATAGACCGTGACACAAATGCTTACAAAGTCATCTTT,45652,5,clonotype19,clonotype19_consensus_2 -ATTATCCGTCCTAGCG-1,True,ATTATCCGTCCTAGCG-1_contig_2,True,527,TRB,TRBV13-3,None,TRBJ2-4,TRBC2,True,True,CASSDWGGQNTLYF,TGTGCCAGCAGTGATTGGGGGGGGCAAAACACCTTGTACTTT,23380,3,clonotype19,clonotype19_consensus_1 -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_1,True,586,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSANERLFF,TGTGCCAGCAGTGCCAACGAAAGATTATTTTTC,964,8,clonotype20,clonotype20_consensus_2 -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_2,True,597,TRA,TRAV12D-2,None,TRAJ49,TRAC,True,True,CALSAPNTGYQNFYF,TGTGCTCTGAGTGCTCCGAACACGGGTTACCAGAACTTCTATTTT,366,4,clonotype20,clonotype20_consensus_1 -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_3,True,328,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,336,2,clonotype20,None -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_4,True,364,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,180,2,clonotype20,None -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_5,True,363,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,176,1,clonotype20,None -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_6,True,571,Multi,TRAV8D-2,None,TRDJ1,TRAC,True,False,CATDVGGRRDTS,TGTGCTACAGACGTGGGGGGGCGGAGGGATACGAGC,260,3,clonotype20,None -CACAAACGTTAAGTAG-1,True,CACAAACGTTAAGTAG-1_contig_1,True,555,TRA,TRAV8D-2,None,TRAJ26,TRAC,True,True,CATDNYAQGLTF,TGTGCTACAGATAACTATGCCCAGGGATTAACCTTC,36432,8,clonotype21,clonotype21_consensus_1 -CACAAACGTTAAGTAG-1,True,CACAAACGTTAAGTAG-1_contig_2,True,518,TRB,TRBV13-1,None,TRBJ2-2,TRBC2,True,True,CASSGDRDTGQLYF,TGTGCCAGCAGCGGGGACAGGGACACCGGGCAGCTCTACTTT,33608,8,clonotype21,clonotype21_consensus_2 -CACAAACGTTAAGTAG-1,True,CACAAACGTTAAGTAG-1_contig_3,True,517,TRA,TRAV6D-4,None,TRAJ31,TRAC,True,False,CSGPNNNRIFF,TGCTCTGGCCCCAACAATAACAGAATCTTCTTT,8522,2,clonotype21,None -CACACAACAGGGTACA-1,True,CACACAACAGGGTACA-1_contig_1,True,544,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGARAWGSYEQYF,TGTGGTGCTAGGGCCTGGGGGTCCTATGAACAGTACTTC,72746,12,clonotype22,clonotype22_consensus_1 -CACACAACAGGGTACA-1,True,CACACAACAGGGTACA-1_contig_2,True,536,Multi,TRDV1,None,TRAJ34,TRAC,True,False,CGGKGRTSNTDKVVF,TGTGGAGGGAAAGGGAGGACTTCCAATACCGACAAAGTCGTCTTT,6188,1,clonotype22,None -CACACCTAGGGCACTA-1,True,CACACCTAGGGCACTA-1_contig_1,True,715,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSIHANTEVFF,TGTGCCAGCAGTATCCACGCAAACACAGAAGTCTTCTTT,1766,26,clonotype23,clonotype23_consensus_1 -CACACCTAGGGCACTA-1,True,CACACCTAGGGCACTA-1_contig_2,True,545,TRA,TRAV9-1,None,TRAJ56,TRAC,True,True,CAVSATGGNNKLTF,TGTGCTGTGAGCGCTACTGGAGGCAATAATAAGCTGACTTTT,256,11,clonotype23,clonotype23_consensus_2 -CACCAGGGTAAGTAGT-1,True,CACCAGGGTAAGTAGT-1_contig_1,True,569,TRB,TRBV2,None,TRBJ2-5,TRBC2,True,True,CASSQDGTGQDTQYF,TGTGCCAGCAGCCAAGACGGGACTGGACAAGACACCCAGTACTTT,1116,11,clonotype24,clonotype24_consensus_1 -CACCAGGGTAAGTAGT-1,True,CACCAGGGTAAGTAGT-1_contig_2,True,565,TRA,TRAV4-4-DV10,None,TRAJ49,TRAC,True,True,CAAEAGPGYQNFYF,TGTGCTGCTGAGGCAGGGCCGGGTTACCAGAACTTCTATTTT,1252,13,clonotype24,clonotype24_consensus_2 -CACCAGGGTAGCGTAG-1,True,CACCAGGGTAGCGTAG-1_contig_1,True,575,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSDKISNERLFF,TGTGCCAGCAGTGATAAAATTTCCAACGAAAGATTATTTTTC,42294,6,clonotype25,clonotype25_consensus_1 -CACCAGGGTAGCGTAG-1,True,CACCAGGGTAGCGTAG-1_contig_2,True,617,TRA,TRAV3-1,None,TRAJ35,TRAC,False,False,CAVSAGFASALTF,TGCGCAGTCAGTGCAGGCTTTGCAAGTGCGCTGACATTT,19912,3,clonotype25,None -CACCAGGGTAGCGTAG-1,True,CACCAGGGTAGCGTAG-1_contig_3,True,335,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,17134,2,clonotype25,None -CACCAGGGTGCCTGGT-1,True,CACCAGGGTGCCTGGT-1_contig_1,True,568,TRB,TRBV1,TRBD2,TRBJ2-7,TRBC2,True,True,CTCSAGLGGPEQYF,TGCACCTGCAGTGCGGGACTGGGGGGGCCGGAACAGTACTTC,43520,7,clonotype26,clonotype26_consensus_2 -CACCAGGGTGCCTGGT-1,True,CACCAGGGTGCCTGGT-1_contig_2,True,567,TRA,TRAV8D-2,None,TRAJ52,TRAC,True,True,CATDRGTGANTGKLTF,TGTGCTACAGATAGGGGCACTGGAGCTAACACTGGAAAGCTCACGTTT,35340,7,clonotype26,clonotype26_consensus_1 -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_1,True,600,TRA,TRAV12D-2,None,TRAJ56,TRAC,True,True,CALSSTGGNNKLTF,TGTGCTCTGAGTTCTACTGGAGGCAATAATAAGCTGACTTTT,5214,30,clonotype27,clonotype27_consensus_1 -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_2,True,575,TRB,TRBV12-1,None,TRBJ2-4,TRBC2,True,True,CASSLEGSQNTLYF,TGTGCCAGCTCTCTCGAGGGTAGTCAAAACACCTTGTACTTT,720,7,clonotype27,clonotype27_consensus_2 -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_3,True,365,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,2052,10,clonotype27,None -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_4,True,326,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,888,3,clonotype27,None -CATGCCTGTATTCGTG-1,True,CATGCCTGTATTCGTG-1_contig_1,True,573,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-1,TRBC2,True,True,CASGDATGLNYAEQFF,TGTGCCAGCGGTGATGCAACAGGGCTAAACTATGCTGAGCAGTTCTTC,1568,15,clonotype28,clonotype28_consensus_2 -CATGCCTGTATTCGTG-1,True,CATGCCTGTATTCGTG-1_contig_2,True,570,TRA,TRAV2,None,TRAJ12,TRAC,True,True,CIVTDTGTGGYKVVF,TGCATTGTGACTGACACCGGGACTGGAGGCTATAAAGTGGTCTTT,918,8,clonotype28,clonotype28_consensus_1 -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_1,True,560,TRB,TRBV2,None,TRBJ1-5,TRBC1,True,True,CASSQDYNQAPLF,TGTGCCAGCAGCCAAGATTACAACCAGGCTCCGCTTTTT,188,2,clonotype29,clonotype29_consensus_1 -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_2,True,354,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,1262,4,clonotype29,None -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_3,True,336,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,342,1,clonotype29,None -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSQGLGDSYEQYF,TGTGCCAGCAGCCAAGGACTGGGGGACTCCTATGAACAGTACTTC,1144,10,clonotype30,clonotype30_consensus_2 -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_2,True,534,TRA,TRAV7-3,None,TRAJ40,TRAC,True,True,CAVSIGTGNYKYVF,TGTGCAGTGAGCATTGGTACAGGAAACTACAAATACGTCTTT,1032,13,clonotype30,clonotype30_consensus_1 -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_3,True,524,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,False,None,None,444,3,clonotype30,None -CCTCTGAAGAGTGACC-1,True,CCTCTGAAGAGTGACC-1_contig_1,True,597,TRA,TRAV7-4,None,TRAJ48,TRAC,True,True,CAASPPNYGNEKITF,TGTGCAGCTAGCCCCCCCAACTATGGAAATGAGAAAATAACTTTT,65014,8,clonotype31,clonotype31_consensus_1 -CCTCTGAAGAGTGACC-1,True,CCTCTGAAGAGTGACC-1_contig_2,True,305,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,12980,1,clonotype31,None -CGAGCCAAGAAACCAT-1,True,CGAGCCAAGAAACCAT-1_contig_1,True,555,TRB,TRBV16,None,TRBJ2-7,TRBC2,True,True,CASSFRDWGASYEQYF,TGTGCAAGCAGCTTCCGGGACTGGGGGGCCTCCTATGAACAGTACTTC,57554,9,clonotype1,clonotype1_consensus_1 -CGAGCCAAGAAACCAT-1,True,CGAGCCAAGAAACCAT-1_contig_2,True,629,TRA,TRAV14D-1,None,TRAJ48,TRAC,True,True,CAASNYGNEKITF,TGTGCAGCAAGTAACTATGGAAATGAGAAAATAACTTTT,14312,2,clonotype1,clonotype1_consensus_2 -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_1,True,519,TRB,TRBV13-3,None,TRBJ1-2,TRBC1,True,True,CASSDAWGPDYTF,TGTGCCAGCAGTGATGCATGGGGCCCCGACTACACCTTC,296,2,clonotype32,clonotype32_consensus_1 -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_2,True,531,TRA,TRAV7-3,None,TRAJ12,None,True,False,CSKTGGYKVVF,TGCAGTAAGACTGGAGGCTATAAAGTGGTCTTT,46,1,clonotype32,None -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_3,True,503,TRB,None,None,TRBJ1-1,TRBC1,False,False,None,None,296,2,clonotype32,None -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_4,True,333,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,1064,3,clonotype32,None -CGGACTGGTCAGGACA-1,True,CGGACTGGTCAGGACA-1_contig_1,True,525,TRB,TRBV5,None,TRBJ1-4,TRBC1,True,True,CASSQEGGLSNERLFF,TGTGCCAGCAGCCAAGAGGGAGGGCTTTCCAACGAAAGATTATTTTTC,52156,7,clonotype33,clonotype33_consensus_2 -CGGACTGGTCAGGACA-1,True,CGGACTGGTCAGGACA-1_contig_2,True,591,TRA,TRAV7-4,None,TRAJ57,TRAC,True,True,CAASEGGSAKLIF,TGTGCAGCTAGTGAAGGAGGGTCTGCGAAGCTCATCTTT,26336,3,clonotype33,clonotype33_consensus_1 -CGGACTGTCCACGAAT-1,True,CGGACTGTCCACGAAT-1_contig_1,True,655,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,582,16,clonotype34,clonotype34_consensus_2 -CGGACTGTCCACGAAT-1,True,CGGACTGTCCACGAAT-1_contig_2,True,520,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,428,6,clonotype34,clonotype34_consensus_1 -CGGACTGTCCACGAAT-1,True,CGGACTGTCCACGAAT-1_contig_3,True,368,TRB,None,None,TRBJ1-5,TRBC1,False,False,None,None,502,4,clonotype34,None -CGGAGTCGTAAGTGGC-1,True,CGGAGTCGTAAGTGGC-1_contig_1,True,718,TRB,TRBV19,None,TRBJ1-3,TRBC1,True,True,CASSPPGEGNTLYF,TGTGCCAGCAGTCCCCCGGGGGAAGGAAATACGCTCTATTTT,57520,8,clonotype35,clonotype35_consensus_2 -CGGAGTCGTAAGTGGC-1,True,CGGAGTCGTAAGTGGC-1_contig_2,True,588,TRA,TRAV7-4,None,TRAJ49,TRAC,True,True,CAGNTGYQNFYF,TGTGCAGGGAACACGGGTTACCAGAACTTCTATTTT,16208,4,clonotype35,clonotype35_consensus_1 -CGGAGTCGTAAGTGGC-1,True,CGGAGTCGTAAGTGGC-1_contig_3,True,466,TRA,None,None,TRAJ32,TRAC,False,False,None,None,2758,1,clonotype35,None -CGTAGCGTCAAGGCTT-1,True,CGTAGCGTCAAGGCTT-1_contig_1,True,513,TRA,TRAV7-3,None,TRAJ40,TRAC,True,True,CAVSMGTGNYKYVF,TGTGCAGTGAGCATGGGTACAGGAAACTACAAATACGTCTTT,52794,8,clonotype36,clonotype36_consensus_1 -CGTCACTAGATACACA-1,True,CGTCACTAGATACACA-1_contig_1,True,513,TRB,TRBV13-1,None,TRBJ1-5,TRBC1,True,True,CASSVSRDRNQAPLF,TGTGCCAGCAGTGTCTCCCGGGACAGAAACCAGGCTCCGCTTTTT,1084,5,clonotype37,clonotype37_consensus_1 -CGTCCATGTTTGGGCC-1,True,CGTCCATGTTTGGGCC-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-1,TRBC2,True,True,CASSQETGVYAEQFF,TGTGCCAGCAGCCAAGAGACTGGGGTCTATGCTGAGCAGTTCTTC,40270,8,clonotype38,clonotype38_consensus_2 -CGTCCATGTTTGGGCC-1,True,CGTCCATGTTTGGGCC-1_contig_2,True,529,TRA,TRAV8D-1,None,TRAJ22,TRAC,True,True,CATDASSGSWQLIF,TGTGCTACTGATGCATCTTCTGGCAGCTGGCAACTCATCTTT,13218,5,clonotype38,clonotype38_consensus_1 -CGTCCATGTTTGGGCC-1,True,CGTCCATGTTTGGGCC-1_contig_3,True,416,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,18384,5,clonotype38,None -CGTCCATGTTTGGGCC-1,True,CGTCCATGTTTGGGCC-1_contig_4,True,344,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,4682,1,clonotype38,None -CGTGTCTAGTGCCAGA-1,True,CGTGTCTAGTGCCAGA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,1190,12,clonotype39,clonotype39_consensus_2 -CGTGTCTAGTGCCAGA-1,True,CGTGTCTAGTGCCAGA-1_contig_2,True,549,TRA,TRAV7-3,None,TRAJ12,TRAC,True,True,CAVSMGTGGYKVVF,TGTGCAGTGAGCATGGGGACTGGAGGCTATAAAGTGGTCTTT,1244,13,clonotype39,clonotype39_consensus_1 -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_1,True,567,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-3,TRBC1,True,True,CASGDDNSGNTLYF,TGTGCCAGCGGTGATGATAATTCTGGAAATACGCTCTATTTT,1530,12,clonotype40,clonotype40_consensus_1 -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_2,True,332,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,684,2,clonotype40,None -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_3,True,381,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,1182,6,clonotype40,None -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_4,True,386,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,484,4,clonotype40,None -CTCGTCAGTCACACGC-1,True,CTCGTCAGTCACACGC-1_contig_1,True,521,TRB,TRBV29,None,TRBJ1-2,TRBC1,True,True,CASIGPNSDYTF,TGTGCTAGCATCGGACCGAACTCCGACTACACCTTC,40120,10,clonotype41,clonotype41_consensus_2 -CTCGTCAGTCACACGC-1,True,CTCGTCAGTCACACGC-1_contig_2,True,544,TRA,TRAV6N-7,None,TRAJ39,TRAC,True,True,CALRNNAGAKLTF,TGTGCTCTGAGGAATAATGCAGGTGCCAAGCTCACATTC,17782,3,clonotype41,clonotype41_consensus_1 -CTCGTCAGTCACACGC-1,True,CTCGTCAGTCACACGC-1_contig_3,True,595,TRA,TRAV13-1,None,TRAJ32,TRAC,True,False,None,None,8258,1,clonotype41,None -CTGAAGTGTGATAAAC-1,True,CTGAAGTGTGATAAAC-1_contig_1,True,559,TRA,TRAV4-3,None,TRAJ22,TRAC,True,True,CAAEAPSGSWQLIF,TGTGCTGCTGAGGCCCCTTCTGGCAGCTGGCAACTCATCTTT,49124,7,clonotype42,clonotype42_consensus_1 -CTGAAGTGTGATAAAC-1,True,CTGAAGTGTGATAAAC-1_contig_2,True,582,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGDGTGGLNQDTQYF,TGTGCCAGCGGTGATGGGACAGGGGGACTTAACCAAGACACCCAGTACTTT,26930,2,clonotype42,clonotype42_consensus_2 -CTGGTCTAGTGTACCT-1,True,CTGGTCTAGTGTACCT-1_contig_1,True,598,TRB,TRBV2,None,TRBJ2-7,TRBC2,True,True,CASSQERDNYEQYF,TGTGCCAGCAGCCAAGAAAGGGACAATTATGAACAGTACTTC,630,8,clonotype43,clonotype43_consensus_2 -CTGGTCTAGTGTACCT-1,True,CTGGTCTAGTGTACCT-1_contig_2,True,512,TRA,TRAV6-6,None,TRAJ34,TRAC,True,True,CALGGANTDKVVF,TGTGCTCTGGGTGGAGCCAATACCGACAAAGTCGTCTTT,1064,8,clonotype43,clonotype43_consensus_1 -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCTGGGACAGGGAACACAGAAGTCTTCTTT,4254,17,clonotype44,clonotype44_consensus_1 -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_2,True,400,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,1186,5,clonotype44,None -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_3,True,474,TRA,TRAV9-4,None,TRAJ17,TRAC,True,False,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,206,3,clonotype44,None -CTTCTCTCATTCCTGC-1,True,CTTCTCTCATTCCTGC-1_contig_1,True,514,TRB,TRBV14,None,TRBJ2-7,TRBC2,True,True,CASRQTVYEQYF,TGTGCCAGCAGACAGACTGTCTATGAACAGTACTTC,29690,15,clonotype45,clonotype45_consensus_1 -CTTCTCTCATTCCTGC-1,True,CTTCTCTCATTCCTGC-1_contig_2,True,538,TRA,TRAV13D-2,None,TRAJ39,TRAC,True,True,CAILNNAGAKLTF,TGTGCTATACTTAATAATGCAGGTGCCAAGCTCACATTC,28570,15,clonotype45,clonotype45_consensus_2 -CTTCTCTCATTCCTGC-1,True,CTTCTCTCATTCCTGC-1_contig_3,True,371,TRA,TRAV17,None,TRAJ52,TRAC,True,False,CTGGSTGANTGKLTF,TGCACTGGAGGATCCACTGGAGCTAACACTGGAAAGCTCACGTTT,8744,4,clonotype45,None -CTTCTCTCATTCCTGC-1,True,CTTCTCTCATTCCTGC-1_contig_4,True,329,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,9400,6,clonotype45,None -GAACGGATCATGTGGT-1,True,GAACGGATCATGTGGT-1_contig_1,True,532,TRB,TRBV20,None,TRBJ1-1,TRBC1,True,True,CGARRQGNTEVFF,TGTGGTGCTAGGAGGCAGGGGAACACAGAAGTCTTCTTT,33068,6,clonotype46,clonotype46_consensus_1 -GAACGGATCATGTGGT-1,True,GAACGGATCATGTGGT-1_contig_2,True,559,TRA,TRAV12D-2,None,TRAJ22,TRAC,True,True,CALSVASGSWQLIF,TGTGCTCTGAGTGTGGCTTCTGGCAGCTGGCAACTCATCTTT,6424,1,clonotype46,clonotype46_consensus_2 -GAACGGATCATGTGGT-1,True,GAACGGATCATGTGGT-1_contig_3,True,363,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,29364,7,clonotype46,None -GACGTTAAGTGTTGAA-1,True,GACGTTAAGTGTTGAA-1_contig_1,True,704,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSSNENTEVFF,TGTGCCAGCAGTTCGAACGAAAACACAGAAGTCTTCTTT,2538,15,clonotype47,clonotype47_consensus_2 -GACGTTAAGTGTTGAA-1,True,GACGTTAAGTGTTGAA-1_contig_2,True,562,TRA,TRAV8D-2,None,TRAJ52,TRAC,True,True,CATDPFGGANTGKLTF,TGTGCTACAGATCCCTTCGGGGGAGCTAACACTGGAAAGCTCACGTTT,148,1,clonotype47,clonotype47_consensus_1 -GACTGCGAGGACCACA-1,True,GACTGCGAGGACCACA-1_contig_1,True,521,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSDAGQGGYEQYF,TGTGCCAGCAGTGATGCGGGACAGGGAGGATATGAACAGTACTTC,51710,9,clonotype48,clonotype48_consensus_1 -GACTGCGAGGACCACA-1,True,GACTGCGAGGACCACA-1_contig_2,True,624,TRB,TRBV15,None,TRBJ2-1,TRBC2,True,False,CQQPGKGEEAEQFF,TGCCAGCAGCCCGGTAAGGGGGAGGAAGCTGAGCAGTTCTTC,7172,3,clonotype48,None -GATCGATGTTAAGACA-1,True,GATCGATGTTAAGACA-1_contig_1,True,563,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-3,TRBC1,True,True,CASGDSGNTLYF,TGTGCCAGCGGTGATTCTGGAAATACGCTCTATTTT,2548,10,clonotype49,clonotype49_consensus_1 -GATCTAGGTTCGGCAC-1,True,GATCTAGGTTCGGCAC-1_contig_1,True,538,TRA,TRAV6-6,None,TRAJ31,TRAC,True,True,CALSANNNNRIFF,TGTGCTCTGAGTGCGAATAACAATAACAGAATCTTCTTT,538,6,clonotype50,clonotype50_consensus_1 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_1,True,526,TRA,TRAV6N-7,None,TRAJ22,TRAC,True,True,CALSDSSGSWQLIF,TGTGCTCTGAGTGACTCTTCTGGCAGCTGGCAACTCATCTTT,158,2,clonotype51,clonotype51_consensus_1 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_2,True,521,TRB,TRBV13-1,None,TRBJ2-5,TRBC2,True,True,CASSDGLGFNQDTQYF,TGTGCCAGCAGTGATGGACTGGGGTTTAACCAAGACACCCAGTACTTT,294,3,clonotype51,clonotype51_consensus_2 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_3,True,537,TRA,TRAV13-1,None,TRAJ22,TRAC,True,True,CAISGSWQLIF,TGTGCTATTTCTGGCAGCTGGCAACTCATCTTT,528,6,clonotype51,clonotype51_consensus_3 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_4,True,361,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,308,1,clonotype51,None -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_5,True,427,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,130,2,clonotype51,None -GCACATACAAGCCGTC-1,True,GCACATACAAGCCGTC-1_contig_1,True,558,TRB,TRBV3,None,TRBJ1-3,TRBC1,True,True,CARGDRHSGNTLYF,TGTGCCAGGGGGGACAGGCATTCTGGAAATACGCTCTATTTT,32094,9,clonotype52,clonotype52_consensus_1 -GCACATACAAGCCGTC-1,True,GCACATACAAGCCGTC-1_contig_2,True,368,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,8500,2,clonotype52,None -GCACATACAAGCCGTC-1,True,GCACATACAAGCCGTC-1_contig_3,True,324,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,23742,3,clonotype52,None -GCACATACAAGCCGTC-1,True,GCACATACAAGCCGTC-1_contig_4,True,435,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,8244,1,clonotype52,None -GCACATACAAGCCGTC-1,True,GCACATACAAGCCGTC-1_contig_5,True,497,TRA,TRAV9-4,None,TRAJ50,TRAC,True,False,CAVSPLIASSSFSKLVF,TGTGCTGTGAGCCCCCTTATAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,6680,1,clonotype52,None -GCACATAGTACTCTCC-1,True,GCACATAGTACTCTCC-1_contig_1,True,557,TRA,TRAV3-3,None,TRAJ47,TRAC,True,True,CAGDYANKMIF,TGCGCGGGGGACTATGCAAACAAGATGATCTTT,1306,11,clonotype53,clonotype53_consensus_2 -GCACATAGTACTCTCC-1,True,GCACATAGTACTCTCC-1_contig_2,True,522,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGARVGVGQYF,TGTGGTGCTAGGGTTGGGGTAGGACAGTACTTC,1610,10,clonotype53,clonotype53_consensus_1 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_1,True,526,TRA,TRAV6N-7,None,TRAJ17,TRAC,True,True,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,258,8,clonotype54,clonotype54_consensus_1 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_2,True,514,TRB,TRBV14,None,TRBJ1-5,TRBC1,True,True,CASSPGTEAPLF,TGTGCCAGCAGTCCCGGGACCGAGGCTCCGCTTTTT,942,20,clonotype54,clonotype54_consensus_2 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_3,True,563,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,360,5,clonotype54,None -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_4,True,330,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,1446,13,clonotype54,None -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_5,True,348,TRA,TRAV6N-6,None,TRAJ17,TRAC,True,False,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,88,1,clonotype54,clonotype54_consensus_1 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_6,True,370,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,590,12,clonotype54,None -GCATGATGTCGCATAT-1,True,GCATGATGTCGCATAT-1_contig_1,True,630,TRA,TRAV5D-4,None,TRAJ57,TRAC,True,True,CAASDQGGSAKLIF,TGTGCTGCAAGTGATCAAGGAGGGTCTGCGAAGCTCATCTTT,678,5,clonotype55,clonotype55_consensus_1 -GCCAAATGTGTTGAGG-1,True,GCCAAATGTGTTGAGG-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-1,TRBC2,True,True,CASSQHWGGGAEQFF,TGTGCCAGCAGCCAACACTGGGGGGGCGGTGCTGAGCAGTTCTTC,14742,3,clonotype56,clonotype56_consensus_2 -GCCAAATGTGTTGAGG-1,True,GCCAAATGTGTTGAGG-1_contig_2,True,514,TRA,TRAV6-6,None,TRAJ34,TRAC,True,True,CALGDPNTDKVVF,TGTGCTCTGGGTGACCCCAATACCGACAAAGTCGTCTTT,14106,2,clonotype56,clonotype56_consensus_1 -GCCAAATGTGTTGAGG-1,True,GCCAAATGTGTTGAGG-1_contig_3,True,316,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,11662,1,clonotype56,None -GCCAAATGTGTTGAGG-1,True,GCCAAATGTGTTGAGG-1_contig_4,True,556,TRA,TRAV3-3,None,TRAJ35,TRAC,False,False,CAVSADRLCKCADIWIW,TGCGCAGTCAGTGCAGACAGGCTTTGCAAGTGCGCTGACATTTGGATCTGG,36902,5,clonotype56,None -GCGGGTTCAGGAATCG-1,True,GCGGGTTCAGGAATCG-1_contig_1,True,547,TRA,TRAV13D-3,None,TRAJ17,TRAC,True,True,CAMERPNSAGNKLTF,TGTGCTATGGAACGTCCTAACAGTGCAGGGAACAAGCTAACTTTT,46258,4,clonotype57,clonotype57_consensus_1 -GCGGGTTCAGGAATCG-1,True,GCGGGTTCAGGAATCG-1_contig_2,True,541,TRB,TRBV29,None,TRBJ1-5,TRBC1,True,True,CASSLTVNNQAPLF,TGTGCTAGCAGTTTAACAGTTAACAACCAGGCTCCGCTTTTT,16090,1,clonotype57,clonotype57_consensus_2 -GCGGGTTCAGGAATCG-1,True,GCGGGTTCAGGAATCG-1_contig_3,True,371,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,15710,1,clonotype57,None -GGAATAAGTTGTCGCG-1,True,GGAATAAGTTGTCGCG-1_contig_1,True,602,TRB,TRBV3,None,TRBJ1-2,TRBC1,True,True,CASSRDDANSDYTF,TGTGCCAGCAGCCGGGACGATGCAAACTCCGACTACACCTTC,716,11,clonotype58,clonotype58_consensus_1 -GGAATAAGTTGTCGCG-1,True,GGAATAAGTTGTCGCG-1_contig_2,True,307,TRB,TRBV17,None,TRBJ1-1,TRBC1,True,False,None,None,710,2,clonotype58,None -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_1,True,502,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQDFPEEVFF,TGTGCCAGCAGCCAAGATTTCCCAGAAGAAGTCTTCTTT,666,6,clonotype59,clonotype59_consensus_2 -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_2,True,493,TRA,TRAV6-5,None,TRAJ32,TRAC,True,True,CALSHYGGSGNKLIF,TGTGCTCTGAGTCATTATGGGGGCAGTGGCAACAAGCTCATCTTT,338,3,clonotype59,clonotype59_consensus_1 -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_3,True,339,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,322,1,clonotype59,None -GGCCGATTCTAACTGG-1,True,GGCCGATTCTAACTGG-1_contig_1,True,725,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CAGTNSAGNKLTF,TGTGCTGGGACTAACAGTGCAGGGAACAAGCTAACTTTT,43940,5,clonotype60,clonotype60_consensus_1 -GGCCGATTCTAACTGG-1,True,GGCCGATTCTAACTGG-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,34672,3,clonotype60,clonotype60_consensus_2 -GGCTGGTTCAAAGACA-1,True,GGCTGGTTCAAAGACA-1_contig_1,True,569,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-4,TRBC2,True,True,CASGQTGGNTLYF,TGTGCCAGCGGTCAGACAGGGGGCAACACCTTGTACTTT,63604,4,clonotype61,clonotype61_consensus_1 -GGGCATCCAATAAGCA-1,True,GGGCATCCAATAAGCA-1_contig_1,True,540,TRB,TRBV20,None,TRBJ1-4,TRBC1,True,True,CGAPRTGGDERLFF,TGTGGTGCCCCCCGGACAGGGGGCGACGAAAGATTATTTTTC,492,4,clonotype62,clonotype62_consensus_1 -GGGCATCCAATAAGCA-1,True,GGGCATCCAATAAGCA-1_contig_2,True,511,TRA,TRAV4-2,None,TRAJ39,TRAC,True,True,CAAFNAGAKLTF,TGTGCTGCCTTTAATGCAGGTGCCAAGCTCACATTC,552,6,clonotype62,clonotype62_consensus_2 -GGGCATCCAATAAGCA-1,True,GGGCATCCAATAAGCA-1_contig_3,True,342,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,646,6,clonotype62,None -GGTGAAGAGTGGGTTG-1,True,GGTGAAGAGTGGGTTG-1_contig_1,True,558,TRB,TRBV13-3,None,TRBJ1-6,TRBC1,True,True,CAGQGARNSPLYF,TGTGCCGGACAGGGGGCGCGAAATTCGCCCCTCTACTTT,27264,6,clonotype63,clonotype63_consensus_1 -GGTGAAGAGTGGGTTG-1,True,GGTGAAGAGTGGGTTG-1_contig_2,True,420,TRB,TRBV31,None,TRBJ1-5,TRBC1,True,False,CLESSDREQAPLF,TGCCTGGAGTCTAGCGACAGGGAACAGGCTCCGCTTTTT,8684,1,clonotype63,None -GGTGAAGAGTGGGTTG-1,True,GGTGAAGAGTGGGTTG-1_contig_3,True,352,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,42352,5,clonotype63,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_1,True,710,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSIDRVGSERLFF,TGTGCCAGCAGTATAGACAGGGTAGGATCCGAAAGATTATTTTTC,1544,16,clonotype64,clonotype64_consensus_1 -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_2,True,567,TRA,TRAV2,None,TRAJ30,TRAC,True,True,CIVTDLTNAYKVIF,TGCATTGTGACTGACCTCACAAATGCTTACAAAGTCATCTTT,1038,12,clonotype64,clonotype64_consensus_2 -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_3,True,308,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,414,2,clonotype64,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_4,True,345,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,530,2,clonotype64,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_5,True,354,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,2548,8,clonotype64,None -GTACTTTCACATGTGT-1,True,GTACTTTCACATGTGT-1_contig_1,True,576,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-4,TRBC2,True,True,CASGDSHASQNTLYF,TGTGCCAGCGGTGATAGCCACGCTAGTCAAAACACCTTGTACTTT,45384,3,clonotype65,clonotype65_consensus_2 -GTACTTTCACATGTGT-1,True,GTACTTTCACATGTGT-1_contig_2,True,558,TRA,TRAV8D-2,None,TRAJ52,TRAC,True,True,CATATGANTGKLTF,TGTGCTACAGCCACTGGAGCTAACACTGGAAAGCTCACGTTT,31030,4,clonotype65,clonotype65_consensus_1 -GTCCTCAGTTTACTCT-1,True,GTCCTCAGTTTACTCT-1_contig_1,True,519,TRB,TRBV5,TRBD1,TRBJ2-7,TRBC2,True,True,CASSHRDRGLEQYF,TGTGCCAGCAGCCACCGGGACAGGGGGCTTGAACAGTACTTC,6544,3,clonotype66,clonotype66_consensus_2 -GTCCTCAGTTTACTCT-1,True,GTCCTCAGTTTACTCT-1_contig_2,True,574,TRA,TRAV4-4-DV10,None,TRAJ50,TRAC,True,True,CAAEAASSSFSKLVF,TGTGCTGCTGAGGCCGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,27224,12,clonotype66,clonotype66_consensus_1 -GTCCTCAGTTTACTCT-1,True,GTCCTCAGTTTACTCT-1_contig_3,True,426,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,44842,14,clonotype66,None -GTCTCGTGTAATCACC-1,True,GTCTCGTGTAATCACC-1_contig_1,True,565,TRB,TRBV1,None,TRBJ1-2,TRBC1,True,True,CTCSAQANSDYTF,TGCACCTGCAGTGCCCAGGCAAACTCCGACTACACCTTC,65594,23,clonotype67,clonotype67_consensus_2 -GTCTCGTGTAATCACC-1,True,GTCTCGTGTAATCACC-1_contig_2,True,524,TRA,TRAV6-4,None,TRAJ15,TRAC,True,True,CALVDVQGGRALIF,TGTGCTCTGGTTGACGTCCAGGGAGGCAGAGCTCTGATATTT,10066,7,clonotype67,clonotype67_consensus_1 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_1,True,512,TRA,TRAV6-5,None,TRAJ5,TRAC,True,True,CALGDTQVVGQLTF,TGTGCTCTGGGTGACACACAGGTTGTGGGGCAGCTCACTTTC,1090,10,clonotype68,clonotype68_consensus_2 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_2,True,513,TRB,TRBV31,None,TRBJ1-3,TRBC1,True,True,CAWRGGGGNTHYF,TGTGCCTGGCGGGGGGGGGGAGGAAATACGCACTATTTT,1620,12,clonotype68,clonotype68_consensus_1 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_3,True,373,TRB,None,None,TRBJ1-1,TRBC1,False,False,None,None,7472,29,clonotype68,None -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_4,True,501,TRA,TRAV12-1,None,TRAJ11,TRAC,True,False,CPVLLCSNSGYNKLTF,TGCCCTGTACTACTGTGCTCTAACTCGGGATACAACAAACTCACTTTT,302,2,clonotype68,None -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_1,True,535,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSAGTGGERLFF,TGTGCCAGCAGTGCCGGGACGGGCGGCGAAAGATTATTTTTC,1346,11,clonotype69,clonotype69_consensus_2 -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_2,True,588,TRA,TRAV7-4,None,TRAJ9,TRAC,True,True,CAARGRGYKLTF,TGTGCAGCTAGGGGGAGGGGCTACAAACTTACCTTC,348,3,clonotype69,clonotype69_consensus_1 -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_3,True,531,TRA,TRAV6-2,None,TRAJ40,None,True,False,CVLGDRYRKLQIRLWSRYQTEGYST,TGTGTTCTGGGTGATAGGTACAGGAAACTACAAATACGTCTTTGGAGCAGGTACCAGACTGAAGGTTATAGCACC,56,1,clonotype69,None -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_4,True,322,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,922,3,clonotype69,None -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_5,True,331,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,990,6,clonotype69,None -TACCTTATCCGCAAGC-1,True,TACCTTATCCGCAAGC-1_contig_1,True,562,TRA,TRAV14D-2,None,TRAJ43,TRAC,True,True,CAALNNNNAPRF,TGTGCAGCACTCAATAACAACAATGCCCCACGATTT,67926,6,clonotype70,clonotype70_consensus_2 -TACCTTATCCGCAAGC-1,True,TACCTTATCCGCAAGC-1_contig_2,True,561,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGDVRYEQYF,TGTGCCAGCGGTGATGTCAGATATGAACAGTACTTC,1286,3,clonotype70,clonotype70_consensus_1 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_1,True,636,TRA,TRAV7-1,None,TRAJ40,TRAC,True,True,CAVSMGTGNYKYVF,TGTGCAGTGAGCATGGGTACAGGAAACTACAAATACGTCTTT,8320,3,clonotype71,clonotype71_consensus_1 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_2,True,543,TRA,TRAV15-1-DV6-1,None,TRAJ33,TRAC,True,True,CALWEPYMDSNYQLIW,TGTGCTCTCTGGGAGCCCTACATGGATAGCAACTATCAGTTGATCTGG,8020,2,clonotype71,clonotype71_consensus_2 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_3,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,20658,6,clonotype71,clonotype71_consensus_3 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_4,True,602,TRA,TRAV14D-2,None,TRAJ33,TRAC,True,False,CALWEPYMDSNYQLIW,TGTGCTCTCTGGGAGCCCTACATGGATAGCAACTATCAGTTGATCTGG,10034,3,clonotype71,clonotype71_consensus_2 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_5,True,311,TRA,None,None,TRAJ34,TRAC,False,False,None,None,13840,4,clonotype71,None -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_6,True,313,TRA,None,None,TRAJ11,TRAC,False,False,None,None,7066,1,clonotype71,None -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_7,True,324,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,7212,1,clonotype71,None -TATCTCACAGTCAGAG-1,True,TATCTCACAGTCAGAG-1_contig_1,True,516,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGYEQYF,TGTGCCAGCAGCCCGGGACTGGGGTATGAACAGTACTTC,50414,3,clonotype72,clonotype72_consensus_1 -TATCTCACAGTCAGAG-1,True,TATCTCACAGTCAGAG-1_contig_2,True,498,TRA,TRAV21-DV12,None,TRAJ40,TRAC,True,True,CILVTGNYKYVF,TGTATCCTTGTTACAGGAAACTACAAATACGTCTTT,28120,3,clonotype72,clonotype72_consensus_2 -TATCTCACATATACGC-1,True,TATCTCACATATACGC-1_contig_1,True,592,TRA,TRAV6N-7,None,TRAJ47,TRAC,True,True,CALGEDYANKMIF,TGTGCTCTGGGTGAGGACTATGCAAACAAGATGATCTTT,13362,3,clonotype73,clonotype73_consensus_3 -TATCTCACATATACGC-1,True,TATCTCACATATACGC-1_contig_2,True,566,TRA,TRAV3-3,None,TRAJ50,TRAC,True,True,CAVSSSSSFSKLVF,TGCGCAGTCAGTTCATCCTCCTCCTTCAGCAAGCTGGTGTTT,13810,4,clonotype73,clonotype73_consensus_2 -TATCTCACATATACGC-1,True,TATCTCACATATACGC-1_contig_3,True,562,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGDRAETLYF,TGTGCCAGCGGTGACCGTGCAGAAACGCTGTATTTT,39610,11,clonotype73,clonotype73_consensus_1 -TATCTCACATATACGC-1,True,TATCTCACATATACGC-1_contig_4,True,1093,TRB,TRBV12-2,None,TRBJ2-3,TRBC2,True,False,None,None,8204,3,clonotype73,None -TATCTCACATATACGC-1,True,TATCTCACATATACGC-1_contig_5,True,690,TRB,TRBV3,None,TRBJ2-7,TRBC2,True,False,None,None,2282,1,clonotype73,None -TCAGATGTCAGAGACG-1,True,TCAGATGTCAGAGACG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,2712,37,clonotype74,clonotype74_consensus_1 -TCAGCAACAAGGTTCT-1,True,TCAGCAACAAGGTTCT-1_contig_1,True,567,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGGGTGEAETLYF,TGTGCCAGCGGTGGTGGGACAGGGGAGGCAGAAACGCTGTATTTT,638,4,clonotype75,clonotype75_consensus_2 -TCAGCAACAAGGTTCT-1,True,TCAGCAACAAGGTTCT-1_contig_2,True,533,TRA,TRAV6-2,None,TRAJ11,TRAC,True,True,CVLGDSGYNKLTF,TGTGTTCTGGGTGACTCGGGATACAACAAACTCACTTTT,1190,7,clonotype75,clonotype75_consensus_1 -TCGTAGATCACGCGGT-1,True,TCGTAGATCACGCGGT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCCGGACAGGGGAACACAGAAGTCTTCTTT,58708,12,clonotype76,clonotype76_consensus_1 -TCGTAGATCACGCGGT-1,True,TCGTAGATCACGCGGT-1_contig_2,True,694,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CAVSASSGQKLVF,TGTGCTGTGAGCGCTTCAAGTGGCCAGAAGCTGGTTTTT,8676,3,clonotype76,clonotype76_consensus_2 -TCGTAGATCACGCGGT-1,True,TCGTAGATCACGCGGT-1_contig_3,True,541,TRA,TRAV6N-7,None,TRAJ34,TRAC,True,False,CTTVLFNTDKVVF,TGTACTACTGTGCTCTTCAATACCGACAAAGTCGTCTTT,4970,1,clonotype76,None -TGACTAGTCGAGAACG-1,True,TGACTAGTCGAGAACG-1_contig_1,True,571,TRB,TRBV1,None,TRBJ2-3,TRBC2,True,True,CTCSADLVSAETLYF,TGCACCTGCAGTGCAGATCTAGTTAGTGCAGAAACGCTGTATTTT,69154,21,clonotype77,clonotype77_consensus_1 -TGACTAGTCGAGAACG-1,True,TGACTAGTCGAGAACG-1_contig_2,True,550,TRA,TRAV10D,None,TRAJ45,TRAC,True,True,CAAGAGGADRLTF,TGTGCAGCTGGGGCAGGAGGTGCAGATAGACTCACCTTT,7960,3,clonotype77,clonotype77_consensus_2 -TGAGCCGCAGTAAGCG-1,True,TGAGCCGCAGTAAGCG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,15432,2,clonotype78,clonotype78_consensus_1 -TGAGCCGCAGTAAGCG-1,True,TGAGCCGCAGTAAGCG-1_contig_2,True,687,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,48952,5,clonotype78,None -TGAGCCGCAGTAAGCG-1,True,TGAGCCGCAGTAAGCG-1_contig_3,True,491,TRA,TRAV12D-2,None,TRAJ17,TRAC,True,False,None,None,14122,2,clonotype78,None -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_1,True,521,TRA,TRAV14-1,None,TRAJ5,TRAC,True,True,CAAGTQVVGQLTF,TGTGCAGCCGGGACACAGGTTGTGGGGCAGCTCACTTTC,388,3,clonotype79,clonotype79_consensus_1 -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_2,True,469,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,180,1,clonotype79,None -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_3,True,426,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,420,3,clonotype79,None -TGTCCCAGTAAGTAGT-1,True,TGTCCCAGTAAGTAGT-1_contig_1,True,721,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,22540,7,clonotype80,clonotype80_consensus_1 -TGTCCCAGTAAGTAGT-1,True,TGTCCCAGTAAGTAGT-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,21012,9,clonotype80,clonotype80_consensus_2 -TGTCCCAGTAAGTAGT-1,True,TGTCCCAGTAAGTAGT-1_contig_3,True,320,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,7892,1,clonotype80,None -TGTCCCAGTAAGTAGT-1,True,TGTCCCAGTAAGTAGT-1_contig_4,True,607,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,24748,5,clonotype80,None -TTCGGTCCATCGGTTA-1,True,TTCGGTCCATCGGTTA-1_contig_1,True,566,TRA,TRAV3-3,None,TRAJ30,TRAC,True,True,CAVSAPTNAYKVIF,TGCGCAGTCAGTGCCCCGACAAATGCTTACAAAGTCATCTTT,37558,6,clonotype81,clonotype81_consensus_1 -TTCGGTCCATCGGTTA-1,True,TTCGGTCCATCGGTTA-1_contig_2,True,545,TRA,TRAV8D-1,None,TRAJ17,TRAC,True,False,None,None,28874,5,clonotype81,None -TTCGGTCCATCGGTTA-1,True,TTCGGTCCATCGGTTA-1_contig_3,True,617,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,False,CASSQGKTANTEVFF,TGTGCCAGCAGCCAAGGGAAAACTGCAAACACAGAAGTCTTCTTT,8300,1,clonotype81,None -TTTATGCAGATACACA-1,True,TTTATGCAGATACACA-1_contig_1,True,597,TRA,TRAV7D-4,None,TRAJ48,TRAC,True,True,CAASRENYGNEKITF,TGTGCAGCTAGTAGGGAGAACTATGGAAATGAGAAAATAACTTTT,10008,19,clonotype82,clonotype82_consensus_1 -TTTATGCAGATACACA-1,True,TTTATGCAGATACACA-1_contig_2,True,357,TRB,TRBV13-2,None,TRBJ2-1,TRBC2,True,False,CASGGWGNYAEQFF,TGTGCCAGCGGTGGCTGGGGTAACTATGCTGAGCAGTTCTTC,57224,4,clonotype82,None -TTTATGCAGCTATGCT-1,True,TTTATGCAGCTATGCT-1_contig_1,True,518,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSEGGRSYEQYF,TGTGCCAGCAGTGAGGGGGGGCGCTCCTATGAACAGTACTTC,42094,5,clonotype83,clonotype83_consensus_1 -TTTATGCAGCTATGCT-1,True,TTTATGCAGCTATGCT-1_contig_2,True,532,TRA,TRAV6N-7,None,TRAJ53,TRAC,True,True,CALSDFGGSNYKLTF,TGTGCTCTGAGTGATTTTGGAGGCAGCAATTACAAACTGACATTT,33472,3,clonotype83,clonotype83_consensus_2 diff --git a/tests/testthat/fixtures/Chariou/h5files/SCAF1714_2_1_filtered_contig_annotations.csv b/tests/testthat/fixtures/Chariou/h5files/SCAF1714_2_1_filtered_contig_annotations.csv deleted file mode 100644 index 243f6cb..0000000 --- a/tests/testthat/fixtures/Chariou/h5files/SCAF1714_2_1_filtered_contig_annotations.csv +++ /dev/null @@ -1,329 +0,0 @@ -barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id -AAATGCCCACGGACAA-1,True,AAATGCCCACGGACAA-1_contig_1,True,623,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSANERLFF,TGTGCCAGCAGTGCCAACGAAAGATTATTTTTC,36008,9,clonotype12,clonotype12_consensus_2 -AAATGCCCACGGACAA-1,True,AAATGCCCACGGACAA-1_contig_2,True,504,TRA,TRAV12D-2,None,TRAJ49,TRAC,True,True,CALSAPNTGYQNFYF,TGTGCTCTGAGTGCCCCTAACACGGGTTACCAGAACTTCTATTTT,21046,5,clonotype12,clonotype12_consensus_1 -AAATGCCCACGGACAA-1,True,AAATGCCCACGGACAA-1_contig_3,True,598,TRB,TRBV3,None,TRBJ2-5,TRBC2,True,False,CQQLAVQDTQYF,TGCCAGCAGCTGGCAGTCCAAGACACCCAGTACTTT,5576,2,clonotype12,None -AAATGCCCACGGACAA-1,True,AAATGCCCACGGACAA-1_contig_4,True,336,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,14804,4,clonotype12,None -AACACGTGTCTAAAGA-1,True,AACACGTGTCTAAAGA-1_contig_1,True,628,TRA,TRAV6N-7,None,TRAJ49,TRAC,True,True,CALGGKKGYQNFYF,TGTGCTCTGGGTGGTAAGAAGGGTTACCAGAACTTCTATTTT,29884,3,clonotype6,clonotype6_consensus_2 -AACACGTGTCTAAAGA-1,True,AACACGTGTCTAAAGA-1_contig_2,True,665,TRB,TRBV19,None,TRBJ2-7,TRBC2,True,True,CASSINWGGEQYF,TGTGCCAGCAGTATAAACTGGGGGGGCGAACAGTACTTC,45260,5,clonotype6,clonotype6_consensus_1 -AACCATGAGACTAAGT-1,True,AACCATGAGACTAAGT-1_contig_1,True,554,TRB,TRBV31,None,TRBJ2-2,TRBC2,True,True,CAWSQKRLGVDTGQLYF,TGTGCCTGGAGTCAAAAAAGACTGGGGGTAGACACCGGGCAGCTCTACTTT,76438,10,clonotype13,clonotype13_consensus_1 -AACCATGCACCGATAT-1,True,AACCATGCACCGATAT-1_contig_1,True,546,TRA,TRAV7-3,None,TRAJ26,TRAC,True,True,CAVSMGYAQGLTF,TGTGCAGTGAGCATGGGCTATGCCCAGGGATTAACCTTC,21636,2,clonotype14,clonotype14_consensus_1 -AACCATGCACCGATAT-1,True,AACCATGCACCGATAT-1_contig_2,True,537,TRA,TRAV15-1-DV6-1,None,TRAJ40,TRAC,True,True,CALWESTGNYKYVF,TGTGCTCTCTGGGAGTCTACAGGAAACTACAAATACGTCTTT,40080,3,clonotype14,clonotype14_consensus_2 -AACCATGCACCGATAT-1,True,AACCATGCACCGATAT-1_contig_3,True,588,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGARQGLGEQYF,TGTGGTGCTAGGCAGGGACTGGGGGAACAGTACTTC,15660,1,clonotype14,clonotype14_consensus_3 -AACCATGCATGTTCCC-1,True,AACCATGCATGTTCCC-1_contig_1,True,659,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,25784,4,clonotype1,clonotype1_consensus_2 -AACCATGCATGTTCCC-1,True,AACCATGCATGTTCCC-1_contig_2,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,47080,5,clonotype1,clonotype1_consensus_1 -AACTGGTGTGCCTGCA-1,True,AACTGGTGTGCCTGCA-1_contig_1,True,550,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,78692,3,clonotype3,clonotype3_consensus_1 -AAGTCTGTCGGAATCT-1,True,AAGTCTGTCGGAATCT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSQGGSSYEQYF,TGTGCCAGCAGCCAGGGGGGAAGCTCCTATGAACAGTACTTC,21974,7,clonotype15,clonotype15_consensus_2 -AAGTCTGTCGGAATCT-1,True,AAGTCTGTCGGAATCT-1_contig_2,True,701,TRB,TRBV19,None,TRBJ1-6,TRBC1,True,True,CASSKDTSYNSPLYF,TGTGCCAGCAGTAAGGACACTTCCTATAATTCGCCCCTCTACTTT,27132,10,clonotype15,clonotype15_consensus_3 -AAGTCTGTCGGAATCT-1,True,AAGTCTGTCGGAATCT-1_contig_3,True,523,TRA,TRAV8D-1,None,TRAJ28,TRAC,True,True,CATGTGSNRLTF,TGTGCTACAGGCACTGGGAGTAACAGGCTCACTTTT,22778,7,clonotype15,clonotype15_consensus_1 -AAGTCTGTCGGAATCT-1,True,AAGTCTGTCGGAATCT-1_contig_4,True,335,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,7062,3,clonotype15,None -ACACCAAAGCTTATCG-1,True,ACACCAAAGCTTATCG-1_contig_1,True,510,TRB,TRBV29,None,TRBJ1-2,TRBC1,True,True,CASVGTTNSDYTF,TGTGCTAGCGTCGGGACAACAAACTCCGACTACACCTTC,36564,10,clonotype16,clonotype16_consensus_2 -ACACCAAAGCTTATCG-1,True,ACACCAAAGCTTATCG-1_contig_2,True,530,TRA,TRAV6N-7,None,TRAJ39,TRAC,True,True,CALRSNNAGAKLTF,TGTGCTCTGAGGTCGAATAATGCAGGTGCCAAGCTCACATTC,8868,3,clonotype16,clonotype16_consensus_1 -ACACCAAAGCTTATCG-1,True,ACACCAAAGCTTATCG-1_contig_3,True,357,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,30974,7,clonotype16,None -ACACCGGTCAGTCAGT-1,True,ACACCGGTCAGTCAGT-1_contig_1,True,529,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQGGGNTEVFF,TGTGCCAGCAGCCAAGGGGGGGGGAACACAGAAGTCTTCTTT,68520,6,clonotype7,clonotype7_consensus_1 -ACACCGGTCAGTCAGT-1,True,ACACCGGTCAGTCAGT-1_contig_2,True,701,TRA,TRAV9D-2,None,TRAJ12,TRAC,True,False,None,None,7128,1,clonotype7,None -ACACTGACATCACGTA-1,True,ACACTGACATCACGTA-1_contig_1,True,590,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-1,TRBC1,True,True,CASGGGQSNTEVFF,TGTGCCAGCGGTGGCGGACAGTCAAACACAGAAGTCTTCTTT,20722,3,clonotype17,clonotype17_consensus_1 -ACACTGACATCACGTA-1,True,ACACTGACATCACGTA-1_contig_2,True,610,TRA,TRAV16N,None,TRAJ37,TRAC,True,True,CAGAGNTRKLIF,TGTGCGGGGGCAGGCAATACTAGAAAACTCATCTTT,12998,1,clonotype17,clonotype17_consensus_2 -ACACTGACATCACGTA-1,True,ACACTGACATCACGTA-1_contig_3,True,331,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,14382,1,clonotype17,None -ACACTGACATCACGTA-1,True,ACACTGACATCACGTA-1_contig_4,True,516,TRA,TRAV13-2,None,TRAJ23,TRAC,True,False,None,None,29454,2,clonotype17,None -ACAGCCGCAGACAGGT-1,True,ACAGCCGCAGACAGGT-1_contig_1,True,563,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,65814,9,clonotype3,clonotype3_consensus_1 -ACGAGGAGTGCTCTTC-1,True,ACGAGGAGTGCTCTTC-1_contig_1,True,668,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTTTGACTAACAGTGCAGGGAACAAGCTAACTTTT,6294,1,clonotype18,clonotype18_consensus_1 -ACGAGGAGTGCTCTTC-1,True,ACGAGGAGTGCTCTTC-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSAGTGNTEVFF,TGTGCCAGCAGCGCCGGGACAGGGAACACAGAAGTCTTCTTT,50176,7,clonotype18,clonotype18_consensus_2 -ACGAGGAGTGCTCTTC-1,True,ACGAGGAGTGCTCTTC-1_contig_3,True,620,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,19384,3,clonotype18,None -ACGATGTAGAGTCTGG-1,True,ACGATGTAGAGTCTGG-1_contig_1,True,520,TRA,TRAV8D-1,None,TRAJ33,TRAC,True,True,CATRRNYQLIW,TGTGCTACTAGGCGCAACTATCAGTTGATCTGG,12340,1,clonotype2,clonotype2_consensus_1 -ACGATGTAGAGTCTGG-1,True,ACGATGTAGAGTCTGG-1_contig_2,True,572,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,17644,2,clonotype2,clonotype2_consensus_2 -ACGATGTAGAGTCTGG-1,True,ACGATGTAGAGTCTGG-1_contig_3,True,374,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,49202,4,clonotype2,None -ACGATGTTCAGCAACT-1,True,ACGATGTTCAGCAACT-1_contig_1,True,558,TRB,TRBV20,None,TRBJ1-1,TRBC1,True,True,CGARGENTEVFF,TGTGGTGCTAGAGGGGAAAACACAGAAGTCTTCTTT,54460,12,clonotype19,clonotype19_consensus_2 -ACGATGTTCAGCAACT-1,True,ACGATGTTCAGCAACT-1_contig_2,True,575,TRA,TRAV7D-2,None,TRAJ39,TRAC,True,True,CAASMGHNAGAKLTF,TGTGCAGCAAGCATGGGTCATAATGCAGGTGCCAAGCTCACATTC,15370,4,clonotype19,clonotype19_consensus_1 -ACGATGTTCAGCAACT-1,True,ACGATGTTCAGCAACT-1_contig_3,True,443,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,5918,2,clonotype19,None -ACGGCCAAGCCTCGTG-1,True,ACGGCCAAGCCTCGTG-1_contig_1,True,591,TRA,TRAV7D-4,None,TRAJ30,TRAC,True,True,CAADDTNAYKVIF,TGTGCAGCTGATGACACAAATGCTTACAAAGTCATCTTT,17380,6,clonotype20,clonotype20_consensus_1 -ACGGCCAAGCCTCGTG-1,True,ACGGCCAAGCCTCGTG-1_contig_2,True,368,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,36760,2,clonotype20,None -ACGGCCAAGCCTCGTG-1,True,ACGGCCAAGCCTCGTG-1_contig_3,True,516,TRB,TRBV26,None,TRBJ1-2,TRBC1,True,False,CQQPGQGGSDYTF,TGCCAGCAGCCGGGACAGGGGGGATCCGACTACACCTTC,24086,4,clonotype20,None -ACGGGCTAGTGTTGAA-1,True,ACGGGCTAGTGTTGAA-1_contig_1,True,694,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASSSDWGLSQNTLYF,TGTGCCAGCAGTAGCGACTGGGGCCTGAGTCAAAACACCTTGTACTTT,38194,3,clonotype21,clonotype21_consensus_2 -ACGGGCTAGTGTTGAA-1,True,ACGGGCTAGTGTTGAA-1_contig_2,True,456,TRA,TRAV16N,None,TRAJ45,None,True,True,CAMRETGGADRLTF,TGTGCTATGAGAGAGACAGGAGGTGCAGATAGACTCACCTTT,10180,1,clonotype21,clonotype21_consensus_1 -ACGGGCTAGTGTTGAA-1,True,ACGGGCTAGTGTTGAA-1_contig_3,True,475,TRA,TRAV12D-2,None,TRAJ42,TRAC,True,False,None,None,28160,2,clonotype21,None -ACTATCTAGAAAGTGG-1,True,ACTATCTAGAAAGTGG-1_contig_1,True,605,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,10062,5,clonotype1,clonotype1_consensus_2 -ACTATCTAGAAAGTGG-1,True,ACTATCTAGAAAGTGG-1_contig_2,True,529,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,17200,8,clonotype1,clonotype1_consensus_1 -ACTATCTAGAAAGTGG-1,True,ACTATCTAGAAAGTGG-1_contig_3,True,375,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,49448,9,clonotype1,None -AGATTGCAGAGAACAG-1,True,AGATTGCAGAGAACAG-1_contig_1,True,552,TRA,TRAV3-3,None,TRAJ15,TRAC,True,True,CAVSYQGGRALIF,TGCGCAGTCAGCTACCAGGGAGGCAGAGCTCTGATATTT,23090,9,clonotype22,clonotype22_consensus_1 -AGATTGCAGAGAACAG-1,True,AGATTGCAGAGAACAG-1_contig_2,True,574,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGAGQGSAETLYF,TGTGCCAGCGGGGCGGGACAGGGGAGTGCAGAAACGCTGTATTTT,33118,11,clonotype22,clonotype22_consensus_3 -AGATTGCAGAGAACAG-1,True,AGATTGCAGAGAACAG-1_contig_3,True,528,TRA,TRAV6-2,None,TRAJ11,TRAC,True,True,CVLGDSGYNKLTF,TGTGTTCTGGGTGACTCGGGATACAACAAACTCACTTTT,8526,4,clonotype22,clonotype22_consensus_2 -AGATTGCAGAGAACAG-1,True,AGATTGCAGAGAACAG-1_contig_4,True,347,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,13902,3,clonotype22,None -AGCCTAAGTGACCAAG-1,True,AGCCTAAGTGACCAAG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ2-2,TRBC2,True,True,CASSQELNTGQLYF,TGTGCCAGCAGCCAAGAACTGAACACCGGGCAGCTCTACTTT,25916,3,clonotype23,clonotype23_consensus_2 -AGCCTAAGTGACCAAG-1,True,AGCCTAAGTGACCAAG-1_contig_2,True,591,TRA,TRAV13-1,None,TRAJ40,TRAC,True,True,CAMERGGNYKYVF,TGTGCTATGGAACGGGGAGGAAACTACAAATACGTCTTT,42470,5,clonotype23,clonotype23_consensus_1 -AGCCTAAGTGACCAAG-1,True,AGCCTAAGTGACCAAG-1_contig_3,True,562,TRA,TRAV12-1,None,TRAJ17,TRAC,True,True,CALRALSAGNKLTF,TGTGCTCTGAGGGCTCTCAGTGCAGGGAACAAGCTAACTTTT,10760,2,clonotype23,clonotype23_consensus_3 -AGGCCGTTCGCTTAGA-1,True,AGGCCGTTCGCTTAGA-1_contig_1,True,562,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSAETYEQYF,TGCACCTGCAGTGCAGAGACATATGAACAGTACTTC,33608,5,clonotype24,clonotype24_consensus_1 -AGGCCGTTCGCTTAGA-1,True,AGGCCGTTCGCTTAGA-1_contig_2,True,570,TRA,TRAV4-4-DV10,None,TRAJ49,TRAC,True,True,CAAEGYQNFYF,TGTGCTGCTGAGGGTTACCAGAACTTCTATTTT,26274,5,clonotype24,clonotype24_consensus_2 -AGGCCGTTCGCTTAGA-1,True,AGGCCGTTCGCTTAGA-1_contig_3,True,337,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,14844,5,clonotype24,None -AGGTCATAGAAGGACA-1,True,AGGTCATAGAAGGACA-1_contig_1,True,521,TRA,TRAV6D-4,None,TRAJ21,TRAC,True,True,CALVKPNYNVLYF,TGTGCTCTGGTTAAGCCTAATTACAACGTGCTTTACTTC,26278,7,clonotype25,clonotype25_consensus_2 -AGGTCATAGAAGGACA-1,True,AGGTCATAGAAGGACA-1_contig_2,True,699,TRB,TRBV19,None,TRBJ1-3,TRBC1,True,True,CASSMTAFSGNTLYF,TGTGCCAGCAGTATGACAGCTTTTTCTGGAAATACGCTCTATTTT,48046,11,clonotype25,clonotype25_consensus_1 -AGGTCATAGCTTATCG-1,True,AGGTCATAGCTTATCG-1_contig_1,True,718,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSTTGYNTEVFF,TGTGCCAGCAGTACTACAGGGTACAACACAGAAGTCTTCTTT,18914,2,clonotype26,clonotype26_consensus_1 -AGGTCATAGCTTATCG-1,True,AGGTCATAGCTTATCG-1_contig_2,True,335,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,54420,4,clonotype26,None -AGTCTTTGTGTAAGTA-1,True,AGTCTTTGTGTAAGTA-1_contig_1,True,536,TRA,TRAV6-2,None,TRAJ33,TRAC,True,True,CVLGDSNYQLIW,TGTGTTCTGGGGGATAGCAACTATCAGTTGATCTGG,61020,5,clonotype27,clonotype27_consensus_1 -AGTCTTTGTGTAAGTA-1,True,AGTCTTTGTGTAAGTA-1_contig_2,True,417,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,14288,3,clonotype27,None -ATCATGGCAATGCCAT-1,True,ATCATGGCAATGCCAT-1_contig_1,True,567,TRA,TRAV2,None,TRAJ43,TRAC,True,True,CIVTDRNNNNAPRF,TGCATTGTGACTGACAGGAATAACAACAATGCCCCACGATTT,40630,3,clonotype28,clonotype28_consensus_2 -ATCATGGCAATGCCAT-1,True,ATCATGGCAATGCCAT-1_contig_2,True,519,TRB,TRBV17,None,TRBJ2-7,TRBC2,True,True,CASSRGRGEQYF,TGTGCTAGCAGTAGAGGGCGGGGGGAACAGTACTTC,37806,3,clonotype28,clonotype28_consensus_1 -ATCATGGCATGTCTCC-1,True,ATCATGGCATGTCTCC-1_contig_1,True,552,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,35824,10,clonotype3,clonotype3_consensus_1 -ATCATGGCATGTCTCC-1,True,ATCATGGCATGTCTCC-1_contig_2,True,368,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,21608,5,clonotype3,None -ATCATGGCATGTCTCC-1,True,ATCATGGCATGTCTCC-1_contig_3,True,352,TRB,TRBV19,None,TRBJ1-6,TRBC1,True,False,None,None,11674,3,clonotype3,None -ATCATGGGTCCCTACT-1,True,ATCATGGGTCCCTACT-1_contig_1,True,724,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASSIWGGLSQNTLYF,TGTGCCAGCAGTATTTGGGGGGGCTTGAGTCAAAACACCTTGTACTTT,43558,5,clonotype29,clonotype29_consensus_1 -ATCATGGGTCCCTACT-1,True,ATCATGGGTCCCTACT-1_contig_2,True,558,TRA,TRAV16N,None,TRAJ56,TRAC,True,True,CAALLATGGNNKLTF,TGTGCTGCCCTTTTGGCTACTGGAGGCAATAATAAGCTGACTTTT,34388,5,clonotype29,clonotype29_consensus_2 -ATCCACCGTACAGCAG-1,True,ATCCACCGTACAGCAG-1_contig_1,True,556,TRA,TRAV8D-2,None,TRAJ49,TRAC,True,True,CATDNTGYQNFYF,TGTGCTACAGACAACACGGGTTACCAGAACTTCTATTTT,9352,1,clonotype30,clonotype30_consensus_2 -ATCCACCGTACAGCAG-1,True,ATCCACCGTACAGCAG-1_contig_2,True,628,TRA,TRAV17,None,TRAJ50,TRAC,True,True,CALDMGASSSFSKLVF,TGTGCACTGGACATGGGGGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,10728,4,clonotype30,clonotype30_consensus_1 -ATCCACCGTACAGCAG-1,True,ATCCACCGTACAGCAG-1_contig_3,True,521,TRB,TRBV13-1,None,TRBJ2-1,TRBC2,True,True,CASSDRWGRWAEQFF,TGTGCCAGCAGTGATCGCTGGGGGAGGTGGGCTGAGCAGTTCTTC,25262,2,clonotype30,clonotype30_consensus_3 -ATCCACCGTACAGCAG-1,True,ATCCACCGTACAGCAG-1_contig_4,True,448,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,32064,2,clonotype30,None -ATGGGAGGTCTCTCTG-1,True,ATGGGAGGTCTCTCTG-1_contig_1,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,33094,2,clonotype1,clonotype1_consensus_1 -ATGGGAGGTCTCTCTG-1,True,ATGGGAGGTCTCTCTG-1_contig_2,True,644,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,30250,3,clonotype1,clonotype1_consensus_2 -ATGGGAGGTCTCTCTG-1,True,ATGGGAGGTCTCTCTG-1_contig_3,True,603,TRB,TRBV3,None,TRBJ2-3,TRBC2,True,False,CTSVPAAWGVSAETLYF,TGTACTTCTGTGCCAGCAGCCTGGGGAGTTAGTGCAGAAACGCTGTATTTT,15442,2,clonotype1,None -ATTGGACCAGGTCCAC-1,True,ATTGGACCAGGTCCAC-1_contig_1,True,547,TRB,TRBV10,None,TRBJ2-5,TRBC2,True,True,CASSQTGGNQDTQYF,TGTGCCAGCAGCCAGACTGGGGGTAACCAAGACACCCAGTACTTT,64478,5,clonotype31,clonotype31_consensus_1 -CAACTAGAGGGATACC-1,True,CAACTAGAGGGATACC-1_contig_1,True,511,TRB,TRBV31,None,TRBJ1-4,TRBC1,True,True,CAWSRGTAPVF,TGTGCCTGGAGTCGCGGGACAGCCCCTGTTTTC,63324,3,clonotype32,clonotype32_consensus_1 -CAACTAGAGGGATACC-1,True,CAACTAGAGGGATACC-1_contig_2,True,548,TRA,TRAV9-1,None,TRAJ52,TRAC,True,True,CAVSAGGANTGKLTF,TGTGCTGTGAGCGCGGGTGGAGCTAACACTGGAAAGCTCACGTTT,5574,2,clonotype32,clonotype32_consensus_2 -CAACTAGAGGGATACC-1,True,CAACTAGAGGGATACC-1_contig_3,True,301,TRA,None,None,TRAJ44,TRAC,False,False,None,None,6878,2,clonotype32,None -CACACCTAGGGCACTA-1,True,CACACCTAGGGCACTA-1_contig_1,True,715,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSIHANTEVFF,TGTGCCAGCAGTATCCACGCAAACACAGAAGTCTTCTTT,29540,14,clonotype33,clonotype33_consensus_1 -CACACCTAGGGCACTA-1,True,CACACCTAGGGCACTA-1_contig_2,True,545,TRA,TRAV9-1,None,TRAJ56,TRAC,True,True,CAVSATGGNNKLTF,TGTGCTGTGAGCGCTACTGGAGGCAATAATAAGCTGACTTTT,12960,10,clonotype33,clonotype33_consensus_2 -CACACCTAGGGCACTA-1,True,CACACCTAGGGCACTA-1_contig_3,True,857,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,29750,14,clonotype33,None -CACACCTAGGGCACTA-1,True,CACACCTAGGGCACTA-1_contig_4,True,533,Multi,TRDV1,None,TRAJ57,TRAC,True,False,None,None,3470,2,clonotype33,None -CACCACTAGTTAGCGG-1,True,CACCACTAGTTAGCGG-1_contig_1,True,571,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,40196,2,clonotype2,clonotype2_consensus_2 -CACCACTAGTTAGCGG-1,True,CACCACTAGTTAGCGG-1_contig_2,True,520,TRA,TRAV8D-1,None,TRAJ33,TRAC,True,True,CATRRNYQLIW,TGTGCTACTAGGCGCAACTATCAGTTGATCTGG,15296,1,clonotype2,clonotype2_consensus_1 -CACCACTAGTTAGCGG-1,True,CACCACTAGTTAGCGG-1_contig_3,True,341,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,23522,1,clonotype2,None -CACCACTGTTTGTTGG-1,True,CACCACTGTTTGTTGG-1_contig_1,True,570,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,33008,5,clonotype2,clonotype2_consensus_2 -CACCACTGTTTGTTGG-1,True,CACCACTGTTTGTTGG-1_contig_2,True,522,TRA,TRAV8D-1,None,TRAJ33,TRAC,True,True,CATRRNYQLIW,TGTGCTACTAGGCGCAACTATCAGTTGATCTGG,14468,2,clonotype2,clonotype2_consensus_1 -CACCACTGTTTGTTGG-1,True,CACCACTGTTTGTTGG-1_contig_3,True,328,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,10842,1,clonotype2,None -CACCACTGTTTGTTGG-1,True,CACCACTGTTTGTTGG-1_contig_4,True,362,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,17386,2,clonotype2,None -CAGCGACGTGAAAGAG-1,True,CAGCGACGTGAAAGAG-1_contig_1,True,547,TRB,TRBV10,None,TRBJ2-2,TRBC2,True,True,CASSYWVANTGQLYF,TGTGCCAGCAGCTACTGGGTCGCAAACACCGGGCAGCTCTACTTT,22272,4,clonotype34,clonotype34_consensus_2 -CAGCGACGTGAAAGAG-1,True,CAGCGACGTGAAAGAG-1_contig_2,True,526,TRA,TRAV13-4-DV7,None,TRAJ13,TRAC,True,True,CAMSNSGTYQRF,TGTGCTATGTCCAATTCTGGGACTTACCAGAGGTTT,37764,6,clonotype34,clonotype34_consensus_1 -CAGCGACGTGAAAGAG-1,True,CAGCGACGTGAAAGAG-1_contig_3,True,346,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,14966,1,clonotype34,None -CATCCACTCCAGATCA-1,True,CATCCACTCCAGATCA-1_contig_1,True,516,TRB,TRBV13-3,None,TRBJ2-1,TRBC2,True,True,CASRVGNEQFF,TGTGCCAGCAGAGTGGGGAATGAGCAGTTCTTC,55066,9,clonotype35,clonotype35_consensus_1 -CATCCACTCCAGATCA-1,True,CATCCACTCCAGATCA-1_contig_2,True,525,TRA,TRAV6-6,None,TRAJ30,TRAC,True,True,CALGDPTNAYKVIF,TGTGCTCTGGGTGATCCCACAAATGCTTACAAAGTCATCTTT,22958,3,clonotype35,clonotype35_consensus_2 -CATGGCGAGGGTTCCC-1,True,CATGGCGAGGGTTCCC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQGGGNTEVFF,TGTGCCAGCAGCCAAGGGGGGGGGAACACAGAAGTCTTCTTT,43382,5,clonotype7,clonotype7_consensus_1 -CATGGCGAGGGTTCCC-1,True,CATGGCGAGGGTTCCC-1_contig_2,True,368,TRA,TRAV9-4,None,TRAJ16,TRAC,True,False,CAVTASSGQKLVF,TGTGCTGTGACGGCTTCAAGTGGCCAGAAGCTGGTTTTT,17390,1,clonotype7,None -CCATTCGTCATTCACT-1,True,CCATTCGTCATTCACT-1_contig_1,True,531,TRB,TRBV13-2,None,TRBJ1-6,TRBC1,True,True,CASGEINYNSPLYF,TGTGCCAGCGGTGAAATCAACTATAATTCGCCCCTCTACTTT,30074,3,clonotype36,clonotype36_consensus_1 -CCATTCGTCATTCACT-1,True,CCATTCGTCATTCACT-1_contig_2,True,553,TRA,TRAV4-3,None,TRAJ34,TRAC,True,True,CAASSNTDKVVF,TGTGCTGCTTCTTCCAATACCGACAAAGTCGTCTTT,45580,7,clonotype36,clonotype36_consensus_2 -CCTATTAAGGAATCGC-1,True,CCTATTAAGGAATCGC-1_contig_1,True,571,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,74296,3,clonotype3,clonotype3_consensus_1 -CCTCAGTCATTGAGCT-1,True,CCTCAGTCATTGAGCT-1_contig_1,True,547,TRA,TRAV6-1,None,TRAJ12,TRAC,True,True,CVLGDPGGYKVVF,TGTGTTCTGGGTGATCCTGGAGGCTATAAAGTGGTCTTT,15670,6,clonotype37,clonotype37_consensus_1 -CCTCAGTCATTGAGCT-1,True,CCTCAGTCATTGAGCT-1_contig_2,True,455,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,12382,5,clonotype37,None -CCTCAGTCATTGAGCT-1,True,CCTCAGTCATTGAGCT-1_contig_3,True,369,TRB,TRBV2,None,TRBJ2-1,TRBC2,True,False,CASSQDRGADYAEQFF,TGTGCCAGCAGCCAAGATAGGGGGGCGGACTATGCTGAGCAGTTCTTC,5944,1,clonotype37,None -CCTCAGTCATTGAGCT-1,True,CCTCAGTCATTGAGCT-1_contig_4,True,434,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,43908,9,clonotype37,None -CCTTCGAAGCACAGGT-1,True,CCTTCGAAGCACAGGT-1_contig_1,True,652,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGETINQDTQYF,TGTGCCAGCGGTGAGACAATTAACCAAGACACCCAGTACTTT,28912,14,clonotype38,clonotype38_consensus_2 -CCTTCGAAGCACAGGT-1,True,CCTTCGAAGCACAGGT-1_contig_2,True,591,TRA,TRAV7D-4,None,TRAJ7,TRAC,True,True,CAARDYSNNRLTL,TGTGCAGCTAGGGACTACAGCAACAACAGACTTACTTTG,7396,3,clonotype38,clonotype38_consensus_1 -CCTTCGAAGCACAGGT-1,True,CCTTCGAAGCACAGGT-1_contig_3,True,531,TRB,TRBV31,None,TRBJ1-4,TRBC1,True,True,CAWSPGQFNERLFF,TGTGCCTGGAGTCCGGGACAATTCAACGAAAGATTATTTTTC,8224,5,clonotype38,clonotype38_consensus_3 -CCTTCGAAGCACAGGT-1,True,CCTTCGAAGCACAGGT-1_contig_4,True,371,TRB,None,None,TRBJ2-4,TRBC2,False,False,None,None,2210,3,clonotype38,None -CCTTCGAAGCACAGGT-1,True,CCTTCGAAGCACAGGT-1_contig_5,True,521,TRB,TRBV17,None,TRBJ2-5,TRBC2,True,False,None,None,16424,6,clonotype38,None -CCTTCGAAGCACAGGT-1,True,CCTTCGAAGCACAGGT-1_contig_6,True,568,TRA,TRAV2,None,TRAJ12,TRAC,True,False,None,None,8518,3,clonotype38,None -CCTTTCTCACATGTGT-1,True,CCTTTCTCACATGTGT-1_contig_1,True,521,TRB,TRBV29,None,TRBJ2-3,TRBC2,True,True,CASSSWGGGAETLYF,TGTGCTAGCAGTTCCTGGGGGGGCGGTGCAGAAACGCTGTATTTT,46320,3,clonotype39,clonotype39_consensus_1 -CCTTTCTCACATGTGT-1,True,CCTTTCTCACATGTGT-1_contig_2,True,335,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,32062,1,clonotype39,None -CGAACATAGCCAGGAT-1,True,CGAACATAGCCAGGAT-1_contig_1,True,567,TRB,TRBV2,None,TRBJ2-5,TRBC2,True,True,CASSQDRWGKDTQYF,TGTGCCAGCAGCCAAGATAGGTGGGGGAAAGACACCCAGTACTTT,44362,6,clonotype40,clonotype40_consensus_2 -CGAACATAGCCAGGAT-1,True,CGAACATAGCCAGGAT-1_contig_2,True,551,TRA,TRAV9-1,None,TRAJ50,TRAC,True,True,CAVTGGASSSFSKLVF,TGTGCTGTGACGGGGGGAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,23390,3,clonotype40,clonotype40_consensus_1 -CGACCTTTCAGAAATG-1,True,CGACCTTTCAGAAATG-1_contig_1,True,556,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-1,TRBC2,True,True,CASGVAGANYAEQFF,TGTGCCAGCGGTGTGGCTGGGGCTAACTATGCTGAGCAGTTCTTC,63510,4,clonotype41,clonotype41_consensus_1 -CGACCTTTCAGAAATG-1,True,CGACCTTTCAGAAATG-1_contig_2,True,544,TRA,TRAV14D-1,None,TRAJ52,TRAC,True,False,None,None,12090,2,clonotype41,None -CGAGAAGCAAACCTAC-1,True,CGAGAAGCAAACCTAC-1_contig_1,True,568,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,53084,2,clonotype2,clonotype2_consensus_2 -CGAGAAGCAAACCTAC-1,True,CGAGAAGCAAACCTAC-1_contig_2,True,538,TRA,TRAV8D-1,None,TRAJ33,TRAC,True,True,CATRRNYQLIW,TGTGCTACTAGGCGCAACTATCAGTTGATCTGG,25904,1,clonotype2,clonotype2_consensus_1 -CGAGCACCACCAGGCT-1,True,CGAGCACCACCAGGCT-1_contig_1,True,514,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSDAGVSSYEQYF,TGTGCCAGCAGTGATGCGGGGGTGAGCTCCTATGAACAGTACTTC,51494,20,clonotype42,clonotype42_consensus_1 -CGAGCACCACCAGGCT-1,True,CGAGCACCACCAGGCT-1_contig_2,True,591,TRA,TRAV7-4,None,TRAJ9,TRAC,True,True,CAASEDMGYKLTF,TGTGCAGCTAGTGAAGACATGGGCTACAAACTTACCTTC,2194,1,clonotype42,clonotype42_consensus_2 -CGAGCACCACCAGGCT-1,True,CGAGCACCACCAGGCT-1_contig_3,True,353,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,3746,1,clonotype42,None -CGAGCACCACCAGGCT-1,True,CGAGCACCACCAGGCT-1_contig_4,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,18838,6,clonotype42,None -CGCGGTAGTCTGATTG-1,True,CGCGGTAGTCTGATTG-1_contig_1,True,571,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,9748,5,clonotype1,clonotype1_consensus_2 -CGCGGTAGTCTGATTG-1,True,CGCGGTAGTCTGATTG-1_contig_2,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,9594,5,clonotype1,clonotype1_consensus_1 -CGCGGTAGTCTGATTG-1,True,CGCGGTAGTCTGATTG-1_contig_3,True,315,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,56320,15,clonotype1,None -CGCGTTTCATCATCCC-1,True,CGCGTTTCATCATCCC-1_contig_1,True,562,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGVTGGYEQYF,TGTGCCAGCGGTGTGACTGGGGGGTATGAACAGTACTTC,8912,4,clonotype43,clonotype43_consensus_1 -CGCGTTTCATCATCCC-1,True,CGCGTTTCATCATCCC-1_contig_2,True,597,TRA,TRAV14D-3-DV8,None,TRAJ43,TRAC,True,True,CAASNNNNAPRF,TGTGCAGCAAGTAATAACAACAATGCCCCACGATTT,13076,6,clonotype43,clonotype43_consensus_2 -CGCGTTTCATCATCCC-1,True,CGCGTTTCATCATCCC-1_contig_3,True,443,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,46608,17,clonotype43,None -CGCGTTTCATCATCCC-1,True,CGCGTTTCATCATCCC-1_contig_4,True,444,TRA,None,None,TRAJ41,TRAC,False,False,None,None,4224,1,clonotype43,None -CGCGTTTCATCATCCC-1,True,CGCGTTTCATCATCCC-1_contig_5,True,317,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,5766,1,clonotype43,None -CGCGTTTCATGATCCA-1,True,CGCGTTTCATGATCCA-1_contig_1,True,583,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALEGGADRLTF,TGTGCTCTGGAGGGAGGTGCAGATAGACTCACCTTT,66552,5,clonotype44,clonotype44_consensus_1 -CGCGTTTCATGATCCA-1,True,CGCGTTTCATGATCCA-1_contig_2,True,670,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASSIYGGTSQNTLYF,TGTGCCAGCAGTATATATGGGGGGACTAGTCAAAACACCTTGTACTTT,11324,1,clonotype44,clonotype44_consensus_2 -CGCTATCAGGTGATTA-1,True,CGCTATCAGGTGATTA-1_contig_1,True,522,TRB,TRBV17,None,TRBJ1-1,TRBC1,True,True,CASSMGANTEVFF,TGTGCTAGCAGTATGGGTGCAAACACAGAAGTCTTCTTT,20564,6,clonotype45,clonotype45_consensus_2 -CGCTATCAGGTGATTA-1,True,CGCTATCAGGTGATTA-1_contig_2,True,549,TRA,TRAV6-6,None,TRAJ16,TRAC,True,True,CALRTSSGQKLVF,TGTGCTCTGAGAACTTCAAGTGGCCAGAAGCTGGTTTTT,12520,4,clonotype45,clonotype45_consensus_1 -CGCTATCAGGTGATTA-1,True,CGCTATCAGGTGATTA-1_contig_3,True,510,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,False,CQQPWGSSYEQYF,TGCCAGCAGCCCTGGGGGAGCTCCTATGAACAGTACTTC,28924,5,clonotype45,None -CGCTATCAGGTGATTA-1,True,CGCTATCAGGTGATTA-1_contig_4,True,388,TRA,TRAV4D-4,None,TRAJ2,TRAC,False,False,None,None,14162,2,clonotype45,None -CGGACTGTCCACGAAT-1,True,CGGACTGTCCACGAAT-1_contig_1,True,579,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,35374,15,clonotype1,clonotype1_consensus_2 -CGGACTGTCCACGAAT-1,True,CGGACTGTCCACGAAT-1_contig_2,True,508,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,27986,7,clonotype1,clonotype1_consensus_1 -CGGACTGTCCACGAAT-1,True,CGGACTGTCCACGAAT-1_contig_3,True,388,TRB,None,None,TRBJ1-5,TRBC1,False,False,None,None,14024,3,clonotype1,None -CGGAGTCCATTCACTT-1,True,CGGAGTCCATTCACTT-1_contig_1,True,524,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,52182,6,clonotype1,clonotype1_consensus_1 -CGGAGTCCATTCACTT-1,True,CGGAGTCCATTCACTT-1_contig_2,True,606,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,20368,3,clonotype1,clonotype1_consensus_2 -CGGCTAGAGTTAGCGG-1,True,CGGCTAGAGTTAGCGG-1_contig_1,True,551,TRA,TRAV9-1,None,TRAJ50,TRAC,True,True,CAVTGGASSSFSKLVF,TGTGCTGTGACGGGGGGAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,39714,7,clonotype46,clonotype46_consensus_1 -CGGCTAGAGTTAGCGG-1,True,CGGCTAGAGTTAGCGG-1_contig_2,True,337,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,29520,2,clonotype46,None -CGTGAGCGTACCGGCT-1,True,CGTGAGCGTACCGGCT-1_contig_1,True,607,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,24242,5,clonotype1,clonotype1_consensus_2 -CGTGAGCGTACCGGCT-1,True,CGTGAGCGTACCGGCT-1_contig_2,True,525,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,49894,9,clonotype1,clonotype1_consensus_1 -CGTTGGGTCGTTGACA-1,True,CGTTGGGTCGTTGACA-1_contig_1,True,701,TRB,TRBV19,None,TRBJ1-2,TRBC1,True,True,CASRDANSDYTF,TGTGCCAGCAGGGACGCAAACTCCGACTACACCTTC,55706,13,clonotype8,clonotype8_consensus_2 -CGTTGGGTCGTTGACA-1,True,CGTTGGGTCGTTGACA-1_contig_2,True,527,TRA,TRAV6N-7,None,TRAJ49,TRAC,True,True,CALGEPGYQNFYF,TGTGCTCTGGGTGAACCGGGTTACCAGAACTTCTATTTT,14996,4,clonotype8,clonotype8_consensus_1 -CGTTGGGTCGTTGACA-1,True,CGTTGGGTCGTTGACA-1_contig_3,True,302,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,2764,1,clonotype8,None -CTAACTTTCGAATCCA-1,True,CTAACTTTCGAATCCA-1_contig_1,True,695,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSIHANTEVFF,TGTGCCAGCAGTATCCACGCAAACACAGAAGTCTTCTTT,12774,3,clonotype47,clonotype47_consensus_1 -CTAACTTTCGAATCCA-1,True,CTAACTTTCGAATCCA-1_contig_2,True,434,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,42260,7,clonotype47,None -CTAACTTTCGAATCCA-1,True,CTAACTTTCGAATCCA-1_contig_3,True,491,TRA,TRAV9-1,None,TRAJ56,TRAC,True,False,CAVSATGGNNKLTF,TGTGCTGTGAGCGCTACTGGAGGCAATAATAAGCTGACTTTT,20918,4,clonotype47,None -CTAGAGTGTTATGCGT-1,True,CTAGAGTGTTATGCGT-1_contig_1,True,543,TRA,TRAV7D-3,None,TRAJ43,TRAC,True,True,CAALNNNNAPRF,TGTGCAGCCTTGAATAACAACAATGCCCCACGATTT,18042,2,clonotype48,clonotype48_consensus_1 -CTAGAGTGTTATGCGT-1,True,CTAGAGTGTTATGCGT-1_contig_2,True,568,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSADGSSYEQYF,TGCACCTGCAGTGCAGACGGAAGCTCCTATGAACAGTACTTC,27708,6,clonotype48,clonotype48_consensus_2 -CTAGAGTGTTATGCGT-1,True,CTAGAGTGTTATGCGT-1_contig_3,True,536,TRA,TRAV6N-7,None,TRAJ42,TRAC,True,False,CSGRYSGGSNAKLTF,TGCTCTGGGCGGTATTCTGGAGGAAGCAATGCAAAGCTAACCTTC,32632,3,clonotype48,None -CTCGGAGCAGTTCCCT-1,True,CTCGGAGCAGTTCCCT-1_contig_1,True,712,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASRTGNTEVFF,TGTGCCAGCAGGACAGGGAACACAGAAGTCTTCTTT,42580,10,clonotype49,clonotype49_consensus_1 -CTCGGAGCAGTTCCCT-1,True,CTCGGAGCAGTTCCCT-1_contig_2,True,588,TRA,TRAV5-1,None,TRAJ12,TRAC,True,True,CSASSSTGGYKVVF,TGCTCAGCAAGTTCCTCGACTGGAGGCTATAAAGTGGTCTTT,12394,4,clonotype49,clonotype49_consensus_2 -CTCGGAGCAGTTCCCT-1,True,CTCGGAGCAGTTCCCT-1_contig_3,True,361,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,23230,4,clonotype49,None -CTGGTCTTCATGGTCA-1,True,CTGGTCTTCATGGTCA-1_contig_1,True,531,TRA,TRAV6-2,None,TRAJ11,TRAC,True,True,CVLGDSGYNKLTF,TGTGTTCTGGGTGACTCGGGATACAACAAACTCACTTTT,29492,3,clonotype50,clonotype50_consensus_2 -CTGGTCTTCATGGTCA-1,True,CTGGTCTTCATGGTCA-1_contig_2,True,563,TRA,TRAV3-3,None,TRAJ15,TRAC,True,True,CAVSYQGGRALIF,TGCGCAGTCAGCTACCAGGGAGGCAGAGCTCTGATATTT,29648,6,clonotype50,clonotype50_consensus_1 -CTGGTCTTCATGGTCA-1,True,CTGGTCTTCATGGTCA-1_contig_3,True,330,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,14914,1,clonotype50,None -CTGTTTATCTGGTGTA-1,True,CTGTTTATCTGGTGTA-1_contig_1,True,565,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,True,CTCSADSDTEVFF,TGCACCTGCAGTGCAGATTCAGACACAGAAGTCTTCTTT,38106,9,clonotype51,clonotype51_consensus_2 -CTGTTTATCTGGTGTA-1,True,CTGTTTATCTGGTGTA-1_contig_2,True,569,TRA,TRAV4-4-DV10,None,TRAJ45,TRAC,True,True,CAAAMNTGGADRLTF,TGTGCTGCTGCCATGAATACAGGAGGTGCAGATAGACTCACCTTT,10718,2,clonotype51,clonotype51_consensus_1 -CTGTTTATCTGGTGTA-1,True,CTGTTTATCTGGTGTA-1_contig_3,True,429,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,27934,4,clonotype51,None -CTTACCGAGGTGGGTT-1,True,CTTACCGAGGTGGGTT-1_contig_1,True,512,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CAVTASSGQKLVF,TGTGCTGTGACGGCTTCAAGTGGCCAGAAGCTGGTTTTT,13218,2,clonotype9,clonotype9_consensus_2 -CTTACCGAGGTGGGTT-1,True,CTTACCGAGGTGGGTT-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQGGGNTEVFF,TGTGCCAGCAGCCAAGGGGGGGGGAACACAGAAGTCTTCTTT,63454,5,clonotype9,clonotype9_consensus_1 -GAAATGAAGGAGCGAG-1,True,GAAATGAAGGAGCGAG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCAGGACAGGGGAACACAGAAGTCTTCTTT,73538,9,clonotype52,clonotype52_consensus_1 -GAAGCAGAGCTCCTCT-1,True,GAAGCAGAGCTCCTCT-1_contig_1,True,603,TRA,TRAV14D-3-DV8,None,TRAJ45,TRAC,True,True,CAARHTGGADRLTF,TGTGCAGCAAGGCATACAGGAGGTGCAGATAGACTCACCTTT,12868,1,clonotype4,clonotype4_consensus_2 -GAAGCAGAGCTCCTCT-1,True,GAAGCAGAGCTCCTCT-1_contig_2,True,607,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASRKGTGGRDTQYF,TGTGCCAGCAGAAAAGGGACTGGGGGGAGAGACACCCAGTACTTT,39380,4,clonotype4,clonotype4_consensus_1 -GAAGCAGAGCTCCTCT-1,True,GAAGCAGAGCTCCTCT-1_contig_3,True,382,TRA,None,None,TRAJ41,TRAC,False,False,None,None,25330,1,clonotype4,None -GACAGAGAGCACCGTC-1,True,GACAGAGAGCACCGTC-1_contig_1,True,600,TRA,TRAV7D-4,None,TRAJ52,TRAC,True,True,CAASGNTGANTGKLTF,TGTGCAGCTAGTGGTAACACTGGAGCTAACACTGGAAAGCTCACGTTT,77450,4,clonotype53,clonotype53_consensus_1 -GACTGCGAGAAACCAT-1,True,GACTGCGAGAAACCAT-1_contig_1,True,516,TRB,TRBV31,None,TRBJ2-3,TRBC2,True,True,CAWRDWGRAETLYF,TGTGCCTGGAGGGACTGGGGGAGGGCAGAAACGCTGTATTTT,48596,7,clonotype10,clonotype10_consensus_1 -GACTGCGAGAAACCAT-1,True,GACTGCGAGAAACCAT-1_contig_2,True,594,TRA,TRAV7-4,None,TRAJ27,TRAC,True,True,CAASEDTNTGKLTF,TGTGCAGCTAGTGAGGACACCAATACAGGCAAATTAACCTTT,30434,5,clonotype10,clonotype10_consensus_2 -GATGAAAAGTGTGAAT-1,True,GATGAAAAGTGTGAAT-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASSRDNQNTLYF,TGTGCCAGCTCGCGGGACAATCAAAACACCTTGTACTTT,43282,12,clonotype54,clonotype54_consensus_2 -GATGAAAAGTGTGAAT-1,True,GATGAAAAGTGTGAAT-1_contig_2,True,586,TRA,TRAV6-6,None,TRAJ43,TRAC,True,True,CALGDRFNNNAPRF,TGTGCTCTGGGTGATCGATTTAACAACAATGCCCCACGATTT,6652,1,clonotype54,clonotype54_consensus_1 -GATGAAAAGTGTGAAT-1,True,GATGAAAAGTGTGAAT-1_contig_3,True,482,TRA,TRAV12D-2,None,TRAJ38,TRAC,True,False,CPVLLCSECLNVGDNSKLIW,TGCCCTGTACTACTGTGCTCTGAGTGCCTTAATGTTGGTGACAACAGTAAGCTGATTTGG,8674,3,clonotype54,None -GATGAAAAGTGTGAAT-1,True,GATGAAAAGTGTGAAT-1_contig_4,True,326,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,19056,3,clonotype54,None -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_1,True,529,TRA,TRAV6N-7,None,TRAJ17,TRAC,True,True,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,9742,8,clonotype5,clonotype5_consensus_1 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_2,True,514,TRB,TRBV14,None,TRBJ1-5,TRBC1,True,True,CASSPGTEAPLF,TGTGCCAGCAGTCCCGGGACCGAGGCTCCGCTTTTT,21206,20,clonotype5,clonotype5_consensus_2 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_3,True,407,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,6202,10,clonotype5,None -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_4,True,701,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,21360,12,clonotype5,None -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_5,True,349,TRA,TRAV6N-6,None,TRAJ17,TRAC,True,False,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,2524,1,clonotype5,clonotype5_consensus_1 -GCAGCCACAAAGGAAG-1,True,GCAGCCACAAAGGAAG-1_contig_6,True,332,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,16022,9,clonotype5,None -GCAGCCACAGTTCATG-1,True,GCAGCCACAGTTCATG-1_contig_1,True,566,TRA,TRAV14D-3-DV8,None,TRAJ40,TRAC,True,True,CAASAVTGNYKYVF,TGTGCAGCAAGTGCAGTTACAGGAAACTACAAATACGTCTTT,23556,6,clonotype55,clonotype55_consensus_1 -GCAGCCACAGTTCATG-1,True,GCAGCCACAGTTCATG-1_contig_2,True,519,TRB,TRBV13-3,None,TRBJ2-5,TRBC2,True,True,CASSDTGEDTQYF,TGTGCCAGCAGTGATACAGGGGAAGACACCCAGTACTTT,21378,5,clonotype55,clonotype55_consensus_2 -GCAGCCACAGTTCATG-1,True,GCAGCCACAGTTCATG-1_contig_3,True,374,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,34082,5,clonotype55,None -GCGAGAATCCTACAGA-1,True,GCGAGAATCCTACAGA-1_contig_1,True,522,TRA,TRAV14D-2,None,TRAJ31,TRAC,True,True,CAASDDNNRIFF,TGTGCAGCAAGTGACGACAATAACAGAATCTTCTTT,45916,6,clonotype56,clonotype56_consensus_1 -GCGGGTTGTAAAGGAG-1,True,GCGGGTTGTAAAGGAG-1_contig_1,True,516,TRB,TRBV31,None,TRBJ2-3,TRBC2,True,True,CAWRDWGRAETLYF,TGTGCCTGGAGGGACTGGGGGAGGGCAGAAACGCTGTATTTT,22152,2,clonotype10,clonotype10_consensus_1 -GCGGGTTGTAAAGGAG-1,True,GCGGGTTGTAAAGGAG-1_contig_2,True,594,TRA,TRAV7-4,None,TRAJ27,TRAC,True,True,CAASEDTNTGKLTF,TGTGCAGCTAGTGAGGACACCAATACAGGCAAATTAACCTTT,29882,2,clonotype10,clonotype10_consensus_2 -GCGGGTTGTAAAGGAG-1,True,GCGGGTTGTAAAGGAG-1_contig_3,True,557,TRA,TRAV4-3,None,TRAJ30,TRAC,True,False,None,None,26254,2,clonotype10,None -GCTGCAGCAAGCCGTC-1,True,GCTGCAGCAAGCCGTC-1_contig_1,True,567,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-2,TRBC2,True,True,CASGEMENTGQLYF,TGTGCCAGCGGTGAAATGGAGAACACCGGGCAGCTCTACTTT,63236,12,clonotype57,clonotype57_consensus_2 -GCTGCAGCAAGCCGTC-1,True,GCTGCAGCAAGCCGTC-1_contig_2,True,676,TRA,TRAV9D-2,None,TRAJ56,TRAC,True,True,CAVSMATGGNNKLTF,TGTGCTGTGAGCATGGCTACTGGAGGCAATAATAAGCTGACTTTT,10264,1,clonotype57,clonotype57_consensus_1 -GCTTCCATCTTTACAC-1,True,GCTTCCATCTTTACAC-1_contig_1,True,511,TRB,TRBV13-1,None,TRBJ2-5,TRBC2,True,True,CASKRLGAQDTQYF,TGTGCCAGCAAAAGACTGGGGGCCCAAGACACCCAGTACTTT,32244,14,clonotype58,clonotype58_consensus_2 -GCTTCCATCTTTACAC-1,True,GCTTCCATCTTTACAC-1_contig_2,True,553,TRA,TRAV4-3,None,TRAJ30,TRAC,True,True,CAAETNAYKVIF,TGTGCTGCTGAAACAAATGCTTACAAAGTCATCTTT,31848,16,clonotype58,clonotype58_consensus_1 -GCTTCCATCTTTACAC-1,True,GCTTCCATCTTTACAC-1_contig_3,True,602,TRA,TRAV8D-2,None,TRAJ24,TRAC,True,False,None,None,3290,1,clonotype58,None -GCTTCCATCTTTACAC-1,True,GCTTCCATCTTTACAC-1_contig_4,True,306,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,5690,6,clonotype58,None -GGACAAGGTCGAACAG-1,True,GGACAAGGTCGAACAG-1_contig_1,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,74196,5,clonotype59,clonotype59_consensus_1 -GGACAGAAGCTTTGGT-1,True,GGACAGAAGCTTTGGT-1_contig_1,True,713,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASSSDWGLSQNTLYF,TGTGCCAGCAGTAGCGACTGGGGCCTGAGTCAAAACACCTTGTACTTT,41660,6,clonotype60,clonotype60_consensus_1 -GGACAGAAGCTTTGGT-1,True,GGACAGAAGCTTTGGT-1_contig_2,True,376,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,22436,2,clonotype60,None -GGACAGAAGCTTTGGT-1,True,GGACAGAAGCTTTGGT-1_contig_3,True,578,TRA,TRAV12D-2,None,TRAJ42,TRAC,True,False,None,None,10464,2,clonotype60,None -GGATTACGTTCGGGCT-1,True,GGATTACGTTCGGGCT-1_contig_1,True,478,TRA,TRAV4-3,None,TRAJ31,None,True,True,CAADNNRIFF,TGTGCTGCTGACAATAACAGAATCTTCTTT,65518,3,clonotype61,clonotype61_consensus_1 -GGATTACGTTCGGGCT-1,True,GGATTACGTTCGGGCT-1_contig_2,True,541,TRB,TRBV10,None,TRBJ2-7,TRBC2,True,True,CASSTDWGYEQYF,TGTGCCAGCAGCACCGACTGGGGCTATGAACAGTACTTC,6690,3,clonotype61,clonotype61_consensus_2 -GGCAATTGTCCCGACA-1,True,GGCAATTGTCCCGACA-1_contig_1,True,517,TRB,TRBV14,None,TRBJ2-4,TRBC2,True,True,CASSFHGKNTLYF,TGTGCCAGCAGTTTCCACGGAAAAAACACCTTGTACTTT,19524,3,clonotype62,clonotype62_consensus_2 -GGCAATTGTCCCGACA-1,True,GGCAATTGTCCCGACA-1_contig_2,True,542,TRA,TRAV9-1,None,TRAJ9,TRAC,True,True,CAVRKNMGYKLTF,TGTGCTGTGAGGAAGAACATGGGCTACAAACTTACCTTC,34030,9,clonotype62,clonotype62_consensus_1 -GGCAATTGTCCCGACA-1,True,GGCAATTGTCCCGACA-1_contig_3,True,357,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,18608,4,clonotype62,None -GGCAATTGTGTCTGAT-1,True,GGCAATTGTGTCTGAT-1_contig_1,True,547,TRB,TRBV10,None,TRBJ2-2,TRBC2,True,True,CASSYWVANTGQLYF,TGTGCCAGCAGCTACTGGGTCGCAAACACCGGGCAGCTCTACTTT,30016,12,clonotype11,clonotype11_consensus_4 -GGCAATTGTGTCTGAT-1,True,GGCAATTGTGTCTGAT-1_contig_2,True,604,TRA,TRAV13-4-DV7,None,TRAJ13,TRAC,True,True,CAMSNSGTYQRF,TGTGCTATGTCCAATTCTGGGACTTACCAGAGGTTT,21508,8,clonotype11,clonotype11_consensus_2 -GGCAATTGTGTCTGAT-1,True,GGCAATTGTGTCTGAT-1_contig_3,True,550,TRB,TRBV10,None,TRBJ2-5,TRBC2,True,True,CASSYKADWGRDTQYF,TGTGCCAGCAGCTATAAGGCAGACTGGGGGAGAGACACCCAGTACTTT,11640,4,clonotype11,clonotype11_consensus_1 -GGCAATTGTGTCTGAT-1,True,GGCAATTGTGTCTGAT-1_contig_4,True,632,TRA,TRAV17,None,TRAJ34,TRAC,True,True,CALEVAASNTDKVVF,TGTGCACTGGAGGTCGCAGCTTCCAATACCGACAAAGTCGTCTTT,13898,4,clonotype11,clonotype11_consensus_3 -GGTGCGTGTGCACGAA-1,True,GGTGCGTGTGCACGAA-1_contig_1,True,514,TRB,TRBV14,None,TRBJ1-5,TRBC1,True,True,CASSPGTEAPLF,TGTGCCAGCAGTCCCGGGACCGAGGCTCCGCTTTTT,28270,20,clonotype5,clonotype5_consensus_2 -GGTGCGTGTGCACGAA-1,True,GGTGCGTGTGCACGAA-1_contig_2,True,542,TRA,TRAV6N-7,None,TRAJ17,TRAC,True,True,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,22156,13,clonotype5,clonotype5_consensus_1 -GGTGCGTGTGCACGAA-1,True,GGTGCGTGTGCACGAA-1_contig_3,True,315,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,2468,1,clonotype5,None -GGTGCGTGTGCACGAA-1,True,GGTGCGTGTGCACGAA-1_contig_4,True,579,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,16600,9,clonotype5,None -GGTGCGTGTGCACGAA-1,True,GGTGCGTGTGCACGAA-1_contig_5,True,326,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,5686,5,clonotype5,None -GGTGTTAAGACCACGA-1,True,GGTGTTAAGACCACGA-1_contig_1,True,570,TRB,TRBV20,None,TRBJ1-2,TRBC1,True,True,CGARRQSNSDYTF,TGTGGTGCTAGACGACAATCAAACTCCGACTACACCTTC,68162,9,clonotype63,clonotype63_consensus_2 -GGTGTTAAGACCACGA-1,True,GGTGTTAAGACCACGA-1_contig_2,True,676,TRA,TRAV9-4,None,TRAJ50,TRAC,True,True,CAVSIASSSFSKLVF,TGTGCTGTGAGCATAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,8316,1,clonotype63,clonotype63_consensus_1 -GTACTCCGTTATTCTC-1,True,GTACTCCGTTATTCTC-1_contig_1,True,597,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,14644,4,clonotype1,clonotype1_consensus_2 -GTACTCCGTTATTCTC-1,True,GTACTCCGTTATTCTC-1_contig_2,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,59060,11,clonotype1,clonotype1_consensus_1 -GTACTTTCACGTCAGC-1,True,GTACTTTCACGTCAGC-1_contig_1,True,521,TRA,TRAV6-5,None,TRAJ30,TRAC,True,True,CALSENTNAYKVIF,TGTGCTCTGAGTGAGAACACAAATGCTTACAAAGTCATCTTT,20710,5,clonotype64,clonotype64_consensus_1 -GTACTTTCACGTCAGC-1,True,GTACTTTCACGTCAGC-1_contig_2,True,612,TRB,TRBV2,None,TRBJ1-6,TRBC1,True,True,CASSQGQGNNSPLYF,TGTGCCAGCAGCCAAGGACAGGGGAATAATTCGCCCCTCTACTTT,19528,6,clonotype64,clonotype64_consensus_2 -GTACTTTCACGTCAGC-1,True,GTACTTTCACGTCAGC-1_contig_3,True,326,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,13394,2,clonotype64,None -GTACTTTCACGTCAGC-1,True,GTACTTTCACGTCAGC-1_contig_4,True,547,TRA,TRAV5-1,None,TRAJ26,TRAC,True,False,None,None,17324,3,clonotype64,None -GTAGTCAGTAAATGAC-1,True,GTAGTCAGTAAATGAC-1_contig_1,True,534,TRA,TRAV6N-7,None,TRAJ58,TRAC,True,True,CALGVQGTGSKLSF,TGTGCTCTGGGTGTGCAAGGCACTGGGTCTAAGCTGTCATTT,34850,6,clonotype65,clonotype65_consensus_1 -GTAGTCAGTAAATGAC-1,True,GTAGTCAGTAAATGAC-1_contig_2,True,525,TRB,TRBV5,None,TRBJ2-3,TRBC2,True,True,CASSQDWVGGAETLYF,TGTGCCAGCAGCCAAGATTGGGTTGGGGGTGCAGAAACGCTGTATTTT,29314,3,clonotype65,clonotype65_consensus_2 -GTAGTCAGTAAATGAC-1,True,GTAGTCAGTAAATGAC-1_contig_3,True,610,TRB,TRBV3,None,TRBJ2-4,TRBC2,True,False,CQQLTGLGTSQNTLYF,TGCCAGCAGCTCACGGGACTGGGGACTAGTCAAAACACCTTGTACTTT,12570,4,clonotype65,None -GTAGTCAGTAAATGAC-1,True,GTAGTCAGTAAATGAC-1_contig_4,True,552,TRA,TRAV15-2-DV6-2,None,TRAJ45,TRAC,True,False,None,None,424,5,clonotype65,None -GTATCTTGTACAAGTA-1,True,GTATCTTGTACAAGTA-1_contig_1,True,529,TRA,TRAV6N-7,None,TRAJ17,TRAC,True,True,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,25644,20,clonotype5,clonotype5_consensus_1 -GTATCTTGTACAAGTA-1,True,GTATCTTGTACAAGTA-1_contig_2,True,515,TRB,TRBV14,None,TRBJ1-5,TRBC1,True,True,CASSPGTEAPLF,TGTGCCAGCAGTCCCGGGACCGAGGCTCCGCTTTTT,22744,9,clonotype5,clonotype5_consensus_2 -GTATCTTGTACAAGTA-1,True,GTATCTTGTACAAGTA-1_contig_3,True,319,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,15054,5,clonotype5,None -GTATCTTGTACAAGTA-1,True,GTATCTTGTACAAGTA-1_contig_4,True,439,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,2778,1,clonotype5,None -GTCACAAGTACCGTTA-1,True,GTCACAAGTACCGTTA-1_contig_1,True,547,TRB,TRBV10,None,TRBJ2-2,TRBC2,True,True,CASSYWVANTGQLYF,TGTGCCAGCAGCTACTGGGTCGCAAACACCGGGCAGCTCTACTTT,16776,3,clonotype11,clonotype11_consensus_4 -GTCACAAGTACCGTTA-1,True,GTCACAAGTACCGTTA-1_contig_2,True,550,TRB,TRBV10,None,TRBJ2-5,TRBC2,True,True,CASSYKADWGRDTQYF,TGTGCCAGCAGCTATAAGGCAGACTGGGGGAGAGACACCCAGTACTTT,12570,3,clonotype11,clonotype11_consensus_1 -GTCACAAGTACCGTTA-1,True,GTCACAAGTACCGTTA-1_contig_3,True,612,TRA,TRAV13-4-DV7,None,TRAJ13,TRAC,True,True,CAMSNSGTYQRF,TGTGCTATGTCCAATTCTGGGACTTACCAGAGGTTT,39452,6,clonotype11,clonotype11_consensus_2 -GTCACAAGTACCGTTA-1,True,GTCACAAGTACCGTTA-1_contig_4,True,601,TRA,TRAV17,None,TRAJ34,TRAC,True,True,CALEVAASNTDKVVF,TGTGCACTGGAGGTCGCAGCTTCCAATACCGACAAAGTCGTCTTT,8030,2,clonotype11,clonotype11_consensus_3 -GTCCTCAGTAGCTAAA-1,True,GTCCTCAGTAGCTAAA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ1-3,TRBC1,True,True,CASSQDRGAGNTLYF,TGTGCCAGCAGCCAAGATCGGGGGGCTGGAAATACGCTCTATTTT,75846,6,clonotype66,clonotype66_consensus_1 -GTCCTCAGTAGCTAAA-1,True,GTCCTCAGTAGCTAAA-1_contig_2,True,345,TRA,TRAV6D-7,None,TRAJ17,TRAC,True,False,CALRTNSAGNKLTF,TGTGCTCTGAGGACTAACAGTGCAGGGAACAAGCTAACTTTT,8,4,clonotype66,None -GTTAAGCCATATACCG-1,True,GTTAAGCCATATACCG-1_contig_1,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,21878,6,clonotype1,clonotype1_consensus_1 -GTTAAGCCATATACCG-1,True,GTTAAGCCATATACCG-1_contig_2,True,531,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,3218,3,clonotype1,clonotype1_consensus_2 -GTTAAGCCATATACCG-1,True,GTTAAGCCATATACCG-1_contig_3,True,427,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,53744,9,clonotype1,None -GTTCATTGTCCCGACA-1,True,GTTCATTGTCCCGACA-1_contig_1,True,656,TRA,TRAV7-1,None,TRAJ7,TRAC,True,True,CAVRAYSNNRLTL,TGTGCAGTGAGGGCCTACAGCAACAACAGACTTACTTTG,21080,7,clonotype67,clonotype67_consensus_2 -GTTCATTGTCCCGACA-1,True,GTTCATTGTCCCGACA-1_contig_2,True,568,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGETINQDTQYF,TGTGCCAGCGGTGAAACAATTAACCAAGACACCCAGTACTTT,26828,9,clonotype67,clonotype67_consensus_1 -GTTCATTGTCCCGACA-1,True,GTTCATTGTCCCGACA-1_contig_3,True,514,TRA,TRAV1,None,TRAJ23,TRAC,True,False,None,None,24160,5,clonotype67,None -GTTCATTGTCCCGACA-1,True,GTTCATTGTCCCGACA-1_contig_4,True,318,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,6176,1,clonotype67,None -GTTCGGGAGTAACCCT-1,True,GTTCGGGAGTAACCCT-1_contig_1,True,732,TRA,TRAV9-4,None,TRAJ2,TRAC,True,True,CALNTGGLSGKLTF,TGTGCTCTGAATACTGGAGGACTAAGTGGTAAATTAACATTC,37020,3,clonotype68,clonotype68_consensus_2 -GTTCGGGAGTAACCCT-1,True,GTTCGGGAGTAACCCT-1_contig_2,True,633,TRB,TRBV13-3,None,TRBJ1-6,TRBC1,True,True,CASSAQNNSPLYF,TGTGCCAGCAGTGCTCAGAATAATTCGCCCCTCTACTTT,25658,2,clonotype68,clonotype68_consensus_1 -GTTCGGGAGTAACCCT-1,True,GTTCGGGAGTAACCCT-1_contig_3,True,506,TRA,TRAV7D-5,None,TRAJ13,TRAC,True,True,CAPIANSGTYQRF,TGTGCACCTATTGCAAATTCTGGGACTTACCAGAGGTTT,15764,1,clonotype68,clonotype68_consensus_3 -GTTCTCGAGTCTCAAC-1,True,GTTCTCGAGTCTCAAC-1_contig_1,True,548,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCAGGGCAAATGCTTACAAAGTCATCTTT,6436,3,clonotype69,clonotype69_consensus_1 -GTTCTCGAGTCTCAAC-1,True,GTTCTCGAGTCTCAAC-1_contig_2,True,627,TRB,TRBV2,None,TRBJ2-2,TRBC2,True,True,CASSQEEGANTGQLYF,TGTGCCAGCAGCCAAGAGGAGGGGGCAAACACCGGGCAGCTCTACTTT,7808,3,clonotype69,clonotype69_consensus_2 -GTTCTCGAGTCTCAAC-1,True,GTTCTCGAGTCTCAAC-1_contig_3,True,424,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,62868,18,clonotype69,None -GTTTCTACATGCCCGA-1,True,GTTTCTACATGCCCGA-1_contig_1,True,526,TRA,TRAV6N-7,None,TRAJ49,TRAC,True,True,CALGEPGYQNFYF,TGTGCTCTGGGTGAACCGGGTTACCAGAACTTCTATTTT,14050,4,clonotype8,clonotype8_consensus_1 -GTTTCTACATGCCCGA-1,True,GTTTCTACATGCCCGA-1_contig_2,True,666,TRB,TRBV19,None,TRBJ1-2,TRBC1,True,True,CASRDANSDYTF,TGTGCCAGCAGGGACGCAAACTCCGACTACACCTTC,52602,15,clonotype8,clonotype8_consensus_2 -GTTTCTACATGCCCGA-1,True,GTTTCTACATGCCCGA-1_contig_3,True,326,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,8110,1,clonotype8,None -TAAGCGTCAAGCGCTC-1,True,TAAGCGTCAAGCGCTC-1_contig_1,True,565,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSGTGGYEQYF,TGCACCTGCAGTGGGACTGGGGGCTATGAACAGTACTTC,53792,12,clonotype70,clonotype70_consensus_2 -TAAGCGTCAAGCGCTC-1,True,TAAGCGTCAAGCGCTC-1_contig_2,True,527,TRA,TRAV6-5,None,TRAJ52,TRAC,True,True,CALRTNTGANTGKLTF,TGTGCTCTGAGGACTAACACTGGAGCTAACACTGGAAAGCTCACGTTT,12504,2,clonotype70,clonotype70_consensus_1 -TAAGCGTCAAGCGCTC-1,True,TAAGCGTCAAGCGCTC-1_contig_3,True,554,TRA,TRAV9-1,None,TRAJ52,TRAC,True,True,CAASPANTGANTGKLTF,TGTGCTGCGAGCCCCGCTAACACTGGAGCTAACACTGGAAAGCTCACGTTT,12274,3,clonotype70,clonotype70_consensus_3 -TAAGTGCTCCTTGCCA-1,True,TAAGTGCTCCTTGCCA-1_contig_1,True,594,TRA,TRAV7-4,None,TRAJ5,TRAC,True,True,CAASGTQVVGQLTF,TGTGCAGCTAGTGGGACACAGGTTGTGGGGCAGCTCACTTTC,31136,5,clonotype71,clonotype71_consensus_1 -TAAGTGCTCCTTGCCA-1,True,TAAGTGCTCCTTGCCA-1_contig_2,True,522,TRB,TRBV31,None,TRBJ1-3,TRBC1,True,True,CAWRQNSGNTLYF,TGTGCCTGGAGACAGAATTCTGGAAATACGCTCTATTTT,33362,5,clonotype71,clonotype71_consensus_2 -TAAGTGCTCCTTGCCA-1,True,TAAGTGCTCCTTGCCA-1_contig_3,True,402,TRA,TRAV6-7-DV9,None,TRAJ13,TRAC,True,False,CALIQILGLTRGLEL,TGTGCTCTGATTCAAATTCTGGGACTTACCAGAGGTTTGGAACTG,13630,1,clonotype71,None -TACGGGCGTCATATGC-1,True,TACGGGCGTCATATGC-1_contig_1,True,552,TRB,TRBV20,TRBD1,TRBJ1-2,TRBC1,True,True,CGVGTGGANSDYTF,TGTGGTGTCGGGACAGGGGGCGCGAACTCCGACTACACCTTC,41534,8,clonotype2,clonotype2_consensus_2 -TACGGGCGTCATATGC-1,True,TACGGGCGTCATATGC-1_contig_2,True,522,TRA,TRAV8D-1,None,TRAJ33,TRAC,True,True,CATRRNYQLIW,TGTGCTACTAGGCGCAACTATCAGTTGATCTGG,7788,1,clonotype2,clonotype2_consensus_1 -TACGGGCGTCATATGC-1,True,TACGGGCGTCATATGC-1_contig_3,True,554,TRA,TRAV10D,None,TRAJ18,TRAC,True,False,None,None,7236,1,clonotype2,None -TACGGGCGTCATATGC-1,True,TACGGGCGTCATATGC-1_contig_4,True,352,TRB,TRBV19,None,TRBJ1-6,TRBC1,True,False,None,None,12526,1,clonotype2,None -TAGTTGGGTATTCTCT-1,True,TAGTTGGGTATTCTCT-1_contig_1,True,514,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,66450,7,clonotype1,clonotype1_consensus_1 -TAGTTGGGTATTCTCT-1,True,TAGTTGGGTATTCTCT-1_contig_2,True,528,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,5722,2,clonotype1,clonotype1_consensus_2 -TATCTCACATGCTGGC-1,True,TATCTCACATGCTGGC-1_contig_1,True,585,TRA,TRAV12-3,None,TRAJ58,TRAC,True,True,CALRQGTGSKLSF,TGTGCTTTGAGGCAAGGCACTGGGTCTAAGCTGTCATTT,51526,7,clonotype72,clonotype72_consensus_1 -TATCTCACATGCTGGC-1,True,TATCTCACATGCTGGC-1_contig_2,True,583,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGDRGQGYEQYF,TGTGCCAGCGGTGATCGGGGACAGGGATATGAACAGTACTTC,23630,2,clonotype72,clonotype72_consensus_2 -TCAACGACATGGTCAT-1,True,TCAACGACATGGTCAT-1_contig_1,True,603,TRA,TRAV14D-3-DV8,None,TRAJ45,TRAC,True,True,CAARHTGGADRLTF,TGTGCAGCAAGGCATACAGGAGGTGCAGATAGACTCACCTTT,25206,4,clonotype4,clonotype4_consensus_2 -TCAACGACATGGTCAT-1,True,TCAACGACATGGTCAT-1_contig_2,True,721,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASRKGTGGRDTQYF,TGTGCCAGCAGAAAAGGGACTGGGGGGAGAGACACCCAGTACTTT,32924,5,clonotype4,clonotype4_consensus_1 -TCAACGACATGGTCAT-1,True,TCAACGACATGGTCAT-1_contig_3,True,329,TRB,TRBV10,None,None,TRBC1,False,False,None,None,15154,1,clonotype4,None -TCAACGACATGGTCAT-1,True,TCAACGACATGGTCAT-1_contig_4,True,599,TRA,TRAV7-4,None,TRAJ49,TRAC,True,False,CAASEQE,TGTGCAGCTAGTGAGCAGGAA,3578,1,clonotype4,None -TCAACGAGTAGCACGA-1,True,TCAACGAGTAGCACGA-1_contig_1,True,521,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSDAGQSSYEQYF,TGTGCCAGCAGTGATGCCGGACAGAGCTCCTATGAACAGTACTTC,55040,18,clonotype73,clonotype73_consensus_2 -TCAACGAGTAGCACGA-1,True,TCAACGAGTAGCACGA-1_contig_2,True,591,TRA,TRAV7D-4,None,TRAJ9,TRAC,True,True,CAASEDMGYKLTF,TGTGCAGCTAGTGAGGACATGGGCTACAAACTTACCTTC,17978,9,clonotype73,clonotype73_consensus_1 -TCAACGAGTAGCACGA-1,True,TCAACGAGTAGCACGA-1_contig_3,True,621,TRB,TRBV1,None,TRBJ2-1,TRBC2,True,False,None,None,4354,2,clonotype73,None -TCAATCTAGCTGCCCA-1,True,TCAATCTAGCTGCCCA-1_contig_1,True,585,TRA,TRAV7D-4,None,TRAJ31,TRAC,True,True,CAANNNNRIFF,TGTGCAGCCAATAACAATAACAGAATCTTCTTT,36166,4,clonotype74,clonotype74_consensus_1 -TCAATCTTCAGAGACG-1,True,TCAATCTTCAGAGACG-1_contig_1,True,600,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,17898,4,clonotype75,clonotype75_consensus_1 -TCAATCTTCAGAGACG-1,True,TCAATCTTCAGAGACG-1_contig_2,True,495,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,False,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,21344,3,clonotype75,None -TCAATCTTCAGAGACG-1,True,TCAATCTTCAGAGACG-1_contig_3,True,347,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,37500,5,clonotype75,None -TCACGAATCAGCTCTC-1,True,TCACGAATCAGCTCTC-1_contig_1,True,718,TRA,TRAV9-4,None,TRAJ34,TRAC,True,True,CAASISNTDKVVF,TGTGCTGCGAGCATCTCCAATACCGACAAAGTCGTCTTT,30010,3,clonotype76,clonotype76_consensus_2 -TCACGAATCAGCTCTC-1,True,TCACGAATCAGCTCTC-1_contig_2,True,698,TRB,TRBV19,None,TRBJ2-3,TRBC2,True,True,CASSSDWGSETLYF,TGTGCCAGCAGTAGTGACTGGGGGTCAGAAACGCTGTATTTT,48138,9,clonotype76,clonotype76_consensus_1 -TCAGATGTCAGAGACG-1,True,TCAGATGTCAGAGACG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,66354,39,clonotype77,clonotype77_consensus_1 -TCAGGATGTATTAGCC-1,True,TCAGGATGTATTAGCC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCTGGACAGGGTAACACAGAAGTCTTCTTT,51466,7,clonotype78,clonotype78_consensus_2 -TCAGGATGTATTAGCC-1,True,TCAGGATGTATTAGCC-1_contig_2,True,718,TRA,TRAV9D-2,None,TRAJ17,TRAC,True,True,CAATNSAGNKLTF,TGTGCTGCGACTAACAGTGCAGGGAACAAGCTAACTTTT,10310,2,clonotype78,clonotype78_consensus_1 -TCAGGATGTATTAGCC-1,True,TCAGGATGTATTAGCC-1_contig_3,True,520,TRA,TRAV15-1-DV6-1,None,TRAJ18,TRAC,True,False,CSLGADRGSALGRLHF,TGCTCTCTGGGAGCCGATAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,3408,2,clonotype78,None -TCAGGATGTATTAGCC-1,True,TCAGGATGTATTAGCC-1_contig_4,True,356,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,9160,3,clonotype78,None -TCATTACGTGTGCGTC-1,True,TCATTACGTGTGCGTC-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-7,TRBC2,True,True,CASSINWGGEQYF,TGTGCCAGCAGTATAAACTGGGGGGGCGAACAGTACTTC,40606,5,clonotype6,clonotype6_consensus_1 -TCATTACGTGTGCGTC-1,True,TCATTACGTGTGCGTC-1_contig_2,True,535,TRA,TRAV6N-7,None,TRAJ49,TRAC,True,True,CALGGKKGYQNFYF,TGTGCTCTGGGTGGTAAGAAGGGTTACCAGAACTTCTATTTT,17558,2,clonotype6,clonotype6_consensus_2 -TCATTACGTGTGCGTC-1,True,TCATTACGTGTGCGTC-1_contig_3,True,350,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,20666,1,clonotype6,None -TCGTAGACAGCTGGCT-1,True,TCGTAGACAGCTGGCT-1_contig_1,True,550,TRA,TRAV6-1,None,TRAJ45,TRAC,True,True,CVLGDEAGGADRLTF,TGTGTTCTGGGTGATGAGGCAGGAGGTGCAGATAGACTCACCTTT,27320,2,clonotype79,clonotype79_consensus_1 -TCGTAGACAGCTGGCT-1,True,TCGTAGACAGCTGGCT-1_contig_2,True,627,TRB,TRBV31,None,TRBJ1-2,TRBC1,True,False,None,None,51778,2,clonotype79,None -TCTATTGGTTGTGGAG-1,True,TCTATTGGTTGTGGAG-1_contig_1,True,555,TRA,TRAV8N-2,None,TRAJ44,TRAC,True,True,CAPVITGSGGKLTL,TGTGCTCCCGTCATTACTGGCAGTGGTGGAAAACTCACTTTG,55542,14,clonotype80,clonotype80_consensus_1 -TCTATTGGTTGTGGAG-1,True,TCTATTGGTTGTGGAG-1_contig_2,True,529,TRB,TRBV20,None,TRBJ2-5,TRBC2,True,True,CGALTGNTQYF,TGTGGTGCTTTGACAGGAAACACCCAGTACTTT,7600,2,clonotype80,clonotype80_consensus_2 -TCTATTGGTTGTGGAG-1,True,TCTATTGGTTGTGGAG-1_contig_3,True,527,TRA,TRAV11,None,TRAJ48,TRAC,True,False,CWMTLPPTSVWWGYGNEKITF,TGCTGGATGACACTGCCACCTACATCTGTGTGGTGGGGCTATGGAAATGAGAAAATAACTTTT,13132,3,clonotype80,None -TCTGAGATCACTCTTA-1,True,TCTGAGATCACTCTTA-1_contig_1,True,579,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASSEPATGGDYEQYF,TGTGCCAGCAGTGAGCCGGCGACGGGGGGCGATTATGAACAGTACTTC,75302,13,clonotype81,clonotype81_consensus_1 -TCTGGAATCGCAGGCT-1,True,TCTGGAATCGCAGGCT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-4,TRBC1,True,True,CASSQEISNERLFF,TGTGCCAGCAGCCAAGAGATTTCCAACGAAAGATTATTTTTC,41650,3,clonotype82,clonotype82_consensus_1 -TCTGGAATCGCAGGCT-1,True,TCTGGAATCGCAGGCT-1_contig_2,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,23452,3,clonotype82,None -TCTGGAATCGCAGGCT-1,True,TCTGGAATCGCAGGCT-1_contig_3,True,500,TRA,TRAV6-5,None,TRAJ34,TRAC,True,False,CTTVLWAPLSNTDKVVF,TGTACTACTGTGCTCTGGGCCCCGCTTTCCAATACCGACAAAGTCGTCTTT,13966,2,clonotype82,None -TGAGCCGGTCCTAGCG-1,True,TGAGCCGGTCCTAGCG-1_contig_1,True,501,TRA,TRAV21-DV12,None,TRAJ50,TRAC,True,True,CILRSSSFSKLVF,TGTATCCTGAGGTCCTCCTCCTTCAGCAAGCTGGTGTTT,20390,6,clonotype83,clonotype83_consensus_1 -TGAGCCGGTCCTAGCG-1,True,TGAGCCGGTCCTAGCG-1_contig_2,True,522,TRB,TRBV31,None,TRBJ1-6,TRBC1,True,True,CAWSRGEGTYNSPLYF,TGTGCCTGGAGTCGCGGGGAAGGGACCTATAATTCGCCCCTCTACTTT,57770,10,clonotype83,clonotype83_consensus_2 -TGCCCATAGATATGGT-1,True,TGCCCATAGATATGGT-1_contig_1,True,537,TRA,TRAV3-3,None,TRAJ49,TRAC,True,True,CAVSVDTGYQNFYF,TGCGCAGTCAGTGTGGACACGGGTTACCAGAACTTCTATTTT,25178,8,clonotype84,clonotype84_consensus_3 -TGCCCATAGATATGGT-1,True,TGCCCATAGATATGGT-1_contig_2,True,525,TRB,TRBV31,None,TRBJ2-1,TRBC2,True,True,CAWSLGTGDPEQFF,TGTGCCTGGAGTCTAGGGACTGGGGATCCTGAGCAGTTCTTC,19524,6,clonotype84,clonotype84_consensus_1 -TGCCCATAGATATGGT-1,True,TGCCCATAGATATGGT-1_contig_3,True,556,TRA,TRAV12-1,None,TRAJ22,TRAC,True,True,CALSSGSWQLIF,TGTGCTCTTTCTTCTGGCAGCTGGCAACTCATCTTT,9356,3,clonotype84,clonotype84_consensus_2 -TGCCCATAGATATGGT-1,True,TGCCCATAGATATGGT-1_contig_4,True,537,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,23606,8,clonotype84,None -TGCGCAGAGAGTGAGA-1,True,TGCGCAGAGAGTGAGA-1_contig_1,True,680,TRA,TRAV7-1,None,TRAJ40,TRAC,True,True,CAVSMGTGNYKYVF,TGTGCAGTGAGCATGGGGACAGGAAACTACAAATACGTCTTT,11978,6,clonotype85,clonotype85_consensus_1 -TGCGCAGAGAGTGAGA-1,True,TGCGCAGAGAGTGAGA-1_contig_2,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCCGGACTGGGGGACTCCTATGAACAGTACTTC,11602,5,clonotype85,clonotype85_consensus_2 -TGCGCAGAGAGTGAGA-1,True,TGCGCAGAGAGTGAGA-1_contig_3,True,375,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,53968,12,clonotype85,None -TGCGGGTCAAGCCGTC-1,True,TGCGGGTCAAGCCGTC-1_contig_1,True,572,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGDGGGRGEQYF,TGTGCCAGCGGTGATGGGGGGGGGCGCGGAGAACAGTACTTC,65734,7,clonotype86,clonotype86_consensus_1 -TGGCGCACACCTCGTT-1,True,TGGCGCACACCTCGTT-1_contig_1,True,518,TRB,TRBV13-1,None,TRBJ2-4,TRBC2,True,True,CASSDSGGQNTLYF,TGTGCCAGCAGTGATTCCGGGGGTCAAAACACCTTGTACTTT,58356,5,clonotype87,clonotype87_consensus_1 -TGGCGCACACCTCGTT-1,True,TGGCGCACACCTCGTT-1_contig_2,True,520,TRA,TRAV6-6,None,TRAJ24,TRAC,True,True,CALGGTTASLGKLQF,TGTGCTCTGGGTGGGACAACTGCCAGTTTGGGGAAACTGCAGTTT,19054,2,clonotype87,clonotype87_consensus_2 -TGGCTGGTCACCATAG-1,True,TGGCTGGTCACCATAG-1_contig_1,True,529,TRB,TRBV13-3,None,TRBJ2-4,TRBC2,True,True,CASSDWGGASQNTLYF,TGTGCCAGCAGTGACTGGGGGGGCGCAAGTCAAAACACCTTGTACTTT,45392,9,clonotype88,clonotype88_consensus_1 -TGGCTGGTCACCATAG-1,True,TGGCTGGTCACCATAG-1_contig_2,True,705,TRA,TRAV9-4,None,TRAJ56,TRAC,True,True,CAVSMKGATGGNNKLTF,TGTGCTGTGAGCATGAAGGGGGCTACTGGAGGCAATAATAAGCTGACTTTT,7320,2,clonotype88,clonotype88_consensus_2 -TGGCTGGTCACCATAG-1,True,TGGCTGGTCACCATAG-1_contig_3,True,698,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,12928,5,clonotype88,None -TGGCTGGTCACCATAG-1,True,TGGCTGGTCACCATAG-1_contig_4,True,595,TRA,TRAV19,None,TRAJ52,TRAC,True,False,None,None,5974,1,clonotype88,None -TGGTTCCCAGCTCCGA-1,True,TGGTTCCCAGCTCCGA-1_contig_1,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,22112,2,clonotype1,clonotype1_consensus_1 -TGGTTCCCAGCTCCGA-1,True,TGGTTCCCAGCTCCGA-1_contig_2,True,729,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,16522,3,clonotype1,clonotype1_consensus_2 -TGGTTCCCAGCTCCGA-1,True,TGGTTCCCAGCTCCGA-1_contig_3,True,425,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,38946,2,clonotype1,None -TGTATTCTCAAGGTAA-1,True,TGTATTCTCAAGGTAA-1_contig_1,True,544,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSDDRGDSDYTF,TGTGCCAGCAGCGATGACAGGGGAGACTCCGACTACACCTTC,58570,14,clonotype1,clonotype1_consensus_1 -TGTATTCTCAAGGTAA-1,True,TGTATTCTCAAGGTAA-1_contig_2,True,690,TRA,TRAV14N-3,None,TRAJ32,TRAC,True,True,CAARSYGGSGNKLIF,TGTGCAGCAAGGTCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,16274,7,clonotype1,clonotype1_consensus_2 -TGTATTCTCACCCTCA-1,True,TGTATTCTCACCCTCA-1_contig_1,True,745,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CAVTASSGQKLVF,TGTGCTGTGACGGCTTCAAGTGGCCAGAAGCTGGTTTTT,14940,9,clonotype9,clonotype9_consensus_2 -TGTATTCTCACCCTCA-1,True,TGTATTCTCACCCTCA-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQGGGNTEVFF,TGTGCCAGCAGCCAAGGGGGGGGGAACACAGAAGTCTTCTTT,56408,26,clonotype9,clonotype9_consensus_1 -TGTATTCTCACCCTCA-1,True,TGTATTCTCACCCTCA-1_contig_3,True,731,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,3930,2,clonotype9,None -TTATGCTGTCCAGTGC-1,True,TTATGCTGTCCAGTGC-1_contig_1,True,712,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSMGVERLFF,TGTGCCAGCAGTATGGGGGTCGAAAGATTATTTTTC,20904,9,clonotype89,clonotype89_consensus_2 -TTATGCTGTCCAGTGC-1,True,TTATGCTGTCCAGTGC-1_contig_2,True,524,TRA,TRAV6N-7,None,TRAJ12,TRAC,True,True,CALTTPGGYKVVF,TGTGCTCTGACCACTCCTGGAGGCTATAAAGTGGTCTTT,15784,5,clonotype89,clonotype89_consensus_1 -TTATGCTGTCCAGTGC-1,True,TTATGCTGTCCAGTGC-1_contig_3,True,329,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,7002,1,clonotype89,None -TTATGCTGTCCAGTGC-1,True,TTATGCTGTCCAGTGC-1_contig_4,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,31842,7,clonotype89,None -TTCTCAAAGCTCCTCT-1,True,TTCTCAAAGCTCCTCT-1_contig_1,True,603,TRA,TRAV14D-3-DV8,None,TRAJ45,TRAC,True,True,CAARHTGGADRLTF,TGTGCAGCAAGGCATACAGGAGGTGCAGATAGACTCACCTTT,34520,3,clonotype4,clonotype4_consensus_2 -TTCTCAAAGCTCCTCT-1,True,TTCTCAAAGCTCCTCT-1_contig_2,True,672,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASRKGTGGRDTQYF,TGTGCCAGCAGAAAAGGGACTGGGGGGAGAGACACCCAGTACTTT,5950,1,clonotype4,clonotype4_consensus_1 -TTCTCAAAGCTCCTCT-1,True,TTCTCAAAGCTCCTCT-1_contig_3,True,553,TRB,TRBV10,None,TRBJ2-3,TRBC2,True,False,None,None,37702,3,clonotype4,None -TTGACTTGTTACGGAG-1,True,TTGACTTGTTACGGAG-1_contig_1,True,571,TRB,TRBV1,None,TRBJ1-4,TRBC1,True,True,CTCSAQGVSNERLFF,TGCACCTGCAGTGCACAGGGGGTTTCCAACGAAAGATTATTTTTC,47750,11,clonotype90,clonotype90_consensus_1 -TTGACTTGTTACGGAG-1,True,TTGACTTGTTACGGAG-1_contig_2,True,406,TRB,TRBV13-3,None,TRBJ2-2,TRBC2,True,False,CASSDALGAAGQLYF,TGTGCCAGCAGTGATGCATTGGGGGCGGCCGGGCAGCTCTACTTT,19412,4,clonotype90,None diff --git a/tests/testthat/fixtures/Chariou/h5files/SCAF1715_3_1_filtered_contig_annotations.csv b/tests/testthat/fixtures/Chariou/h5files/SCAF1715_3_1_filtered_contig_annotations.csv deleted file mode 100644 index 1d363bb..0000000 --- a/tests/testthat/fixtures/Chariou/h5files/SCAF1715_3_1_filtered_contig_annotations.csv +++ /dev/null @@ -1,142 +0,0 @@ -barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id -AAGTCTGAGTGGTAGC-1,True,AAGTCTGAGTGGTAGC-1_contig_1,True,530,TRA,TRAV16N,None,TRAJ45,TRAC,True,True,CAMREANTGGADRLTF,TGTGCTATGAGAGAGGCTAATACAGGAGGTGCAGATAGACTCACCTTT,18318,5,clonotype1,clonotype1_consensus_1 -AAGTCTGAGTGGTAGC-1,True,AAGTCTGAGTGGTAGC-1_contig_2,True,645,TRB,TRBV2,None,TRBJ1-6,TRBC1,True,True,CASSQDGGYNSPLYF,TGTGCCAGCAGCCAAGATGGGGGCTATAATTCGCCCCTCTACTTT,16650,6,clonotype1,clonotype1_consensus_2 -AAGTCTGAGTGGTAGC-1,True,AAGTCTGAGTGGTAGC-1_contig_3,True,328,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,39518,10,clonotype1,None -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_1,True,570,TRA,TRAV2,None,TRAJ15,TRAC,True,True,CIVTVPYQGGRALIF,TGCATTGTGACTGTCCCCTACCAGGGAGGCAGAGCTCTGATATTT,10830,6,clonotype2,clonotype2_consensus_3 -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_2,True,538,TRA,TRAV6-2,None,TRAJ9,TRAC,True,True,CVRGNMGYKLTF,TGTGTTAGAGGGAACATGGGCTACAAACTTACCTTC,16732,8,clonotype2,clonotype2_consensus_2 -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_3,True,670,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASRDRSYNYAEQFF,TGTGCCAGCAGGGACAGGTCCTATAACTATGCTGAGCAGTTCTTC,25508,13,clonotype2,clonotype2_consensus_1 -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_4,True,505,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,20654,10,clonotype2,None -ACCTTTAAGCTGAAAT-1,True,ACCTTTAAGCTGAAAT-1_contig_5,True,348,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,3984,1,clonotype2,None -ACGGGCTTCCATTCTA-1,True,ACGGGCTTCCATTCTA-1_contig_1,True,567,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-3,TRBC1,True,True,CASGDGNSGNTLYF,TGTGCCAGCGGTGATGGCAATTCTGGAAATACGCTCTATTTT,74284,6,clonotype3,clonotype3_consensus_1 -AGCTCTCCACGAAACG-1,True,AGCTCTCCACGAAACG-1_contig_1,True,492,TRA,TRAV1,None,TRAJ33,TRAC,True,True,CAVRDSNYQLIW,TGTGCTGTGAGGGATAGCAACTATCAGTTGATCTGG,8748,1,clonotype4,clonotype4_consensus_1 -AGCTCTCCACGAAACG-1,True,AGCTCTCCACGAAACG-1_contig_2,True,525,TRB,TRBV13-3,None,TRBJ1-5,TRBC1,True,True,CASSAGTDNQAPLF,TGTGCCAGCAGTGCCGGGACAGACAACCAGGCTCCGCTTTTT,42160,6,clonotype4,clonotype4_consensus_2 -AGCTCTCCACGAAACG-1,True,AGCTCTCCACGAAACG-1_contig_3,True,452,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,11306,1,clonotype4,None -AGCTCTCCACGAAACG-1,True,AGCTCTCCACGAAACG-1_contig_4,True,546,TRA,TRAV8D-1,None,TRAJ6,TRAC,True,False,None,None,16050,3,clonotype4,None -AGGGTGAGTCAGCTAT-1,True,AGGGTGAGTCAGCTAT-1_contig_1,True,636,TRA,TRAV5D-4,None,TRAJ6,TRAC,True,True,CAASAGGNYKPTF,TGTGCTGCAAGTGCAGGAGGAAACTACAAACCTACGTTT,23148,3,clonotype5,clonotype5_consensus_1 -AGGGTGAGTCAGCTAT-1,True,AGGGTGAGTCAGCTAT-1_contig_2,True,718,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASKTGGSQNTLYF,TGTGCCAGCAAAACTGGGGGGAGTCAAAACACCTTGTACTTT,56110,2,clonotype5,clonotype5_consensus_2 -ATTACTCCATGCCCGA-1,True,ATTACTCCATGCCCGA-1_contig_1,True,513,TRA,TRAV6-6,None,TRAJ15,TRAC,True,True,CALGDPQGGRALIF,TGTGCTCTGGGTGATCCCCAGGGAGGCAGAGCTCTGATATTT,27020,4,clonotype6,clonotype6_consensus_1 -ATTACTCCATGCCCGA-1,True,ATTACTCCATGCCCGA-1_contig_2,True,643,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,True,CTCSAQGAQGTEVFF,TGCACCTGCAGTGCGCAGGGGGCGCAGGGCACAGAAGTCTTCTTT,52090,7,clonotype6,clonotype6_consensus_2 -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_1,True,586,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSANERLFF,TGTGCCAGCAGTGCCAACGAAAGATTATTTTTC,32168,9,clonotype7,clonotype7_consensus_2 -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_2,True,603,TRA,TRAV12D-2,None,TRAJ49,TRAC,True,True,CALSAPNTGYQNFYF,TGTGCTCTGAGTGCTCCGAACACGGGTTACCAGAACTTCTATTTT,17612,4,clonotype7,clonotype7_consensus_1 -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_3,True,332,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,8526,1,clonotype7,None -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_4,True,571,Multi,TRAV8D-2,None,TRDJ1,TRAC,True,False,CATDVGGRRDTS,TGTGCTACAGACGTGGGGGGGCGGAGGGATACGAGC,9822,3,clonotype7,None -CAAGGCCAGTAGGTGC-1,True,CAAGGCCAGTAGGTGC-1_contig_5,True,372,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,6176,2,clonotype7,None -CACCAGGAGAGACTTA-1,True,CACCAGGAGAGACTTA-1_contig_1,True,511,TRB,TRBV10,None,TRBJ1-2,TRBC1,True,True,CASSRQGGSDYTF,TGTGCCAGCAGCCGACAGGGCGGCTCCGACTACACCTTC,64360,8,clonotype8,clonotype8_consensus_2 -CACCAGGAGAGACTTA-1,True,CACCAGGAGAGACTTA-1_contig_2,True,546,TRA,TRAV8N-2,None,TRAJ34,TRAC,True,True,CATANTDKVVF,TGTGCTACTGCCAATACCGACAAAGTCGTCTTT,8018,2,clonotype8,clonotype8_consensus_1 -CACCAGGGTAAGTAGT-1,True,CACCAGGGTAAGTAGT-1_contig_1,True,569,TRB,TRBV2,None,TRBJ2-5,TRBC2,True,True,CASSQDGTGQDTQYF,TGTGCCAGCAGCCAAGACGGGACTGGACAAGACACCCAGTACTTT,26388,9,clonotype9,clonotype9_consensus_1 -CACCAGGGTAAGTAGT-1,True,CACCAGGGTAAGTAGT-1_contig_2,True,567,TRA,TRAV4-4-DV10,None,TRAJ49,TRAC,True,True,CAAEAGPGYQNFYF,TGTGCTGCTGAGGCAGGGCCGGGTTACCAGAACTTCTATTTT,41438,13,clonotype9,clonotype9_consensus_2 -CACCAGGGTAAGTAGT-1,True,CACCAGGGTAAGTAGT-1_contig_3,True,614,TRB,None,None,TRBJ1-1,TRBC1,False,False,None,None,10066,3,clonotype9,None -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_1,True,600,TRA,TRAV12D-2,None,TRAJ56,TRAC,True,True,CALSSTGGNNKLTF,TGTGCTCTGAGTTCTACTGGAGGCAATAATAAGCTGACTTTT,49126,30,clonotype10,clonotype10_consensus_1 -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_2,True,574,TRB,TRBV12-1,None,TRBJ2-4,TRBC2,True,True,CASSLEGSQNTLYF,TGTGCCAGCTCTCTCGAGGGTAGTCAAAACACCTTGTACTTT,7982,7,clonotype10,clonotype10_consensus_2 -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_3,True,328,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,6266,3,clonotype10,None -CATCAGAGTCTCGTTC-1,True,CATCAGAGTCTCGTTC-1_contig_4,True,369,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,13520,9,clonotype10,None -CATGCCTGTATTCGTG-1,True,CATGCCTGTATTCGTG-1_contig_1,True,580,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-1,TRBC2,True,True,CASGDATGLNYAEQFF,TGTGCCAGCGGTGATGCAACAGGGCTAAACTATGCTGAGCAGTTCTTC,28996,16,clonotype11,clonotype11_consensus_2 -CATGCCTGTATTCGTG-1,True,CATGCCTGTATTCGTG-1_contig_2,True,628,TRA,TRAV3-1,None,TRAJ15,TRAC,True,True,CAVRPFYQGGRALIF,TGCGCAGTCAGGCCCTTCTACCAGGGAGGCAGAGCTCTGATATTT,34032,12,clonotype11,clonotype11_consensus_3 -CATGCCTGTATTCGTG-1,True,CATGCCTGTATTCGTG-1_contig_3,True,570,TRA,TRAV2,None,TRAJ12,TRAC,True,True,CIVTDTGTGGYKVVF,TGCATTGTGACTGACACCGGGACTGGAGGCTATAAAGTGGTCTTT,10140,5,clonotype11,clonotype11_consensus_1 -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_1,True,524,TRA,TRAV6-5,None,TRAJ56,TRAC,True,True,CALSAVTGGNNKLTF,TGTGCTCTGAGTGCCGTAACTGGAGGCAATAATAAGCTGACTTTT,11472,3,clonotype12,clonotype12_consensus_2 -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_2,True,560,TRB,TRBV2,None,TRBJ1-5,TRBC1,True,True,CASSQDYNQAPLF,TGTGCCAGCAGCCAAGATTACAACCAGGCTCCGCTTTTT,10964,2,clonotype12,clonotype12_consensus_1 -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_3,True,341,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,13656,1,clonotype12,None -CCACGGAAGCCTATGT-1,True,CCACGGAAGCCTATGT-1_contig_4,True,362,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,40694,4,clonotype12,None -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSQGLGDSYEQYF,TGTGCCAGCAGCCAAGGACTGGGGGACTCCTATGAACAGTACTTC,32308,10,clonotype13,clonotype13_consensus_2 -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_2,True,606,TRA,TRAV7-4,None,TRAJ42,TRAC,True,True,CAASEHENSGGSNAKLTF,TGTGCAGCTAGTGAGCATGAAAATTCTGGAGGAAGCAATGCAAAGCTAACCTTC,11948,6,clonotype13,clonotype13_consensus_3 -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_3,True,534,TRA,TRAV7-3,None,TRAJ40,TRAC,True,True,CAVSIGTGNYKYVF,TGTGCAGTGAGCATTGGTACAGGAAACTACAAATACGTCTTT,21812,7,clonotype13,clonotype13_consensus_1 -CCCTCCTGTAACGCGA-1,True,CCCTCCTGTAACGCGA-1_contig_4,True,528,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,False,None,None,12054,3,clonotype13,None -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_1,True,520,TRB,TRBV13-3,None,TRBJ1-2,TRBC1,True,True,CASSDAWGPDYTF,TGTGCCAGCAGTGATGCATGGGGCCCCGACTACACCTTC,17728,2,clonotype14,clonotype14_consensus_1 -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_2,True,540,TRA,TRAV11,None,TRAJ18,TRAC,True,True,CVVGDRGSALGRLHF,TGTGTGGTGGGCGATAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,4268,1,clonotype14,clonotype14_consensus_2 -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_3,True,864,TRB,None,None,TRBJ1-1,TRBC1,False,False,None,None,14612,2,clonotype14,None -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_4,True,705,TRA,TRAV7-3,None,TRAJ12,TRAC,True,False,CSKTGGYKVVF,TGCAGTAAGACTGGAGGCTATAAAGTGGTCTTT,2870,1,clonotype14,None -CGCCAAGAGCCACGCT-1,True,CGCCAAGAGCCACGCT-1_contig_5,True,340,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,38948,3,clonotype14,None -CGGTTAAGTAGCGTCC-1,True,CGGTTAAGTAGCGTCC-1_contig_1,True,555,TRA,TRAV8N-2,None,TRAJ32,TRAC,True,True,CATPYGGSGNKLIF,TGTGCTACTCCTTATGGGGGCAGTGGCAACAAGCTCATCTTT,59298,8,clonotype15,clonotype15_consensus_2 -CGGTTAAGTAGCGTCC-1,True,CGGTTAAGTAGCGTCC-1_contig_2,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSQDWGAIYEQYF,TGTGCCAGCAGCCAAGACTGGGGGGCTATATATGAACAGTACTTC,20054,3,clonotype15,clonotype15_consensus_1 -CGTCACTAGATACACA-1,True,CGTCACTAGATACACA-1_contig_1,True,572,TRA,TRAV6-6,None,TRAJ16,TRAC,True,True,CALGATSSGQKLVF,TGTGCTCTGGGTGCAACTTCAAGTGGCCAGAAGCTGGTTTTT,4392,2,clonotype16,clonotype16_consensus_2 -CGTCACTAGATACACA-1,True,CGTCACTAGATACACA-1_contig_2,True,513,TRB,TRBV13-1,None,TRBJ1-5,TRBC1,True,True,CASSVSRDRNQAPLF,TGTGCCAGCAGTGTCTCCCGGGACAGAAACCAGGCTCCGCTTTTT,72618,5,clonotype16,clonotype16_consensus_1 -CGTGTCTAGTGCCAGA-1,True,CGTGTCTAGTGCCAGA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,30426,9,clonotype17,clonotype17_consensus_2 -CGTGTCTAGTGCCAGA-1,True,CGTGTCTAGTGCCAGA-1_contig_2,True,549,TRA,TRAV7-3,None,TRAJ12,TRAC,True,True,CAVSMGTGGYKVVF,TGTGCAGTGAGCATGGGGACTGGAGGCTATAAAGTGGTCTTT,43770,13,clonotype17,clonotype17_consensus_1 -CGTGTCTAGTGCCAGA-1,True,CGTGTCTAGTGCCAGA-1_contig_3,True,758,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,4346,3,clonotype17,None -CTACATTAGGTGGGTT-1,True,CTACATTAGGTGGGTT-1_contig_1,True,538,TRB,TRBV2,None,TRBJ1-2,None,True,True,CASSQRTANSDYTF,TGTGCCAGCAGCCAACGGACAGCAAACTCCGACTACACCTTC,5594,1,clonotype18,clonotype18_consensus_1 -CTACATTAGGTGGGTT-1,True,CTACATTAGGTGGGTT-1_contig_2,True,548,TRA,TRAV9-1,None,TRAJ47,TRAC,True,True,CAVSAKEDYANKMIF,TGTGCTGTGAGCGCGAAGGAGGACTATGCAAACAAGATGATCTTT,24434,5,clonotype18,clonotype18_consensus_2 -CTACATTAGGTGGGTT-1,True,CTACATTAGGTGGGTT-1_contig_3,True,392,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,30556,3,clonotype18,None -CTACATTAGGTGGGTT-1,True,CTACATTAGGTGGGTT-1_contig_4,True,429,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,16218,2,clonotype18,None -CTCGAGGTCACATACG-1,True,CTCGAGGTCACATACG-1_contig_1,True,564,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGDARGDTQYF,TGTGCCAGCGGTGATGCCCGGGGAGACACCCAGTACTTT,58876,29,clonotype19,clonotype19_consensus_2 -CTCGAGGTCACATACG-1,True,CTCGAGGTCACATACG-1_contig_2,True,542,TRA,TRAV6-1,None,TRAJ13,TRAC,True,True,CVLGENSGTYQRF,TGTGTTCTGGGTGAGAATTCTGGGACTTACCAGAGGTTT,14738,4,clonotype19,clonotype19_consensus_1 -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_1,True,568,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-3,TRBC1,True,True,CASGDDNSGNTLYF,TGTGCCAGCGGTGATGATAATTCTGGAAATACGCTCTATTTT,32644,11,clonotype20,clonotype20_consensus_1 -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_2,True,432,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,31900,10,clonotype20,None -CTCGGAGCACAGACAG-1,True,CTCGGAGCACAGACAG-1_contig_3,True,339,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,13178,2,clonotype20,None -CTGGTCTAGTGTACCT-1,True,CTGGTCTAGTGTACCT-1_contig_1,True,648,TRB,TRBV2,None,TRBJ2-7,TRBC2,True,True,CASSQERDNYEQYF,TGTGCCAGCAGCCAAGAAAGGGACAATTATGAACAGTACTTC,31272,9,clonotype21,clonotype21_consensus_2 -CTGGTCTAGTGTACCT-1,True,CTGGTCTAGTGTACCT-1_contig_2,True,533,TRA,TRAV6-6,None,TRAJ34,TRAC,True,True,CALGGANTDKVVF,TGTGCTCTGGGTGGAGCCAATACCGACAAAGTCGTCTTT,46728,9,clonotype21,clonotype21_consensus_1 -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_1,True,598,TRA,TRAV3-1,None,TRAJ4,TRAC,True,True,CAVSPSSGSFNKLTF,TGCGCAGTCAGTCCCTCATCTGGTAGCTTCAATAAGTTGACCTTT,7212,4,clonotype22,clonotype22_consensus_1 -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCTGGGACAGGGAACACAGAAGTCTTCTTT,49116,17,clonotype22,clonotype22_consensus_2 -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_3,True,473,TRA,TRAV9-4,None,TRAJ17,TRAC,True,False,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,3080,1,clonotype22,None -CTTAACTTCTTCAACT-1,True,CTTAACTTCTTCAACT-1_contig_4,True,405,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,15812,5,clonotype22,None -GACGTGCCACAGGTTT-1,True,GACGTGCCACAGGTTT-1_contig_1,True,524,TRA,TRAV6-4,None,TRAJ13,TRAC,True,True,CALVGTNSGTYQRF,TGTGCTCTGGTTGGTACAAATTCTGGGACTTACCAGAGGTTT,10990,1,clonotype23,clonotype23_consensus_1 -GACGTGCCACAGGTTT-1,True,GACGTGCCACAGGTTT-1_contig_2,True,568,TRB,TRBV1,None,TRBJ2-2,TRBC2,True,True,CTCSADRDTGQLYF,TGCACCTGCAGTGCAGACAGGGACACCGGGCAGCTCTACTTT,53964,5,clonotype23,clonotype23_consensus_2 -GACGTGCCACAGGTTT-1,True,GACGTGCCACAGGTTT-1_contig_3,True,539,TRA,TRAV3-3,None,TRAJ37,TRAC,True,False,CAVSEGQAILENSSLGW,TGCGCAGTCAGTGAGGGGCAGGCAATACTAGAAAACTCATCTTTGGGCTGG,13374,1,clonotype23,None -GACGTTAAGTGTTGAA-1,True,GACGTTAAGTGTTGAA-1_contig_1,True,601,TRA,TRAV8D-2,None,TRAJ52,TRAC,True,True,CATDPFGGANTGKLTF,TGTGCTACAGATCCCTTCGGGGGAGCTAACACTGGAAAGCTCACGTTT,4660,1,clonotype24,clonotype24_consensus_1 -GACGTTAAGTGTTGAA-1,True,GACGTTAAGTGTTGAA-1_contig_2,True,704,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSSNENTEVFF,TGTGCCAGCAGTTCGAACGAAAACACAGAAGTCTTCTTT,68202,14,clonotype24,clonotype24_consensus_2 -GATCGATGTTAAGACA-1,True,GATCGATGTTAAGACA-1_contig_1,True,569,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-3,TRBC1,True,True,CASGDSGNTLYF,TGTGCCAGCGGTGATTCTGGAAATACGCTCTATTTT,10804,4,clonotype25,clonotype25_consensus_1 -GATCGATGTTAAGACA-1,True,GATCGATGTTAAGACA-1_contig_2,True,305,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,67442,6,clonotype25,None -GATCTAGGTTCGGCAC-1,True,GATCTAGGTTCGGCAC-1_contig_1,True,538,TRA,TRAV6-6,None,TRAJ31,TRAC,True,True,CALSANNNNRIFF,TGTGCTCTGAGTGCGAATAACAATAACAGAATCTTCTTT,22644,9,clonotype26,clonotype26_consensus_1 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_1,True,524,TRB,TRBV13-1,None,TRBJ2-5,TRBC2,True,True,CASSDGLGFNQDTQYF,TGTGCCAGCAGTGATGGACTGGGGTTTAACCAAGACACCCAGTACTTT,16152,3,clonotype27,clonotype27_consensus_2 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_2,True,530,TRA,TRAV6N-7,None,TRAJ22,TRAC,True,True,CALSDSSGSWQLIF,TGTGCTCTGAGTGACTCTTCTGGCAGCTGGCAACTCATCTTT,10344,2,clonotype27,clonotype27_consensus_1 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_3,True,540,TRA,TRAV13-1,None,TRAJ22,TRAC,True,True,CAISGSWQLIF,TGTGCTATTTCTGGCAGCTGGCAACTCATCTTT,31908,7,clonotype27,clonotype27_consensus_3 -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_4,True,433,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,4944,1,clonotype27,None -GATCTAGTCGTCTGAA-1,True,GATCTAGTCGTCTGAA-1_contig_5,True,368,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,13264,1,clonotype27,None -GCACATAGTACTCTCC-1,True,GCACATAGTACTCTCC-1_contig_1,True,557,TRA,TRAV3-3,None,TRAJ47,TRAC,True,True,CAGDYANKMIF,TGCGCGGGGGACTATGCAAACAAGATGATCTTT,24500,8,clonotype28,clonotype28_consensus_2 -GCACATAGTACTCTCC-1,True,GCACATAGTACTCTCC-1_contig_2,True,526,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGARVGVGQYF,TGTGGTGCTAGGGTTGGGGTAGGACAGTACTTC,33672,10,clonotype28,clonotype28_consensus_1 -GCACATAGTACTCTCC-1,True,GCACATAGTACTCTCC-1_contig_3,True,576,TRA,TRAV13-1,None,TRAJ50,TRAC,True,False,None,None,15688,3,clonotype28,None -GCATGATGTCGCATAT-1,True,GCATGATGTCGCATAT-1_contig_1,True,631,TRA,TRAV5D-4,None,TRAJ57,TRAC,True,True,CAASDQGGSAKLIF,TGTGCTGCAAGTGATCAAGGAGGGTCTGCGAAGCTCATCTTT,37846,8,clonotype29,clonotype29_consensus_1 -GCCAAATGTCACCTAA-1,True,GCCAAATGTCACCTAA-1_contig_1,True,541,TRB,TRBV20,None,TRBJ1-5,TRBC1,True,True,CGAGQGAKAPLF,TGTGGTGCTGGACAGGGGGCGAAGGCTCCGCTTTTT,64196,6,clonotype30,clonotype30_consensus_1 -GCGCCAAAGCGTTCCG-1,True,GCGCCAAAGCGTTCCG-1_contig_1,True,524,TRA,TRAV16N,None,TRAJ37,TRAC,True,True,CAMRGITGNTRKLIF,TGTGCTATGAGAGGTATAACAGGCAATACTAGAAAACTCATCTTT,23390,1,clonotype31,clonotype31_consensus_1 -GCGCCAAAGCGTTCCG-1,True,GCGCCAAAGCGTTCCG-1_contig_2,True,682,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSITGPNYAEQFF,TGTGCCAGCAGTATAACTGGACCTAACTATGCTGAGCAGTTCTTC,55252,5,clonotype31,clonotype31_consensus_2 -GGAACTTCATCTGGTA-1,True,GGAACTTCATCTGGTA-1_contig_1,True,672,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASTWGEAVFF,TGTGCCAGCACCTGGGGTGAGGCAGTCTTCTTT,61414,13,clonotype32,clonotype32_consensus_2 -GGAACTTCATCTGGTA-1,True,GGAACTTCATCTGGTA-1_contig_2,True,537,TRA,TRAV12-3,None,TRAJ39,TRAC,True,True,CALRNNNAGAKLTF,TGTGCTTTGAGGAATAATAATGCAGGTGCCAAGCTCACATTC,2326,2,clonotype32,clonotype32_consensus_1 -GGAACTTCATCTGGTA-1,True,GGAACTTCATCTGGTA-1_contig_3,True,483,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,14562,2,clonotype32,None -GGAATAAGTTGTCGCG-1,True,GGAATAAGTTGTCGCG-1_contig_1,True,602,TRB,TRBV3,None,TRBJ1-2,TRBC1,True,True,CASSRDDANSDYTF,TGTGCCAGCAGCCGGGACGATGCAAACTCCGACTACACCTTC,76576,13,clonotype33,clonotype33_consensus_1 -GGAATAAGTTGTCGCG-1,True,GGAATAAGTTGTCGCG-1_contig_2,True,596,TRA,TRAV7-4,None,TRAJ56,TRAC,True,False,CAGGRLLE,TGTGCAGGAGGGAGGCTACTGGAG,590,1,clonotype33,None -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_1,True,515,TRA,TRAV6-5,None,TRAJ32,TRAC,True,True,CALSHYGGSGNKLIF,TGTGCTCTGAGTCATTATGGGGGCAGTGGCAACAAGCTCATCTTT,16344,2,clonotype34,clonotype34_consensus_1 -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_2,True,502,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQDFPEEVFF,TGTGCCAGCAGCCAAGATTTCCCAGAAGAAGTCTTCTTT,40442,5,clonotype34,clonotype34_consensus_2 -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_3,True,542,TRA,TRAV5D-4,None,TRAJ49,TRAC,True,False,None,None,5878,1,clonotype34,None -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_4,True,344,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,14718,1,clonotype34,None -GGACAGATCTCGAGTA-1,True,GGACAGATCTCGAGTA-1_contig_5,True,586,TRB,TRBV13-1,None,TRBJ1-1,TRBC1,True,False,None,None,1530,1,clonotype34,None -GGCTGGTGTCCTCCAT-1,True,GGCTGGTGTCCTCCAT-1_contig_1,True,531,TRA,TRAV6-6,None,TRAJ18,TRAC,True,True,CALGDRGSALGRLHF,TGTGCTCTGGGTGATAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,36546,3,clonotype35,clonotype35_consensus_1 -GGCTGGTGTCCTCCAT-1,True,GGCTGGTGTCCTCCAT-1_contig_2,True,409,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,42384,2,clonotype35,None -GGGCATCCAATAAGCA-1,True,GGGCATCCAATAAGCA-1_contig_1,True,511,TRA,TRAV4-2,None,TRAJ39,TRAC,True,True,CAAFNAGAKLTF,TGTGCTGCCTTTAATGCAGGTGCCAAGCTCACATTC,24674,9,clonotype36,clonotype36_consensus_2 -GGGCATCCAATAAGCA-1,True,GGGCATCCAATAAGCA-1_contig_2,True,660,TRB,TRBV19,None,TRBJ2-7,TRBC2,True,True,CASSMGGSSYEQYF,TGTGCCAGCAGTATGGGGGGGAGCTCCTATGAACAGTACTTC,28476,6,clonotype36,clonotype36_consensus_3 -GGGCATCCAATAAGCA-1,True,GGGCATCCAATAAGCA-1_contig_3,True,543,TRB,TRBV20,None,TRBJ1-4,TRBC1,True,True,CGAPRTGGDERLFF,TGTGGTGCCCCCCGGACAGGGGGCGACGAAAGATTATTTTTC,23282,4,clonotype36,clonotype36_consensus_1 -GGTGCGTTCAGCTCTC-1,True,GGTGCGTTCAGCTCTC-1_contig_1,True,564,TRA,TRAV5-1,None,TRAJ4,TRAC,True,True,CSASIGLLSGSFNKLTF,TGCTCAGCAAGTATTGGATTGTTATCTGGTAGCTTCAATAAGTTGACCTTT,14122,2,clonotype37,clonotype37_consensus_2 -GGTGCGTTCAGCTCTC-1,True,GGTGCGTTCAGCTCTC-1_contig_2,True,544,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGASLFRDWGLSYEQYF,TGTGGTGCTAGTCTCTTCCGGGACTGGGGCCTCTCCTATGAACAGTACTTC,31838,5,clonotype37,clonotype37_consensus_1 -GGTGCGTTCAGCTCTC-1,True,GGTGCGTTCAGCTCTC-1_contig_3,True,557,TRA,TRAV6-6,None,TRAJ17,TRAC,True,False,None,None,31062,3,clonotype37,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_1,True,710,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSIDRVGSERLFF,TGTGCCAGCAGTATAGACAGGGTAGGATCCGAAAGATTATTTTTC,23014,16,clonotype38,clonotype38_consensus_1 -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_2,True,567,TRA,TRAV2,None,TRAJ30,TRAC,True,True,CIVTDLTNAYKVIF,TGCATTGTGACTGACCTCACAAATGCTTACAAAGTCATCTTT,17552,11,clonotype38,clonotype38_consensus_2 -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_3,True,401,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,5264,1,clonotype38,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_4,True,324,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,4612,2,clonotype38,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_5,True,345,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,5806,2,clonotype38,None -GTACTCCCACCTCGGA-1,True,GTACTCCCACCTCGGA-1_contig_6,True,361,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,22048,7,clonotype38,None -GTGAAGGTCTGTCAAG-1,True,GTGAAGGTCTGTCAAG-1_contig_1,True,571,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGDADSSYEQYF,TGTGCCAGCGGTGATGCGGACAGCTCCTATGAACAGTACTTC,33696,2,clonotype39,clonotype39_consensus_1 -GTGAAGGTCTGTCAAG-1,True,GTGAAGGTCTGTCAAG-1_contig_2,True,369,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,12866,6,clonotype39,None -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_1,True,510,TRA,TRAV6-5,None,TRAJ5,TRAC,True,True,CALGDTQVVGQLTF,TGTGCTCTGGGTGACACACAGGTTGTGGGGCAGCTCACTTTC,9862,10,clonotype40,clonotype40_consensus_1 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_2,True,415,TRB,TRBV31,None,TRBJ1-3,None,True,True,CAWRGGGGNTLYF,TGTGCCTGGCGGGGGGGGGGAGGAAATACGCTCTATTTT,15148,13,clonotype40,clonotype40_consensus_2 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_3,True,414,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,49186,29,clonotype40,None -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_4,True,507,TRA,TRAV12-1,None,TRAJ11,TRAC,True,False,CPVLLCSNSGYNKLTF,TGCCCTGTACTACTGTGCTCTAACTCGGGATACAACAAACTCACTTTT,3054,2,clonotype40,None -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_1,True,588,TRA,TRAV7-4,None,TRAJ9,TRAC,True,True,CAARGRGYKLTF,TGTGCAGCTAGGGGGAGGGGCTACAAACTTACCTTC,8002,3,clonotype41,clonotype41_consensus_1 -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_2,True,560,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSAGTGGERLFF,TGTGCCAGCAGTGCCGGGACGGGCGGCGAAAGATTATTTTTC,31080,10,clonotype41,clonotype41_consensus_2 -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_3,True,336,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,7710,3,clonotype41,None -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_4,True,679,TRA,TRAV6-2,None,TRAJ39,TRAC,True,False,CVLGDRYRKLQIRLWSRYQTEGYST,TGTGTTCTGGGTGATAGGTACAGGAAACTACAAATACGTCTTTGGAGCAGGTACCAGACTGAAGGTTATAGCACC,2238,1,clonotype41,None -GTTTCTATCTAACTGG-1,True,GTTTCTATCTAACTGG-1_contig_5,True,326,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,26900,5,clonotype41,None -TATGCCCAGATATGCA-1,True,TATGCCCAGATATGCA-1_contig_1,True,584,TRA,TRAV6-2,None,TRAJ26,TRAC,True,True,CVLGDQNYAQGLTF,TGTGTTCTGGGTGATCAAAACTATGCCCAGGGATTAACCTTC,75622,5,clonotype42,clonotype42_consensus_2 -TATGCCCAGATATGCA-1,True,TATGCCCAGATATGCA-1_contig_2,True,714,TRB,TRBV2,None,TRBJ2-7,TRBC2,True,True,CASSHPGVSSYEQYF,TGTGCCAGCAGCCATCCCGGGGTTAGCTCCTATGAACAGTACTTC,3310,1,clonotype42,clonotype42_consensus_1 -TCAGCAACAAGGTTCT-1,True,TCAGCAACAAGGTTCT-1_contig_1,True,538,TRA,TRAV6-2,None,TRAJ11,TRAC,True,True,CVLGDSGYNKLTF,TGTGTTCTGGGTGACTCGGGATACAACAAACTCACTTTT,51778,7,clonotype43,clonotype43_consensus_1 -TCAGCAACAAGGTTCT-1,True,TCAGCAACAAGGTTCT-1_contig_2,True,561,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGGGTGEAETLYF,TGTGCCAGCGGTGGTGGGACAGGGGAGGCAGAAACGCTGTATTTT,25892,4,clonotype43,clonotype43_consensus_2 -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_1,True,528,TRA,TRAV14-1,None,TRAJ5,TRAC,True,True,CAAGTQVVGQLTF,TGTGCAGCCGGGACACAGGTTGTGGGGCAGCTCACTTTC,31486,5,clonotype44,clonotype44_consensus_2 -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_2,True,707,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASRTGGSNERLFF,TGTGCCAGCAGAACAGGGGGCTCCAACGAAAGATTATTTTTC,8964,2,clonotype44,clonotype44_consensus_1 -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_3,True,473,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,22010,2,clonotype44,None -TGGTTAGGTGTCTGAT-1,True,TGGTTAGGTGTCTGAT-1_contig_4,True,431,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,13840,1,clonotype44,None -TTAGGACGTTACGTCA-1,True,TTAGGACGTTACGTCA-1_contig_1,True,514,TRA,TRAV4-2,None,TRAJ45,TRAC,True,True,CAADTGGADRLTF,TGTGCTGCGGATACAGGAGGTGCAGATAGACTCACCTTT,15494,3,clonotype45,clonotype45_consensus_1 -TTAGGACGTTACGTCA-1,True,TTAGGACGTTACGTCA-1_contig_2,True,739,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGARRNYEQYF,TGTGGTGCTAGAAGGAATTATGAACAGTACTTC,51036,8,clonotype45,clonotype45_consensus_2 -TTAGGACGTTACGTCA-1,True,TTAGGACGTTACGTCA-1_contig_3,True,544,TRA,TRAV8D-2,None,TRAJ31,TRAC,True,False,None,None,7462,1,clonotype45,None -TTCTACAGTCTTGTCC-1,True,TTCTACAGTCTTGTCC-1_contig_1,True,648,TRB,TRBV2,None,TRBJ2-4,TRBC2,True,True,CASSQEDAGRQNTLYF,TGTGCCAGCAGCCAAGAAGATGCTGGGCGTCAAAACACCTTGTACTTT,46314,3,clonotype46,clonotype46_consensus_1 -TTCTACAGTCTTGTCC-1,True,TTCTACAGTCTTGTCC-1_contig_2,True,599,TRA,TRAV19,None,TRAJ17,TRAC,True,True,CAAGRLTNSAGNKLTF,TGCGCAGCAGGGCGGTTGACTAACAGTGCAGGGAACAAGCTAACTTTT,30142,4,clonotype46,clonotype46_consensus_2 -TTCTACAGTCTTGTCC-1,True,TTCTACAGTCTTGTCC-1_contig_3,True,436,TRB,TRBV5,None,TRBJ1-1,None,True,False,CASSPGTGNTEVFF,TGTGCCAGCAGCCCTGGGACAGGGAACACAGAAGTCTTCTTT,4,2,clonotype46,None -TTCTTAGGTCAGTGGA-1,True,TTCTTAGGTCAGTGGA-1_contig_1,True,567,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGARDLGGGGYEQYF,TGTGGTGCTAGGGATCTGGGGGGAGGCGGCTATGAACAGTACTTC,36732,6,clonotype47,clonotype47_consensus_1 -TTCTTAGGTCAGTGGA-1,True,TTCTTAGGTCAGTGGA-1_contig_2,True,632,TRA,TRAV5D-4,None,TRAJ27,TRAC,True,True,CAASRNTNTGKLTF,TGTGCTGCAAGCAGGAACACCAATACAGGCAAATTAACCTTT,36896,5,clonotype47,clonotype47_consensus_2 -TTCTTAGGTCAGTGGA-1,True,TTCTTAGGTCAGTGGA-1_contig_3,True,416,TRA,None,None,TRAJ26,TRAC,False,False,None,None,4894,1,clonotype47,None diff --git a/tests/testthat/fixtures/Chariou/h5files/SCAF1716_4_1_filtered_contig_annotations.csv b/tests/testthat/fixtures/Chariou/h5files/SCAF1716_4_1_filtered_contig_annotations.csv deleted file mode 100644 index 527c02a..0000000 --- a/tests/testthat/fixtures/Chariou/h5files/SCAF1716_4_1_filtered_contig_annotations.csv +++ /dev/null @@ -1,478 +0,0 @@ -barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id -AAACGGGCAGTAACGG-1,True,AAACGGGCAGTAACGG-1_contig_1,True,714,TRB,TRBV2,None,TRBJ1-1,TRBC1,True,True,CASSQEEGANTEVFF,TGTGCCAGCAGCCAAGAGGAGGGTGCAAACACAGAAGTCTTCTTT,21738,6,clonotype6,clonotype6_consensus_2 -AAACGGGCAGTAACGG-1,True,AAACGGGCAGTAACGG-1_contig_2,True,576,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCCGGGCAAATGCTTACAAAGTCATCTTT,28238,6,clonotype6,clonotype6_consensus_1 -AAACGGGCAGTAACGG-1,True,AAACGGGCAGTAACGG-1_contig_3,True,410,TRB,None,None,TRBJ2-4,TRBC2,False,False,None,None,4260,3,clonotype6,None -AAACGGGCAGTAACGG-1,True,AAACGGGCAGTAACGG-1_contig_4,True,349,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,23282,8,clonotype6,None -AAACGGGGTCTGGAGA-1,True,AAACGGGGTCTGGAGA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,11582,3,clonotype7,clonotype7_consensus_1 -AAACGGGGTCTGGAGA-1,True,AAACGGGGTCTGGAGA-1_contig_2,True,435,TRA,TRAV9-4,None,TRAJ17,TRAC,True,False,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,21132,2,clonotype7,None -AAACGGGGTCTGGAGA-1,True,AAACGGGGTCTGGAGA-1_contig_3,True,447,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,28844,3,clonotype7,None -AAACGGGGTCTGGAGA-1,True,AAACGGGGTCTGGAGA-1_contig_4,True,320,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,2242,1,clonotype7,None -AAACGGGGTCTGGAGA-1,True,AAACGGGGTCTGGAGA-1_contig_5,True,342,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,13278,2,clonotype7,None -AAAGATGGTGTGACGA-1,True,AAAGATGGTGTGACGA-1_contig_1,True,550,TRB,TRBV31,None,TRBJ2-7,TRBC2,True,True,CAWSLRSYEQYF,TGTGCCTGGAGTCTACGCTCCTATGAACAGTACTTC,45190,13,clonotype25,clonotype25_consensus_1 -AAAGATGGTGTGACGA-1,True,AAAGATGGTGTGACGA-1_contig_2,True,565,TRA,TRAV14D-1,None,TRAJ42,TRAC,True,True,CAASRGGGSNAKLTF,TGTGCAGCAAGTAGGGGGGGAGGAAGCAATGCAAAGCTAACCTTC,5400,3,clonotype25,clonotype25_consensus_2 -AAAGATGGTGTGACGA-1,True,AAAGATGGTGTGACGA-1_contig_3,True,397,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,24024,6,clonotype25,None -AAATGCCCAAGTACCT-1,True,AAATGCCCAAGTACCT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSVGQGNTEVFF,TGTGCCAGCAGCGTCGGACAGGGAAACACAGAAGTCTTCTTT,60994,15,clonotype14,clonotype14_consensus_1 -AAATGCCCAAGTACCT-1,True,AAATGCCCAAGTACCT-1_contig_2,True,723,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CAVSTSSGQKLVF,TGTGCTGTGAGCACTTCAAGTGGCCAGAAGCTGGTTTTT,15780,4,clonotype14,clonotype14_consensus_2 -AAATGCCCAATAACGA-1,True,AAATGCCCAATAACGA-1_contig_1,True,561,TRB,TRBV13-3,None,TRBJ2-1,TRBC2,True,True,CASKLTGGNYAEQFF,TGTGCCAGCAAGCTGACTGGGGGTAACTATGCTGAGCAGTTCTTC,45318,4,clonotype26,clonotype26_consensus_3 -AAATGCCCAATAACGA-1,True,AAATGCCCAATAACGA-1_contig_2,True,732,TRA,TRAV9D-2,None,TRAJ48,TRAC,True,True,CAVSMDYGNEKITF,TGTGCTGTGAGCATGGACTATGGAAATGAGAAAATAACTTTT,13394,2,clonotype26,clonotype26_consensus_2 -AAATGCCCAATAACGA-1,True,AAATGCCCAATAACGA-1_contig_3,True,549,TRA,TRAV16N,None,TRAJ53,TRAC,True,True,CAMREDLLRGGSNYKLTF,TGTGCTATGAGAGAGGACCTCCTCCGTGGAGGCAGCAATTACAAACTGACATTT,18750,2,clonotype26,clonotype26_consensus_1 -AACGTTGGTAGTACCT-1,True,AACGTTGGTAGTACCT-1_contig_1,True,515,TRB,TRBV13-1,None,TRBJ1-1,TRBC1,True,True,CASSSLGDTEVFF,TGTGCCAGCAGTTCGTTGGGGGACACAGAAGTCTTCTTT,62126,10,clonotype27,clonotype27_consensus_1 -AACGTTGGTAGTACCT-1,True,AACGTTGGTAGTACCT-1_contig_2,True,731,TRA,TRAV3-1,None,TRAJ30,TRAC,True,False,CTSAQSVKVIF,TGTACTTCTGCGCAGTCAGTGAAAGTCATCTTT,11230,2,clonotype27,None -AAGACCTCAGGGAGAG-1,True,AAGACCTCAGGGAGAG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGAAACACAGAAGTCTTCTTT,6816,3,clonotype28,clonotype28_consensus_1 -AAGACCTCAGGGAGAG-1,True,AAGACCTCAGGGAGAG-1_contig_2,True,636,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,68476,15,clonotype28,None -AAGCCGCGTAGAGTGC-1,True,AAGCCGCGTAGAGTGC-1_contig_1,True,546,TRA,TRAV7D-3,None,TRAJ26,TRAC,True,True,CAVSLNYAQGLTF,TGTGCAGTGAGCCTCAACTATGCCCAGGGATTAACCTTC,20840,5,clonotype15,clonotype15_consensus_1 -AAGCCGCGTAGAGTGC-1,True,AAGCCGCGTAGAGTGC-1_contig_2,True,558,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASSAPGLGSYEQYF,TGTGCCAGCAGTGCCCCGGGACTGGGGTCCTATGAACAGTACTTC,55528,13,clonotype15,clonotype15_consensus_2 -AAGGAGCAGACAAAGG-1,True,AAGGAGCAGACAAAGG-1_contig_1,True,594,TRA,TRAV7D-4,None,TRAJ40,TRAC,True,True,CAASEGTGNYKYVF,TGTGCAGCTAGTGAAGGTACAGGAAACTACAAATACGTCTTT,55564,7,clonotype16,clonotype16_consensus_2 -AAGGAGCAGACAAAGG-1,True,AAGGAGCAGACAAAGG-1_contig_2,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCAGGACTGGGGGACTCCTATGAACAGTACTTC,3742,1,clonotype16,clonotype16_consensus_1 -AAGGAGCAGACAAAGG-1,True,AAGGAGCAGACAAAGG-1_contig_3,True,510,TRA,TRAV13D-2,None,TRAJ31,TRAC,True,False,None,None,18872,4,clonotype16,None -AAGGTTCCAGCATACT-1,True,AAGGTTCCAGCATACT-1_contig_1,True,544,TRB,TRBV13-3,None,TRBJ1-3,TRBC1,True,True,CASSGDRGGNTLYF,TGTGCCAGCAGTGGGGACAGGGGTGGAAATACGCTCTATTTT,22572,10,clonotype8,clonotype8_consensus_1 -AAGGTTCCAGCATACT-1,True,AAGGTTCCAGCATACT-1_contig_2,True,516,TRB,TRBV17,None,TRBJ1-6,TRBC1,True,True,CGVQDNSPLYF,TGTGGGGTACAGGATAATTCGCCCCTCTACTTT,38134,20,clonotype8,clonotype8_consensus_3 -AAGGTTCCAGCATACT-1,True,AAGGTTCCAGCATACT-1_contig_3,True,530,TRA,TRAV16N,None,TRAJ56,TRAC,True,True,CAMREGPGGNNKLTF,TGTGCTATGAGAGAGGGACCTGGAGGCAATAATAAGCTGACTTTT,6254,2,clonotype8,clonotype8_consensus_2 -AAGGTTCCAGCATACT-1,True,AAGGTTCCAGCATACT-1_contig_4,True,364,TRA,TRAV17,None,TRAJ56,TRAC,True,False,None,None,8806,3,clonotype8,None -AATCGGTAGAAGGGTA-1,True,AATCGGTAGAAGGGTA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,34280,21,clonotype2,clonotype2_consensus_2 -AATCGGTAGAAGGGTA-1,True,AATCGGTAGAAGGGTA-1_contig_2,True,669,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,12154,7,clonotype2,clonotype2_consensus_1 -AATCGGTAGAAGGGTA-1,True,AATCGGTAGAAGGGTA-1_contig_3,True,318,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,26078,10,clonotype2,None -AATCGGTAGAAGGGTA-1,True,AATCGGTAGAAGGGTA-1_contig_4,True,319,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,3912,1,clonotype2,None -AATCGGTTCCACGACG-1,True,AATCGGTTCCACGACG-1_contig_1,True,534,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,29406,2,clonotype7,clonotype7_consensus_1 -AATCGGTTCCACGACG-1,True,AATCGGTTCCACGACG-1_contig_2,True,361,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,41102,3,clonotype7,None -ACACCAAGTTCTGGTA-1,True,ACACCAAGTTCTGGTA-1_contig_1,True,672,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,12668,2,clonotype17,clonotype17_consensus_1 -ACACCAAGTTCTGGTA-1,True,ACACCAAGTTCTGGTA-1_contig_2,True,403,TRA,TRAV6-6,None,TRAJ45,TRAC,True,False,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,19680,1,clonotype17,None -ACACCAAGTTCTGGTA-1,True,ACACCAAGTTCTGGTA-1_contig_3,True,328,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,39416,3,clonotype17,None -ACACTGAAGGCCCTCA-1,True,ACACTGAAGGCCCTCA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,62836,25,clonotype9,clonotype9_consensus_2 -ACACTGAAGGCCCTCA-1,True,ACACTGAAGGCCCTCA-1_contig_2,True,731,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,5352,2,clonotype9,clonotype9_consensus_1 -ACACTGAAGGCCCTCA-1,True,ACACTGAAGGCCCTCA-1_contig_3,True,428,TRA,TRAV9-4,None,TRAJ17,TRAC,True,False,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,4936,1,clonotype9,None -ACCAGTACACGAAACG-1,True,ACCAGTACACGAAACG-1_contig_1,True,577,TRA,TRAV6-6,None,TRAJ11,TRAC,True,True,CALGAPDSGYNKLTF,TGTGCTCTGGGTGCCCCCGACTCGGGATACAACAAACTCACTTTT,19298,3,clonotype29,clonotype29_consensus_2 -ACCAGTACACGAAACG-1,True,ACCAGTACACGAAACG-1_contig_2,True,554,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-5,TRBC1,True,True,CASGDWAPLF,TGTGCCAGCGGTGATTGGGCTCCGCTTTTT,46552,4,clonotype29,clonotype29_consensus_1 -ACCCACTGTCAATGTC-1,True,ACCCACTGTCAATGTC-1_contig_1,True,521,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSDAGTGGYEQYF,TGTGCCAGCAGTGATGCCGGGACTGGGGGGTATGAACAGTACTTC,69384,15,clonotype30,clonotype30_consensus_2 -ACCCACTGTCAATGTC-1,True,ACCCACTGTCAATGTC-1_contig_2,True,591,TRA,TRAV7-4,None,TRAJ9,TRAC,True,True,CAASEDMGYKLTF,TGTGCAGCTAGTGAGGACATGGGCTACAAACTTACCTTC,6914,3,clonotype30,clonotype30_consensus_1 -ACGAGCCGTACAGACG-1,True,ACGAGCCGTACAGACG-1_contig_1,True,517,TRB,TRBV14,None,TRBJ1-1,TRBC1,True,True,CASSFGTVTEVFF,TGTGCCAGCAGTTTTGGGACCGTCACAGAAGTCTTCTTT,22562,14,clonotype18,clonotype18_consensus_1 -ACGAGCCGTACAGACG-1,True,ACGAGCCGTACAGACG-1_contig_2,True,362,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,30554,14,clonotype18,None -ACGAGCCGTACAGACG-1,True,ACGAGCCGTACAGACG-1_contig_3,True,504,TRA,TRAV12-3,None,TRAJ31,TRAC,True,False,CPVLLCF,TGCCCTGTACTACTGTGCTTT,1750,1,clonotype18,None -ACGAGCCGTACAGACG-1,True,ACGAGCCGTACAGACG-1_contig_4,True,570,Multi,TRDV1,None,TRAJ17,TRAC,True,False,CGGKEARAGNKLTF,TGTGGAGGGAAAGAGGCCCGTGCAGGGAACAAGCTAACTTTT,20488,8,clonotype18,None -ACGATGTTCGTGTAGT-1,True,ACGATGTTCGTGTAGT-1_contig_1,True,525,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,29780,5,clonotype31,clonotype31_consensus_1 -ACGATGTTCGTGTAGT-1,True,ACGATGTTCGTGTAGT-1_contig_2,True,731,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,False,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,5860,4,clonotype31,None -ACGCAGCAGATACACA-1,True,ACGCAGCAGATACACA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQGQGNTEVFF,TGTGCCAGCAGCCAGGGACAGGGGAACACAGAAGTCTTCTTT,27454,13,clonotype32,clonotype32_consensus_1 -ACGCAGCAGATACACA-1,True,ACGCAGCAGATACACA-1_contig_2,True,669,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CALSASSGQKLVF,TGTGCTCTGAGCGCTTCAAGTGGCCAGAAGCTGGTTTTT,5888,3,clonotype32,clonotype32_consensus_2 -ACGCAGCAGATACACA-1,True,ACGCAGCAGATACACA-1_contig_3,True,673,TRB,TRBV20,None,TRBJ1-1,TRBC1,True,False,None,None,13136,8,clonotype32,None -ACGCAGCAGATACACA-1,True,ACGCAGCAGATACACA-1_contig_4,True,567,TRA,TRAV3-3,None,TRAJ40,TRAC,True,False,None,None,29222,15,clonotype32,None -ACGGGTCAGAGTACAT-1,True,ACGGGTCAGAGTACAT-1_contig_1,True,721,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSIGGASNERLFF,TGTGCCAGCAGTATAGGGGGGGCGTCCAACGAAAGATTATTTTTC,25348,16,clonotype10,clonotype10_consensus_2 -ACGGGTCAGAGTACAT-1,True,ACGGGTCAGAGTACAT-1_contig_2,True,603,TRA,TRAV13-1,None,TRAJ53,TRAC,True,True,CAILSGGSNYKLTF,TGTGCTATCCTCAGTGGAGGCAGCAATTACAAACTGACATTT,21974,12,clonotype10,clonotype10_consensus_1 -ACGGGTCAGAGTACAT-1,True,ACGGGTCAGAGTACAT-1_contig_3,True,430,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,14014,4,clonotype10,None -ACGGGTCAGAGTACAT-1,True,ACGGGTCAGAGTACAT-1_contig_4,True,328,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,15284,7,clonotype10,None -ACTATCTCAGTCTTCC-1,True,ACTATCTCAGTCTTCC-1_contig_1,True,520,TRA,TRAV6-6,None,TRAJ42,TRAC,True,True,CALGLGGSNAKLTF,TGTGCTCTGGGCCTTGGAGGAAGCAATGCAAAGCTAACCTTC,21896,2,clonotype33,clonotype33_consensus_1 -ACTATCTCAGTCTTCC-1,True,ACTATCTCAGTCTTCC-1_contig_2,True,311,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,17254,4,clonotype33,None -ACTATCTCAGTCTTCC-1,True,ACTATCTCAGTCTTCC-1_contig_3,True,441,TRA,None,None,TRAJ41,TRAC,False,False,None,None,29568,6,clonotype33,None -ACTGATGAGTCCTCCT-1,True,ACTGATGAGTCCTCCT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSQGQGNTEVFF,TGTGCCAGCAGCCAGGGACAGGGGAACACAGAAGTCTTCTTT,64020,21,clonotype34,clonotype34_consensus_1 -ACTGATGAGTCCTCCT-1,True,ACTGATGAGTCCTCCT-1_contig_2,True,567,TRA,TRAV3-3,None,TRAJ40,TRAC,True,False,None,None,8264,3,clonotype34,None -AGAGCGACAGCCACCA-1,True,AGAGCGACAGCCACCA-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,47560,15,clonotype1,clonotype1_consensus_2 -AGAGCGACAGCCACCA-1,True,AGAGCGACAGCCACCA-1_contig_2,True,526,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,10018,4,clonotype1,clonotype1_consensus_1 -AGAGCGACAGCCACCA-1,True,AGAGCGACAGCCACCA-1_contig_3,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,20944,4,clonotype1,None -AGAGCTTGTCAACATC-1,True,AGAGCTTGTCAACATC-1_contig_1,True,507,TRA,TRAV21-DV12,None,TRAJ56,TRAC,True,True,CILRGATGGNNKLTF,TGTATCCTGAGGGGGGCTACTGGAGGCAATAATAAGCTGACTTTT,17276,5,clonotype19,clonotype19_consensus_1 -AGAGCTTGTCAACATC-1,True,AGAGCTTGTCAACATC-1_contig_2,True,562,TRB,TRBV2,None,TRBJ2-4,TRBC2,True,True,CASSQRQGQNTLYF,TGTGCCAGCAGCCAAAGACAGGGCCAAAACACCTTGTACTTT,36978,9,clonotype19,clonotype19_consensus_2 -AGAGCTTGTCAACATC-1,True,AGAGCTTGTCAACATC-1_contig_3,True,405,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,17060,5,clonotype19,None -AGAGCTTTCCAGTATG-1,True,AGAGCTTTCCAGTATG-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,43516,9,clonotype11,clonotype11_consensus_1 -AGAGCTTTCCAGTATG-1,True,AGAGCTTTCCAGTATG-1_contig_2,True,637,TRA,TRAV7-1,None,TRAJ12,TRAC,True,True,CAVSIGTGGYKVVF,TGTGCAGTGAGCATTGGGACTGGAGGCTATAAAGTGGTCTTT,19834,4,clonotype11,clonotype11_consensus_2 -AGAGCTTTCCAGTATG-1,True,AGAGCTTTCCAGTATG-1_contig_3,True,653,TRA,TRAV14N-3,None,TRAJ7,TRAC,True,False,None,None,12874,5,clonotype11,None -AGCAGCCAGGGATGGG-1,True,AGCAGCCAGGGATGGG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,57944,5,clonotype20,clonotype20_consensus_1 -AGCAGCCAGGGATGGG-1,True,AGCAGCCAGGGATGGG-1_contig_2,True,428,TRA,TRAV9-4,None,TRAJ16,TRAC,True,False,CALSSSSGQKLVF,TGTGCTCTGAGTTCTTCAAGTGGCCAGAAGCTGGTTTTT,18512,1,clonotype20,None -AGCGTATCAGTAAGCG-1,True,AGCGTATCAGTAAGCG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGGAACACAGAAGTCTTCTTT,30952,6,clonotype3,clonotype3_consensus_2 -AGCGTATCAGTAAGCG-1,True,AGCGTATCAGTAAGCG-1_contig_2,True,667,TRA,TRAV9-4,None,TRAJ22,TRAC,True,True,CAVTSSGSWQLIF,TGTGCTGTGACATCTTCTGGCAGCTGGCAACTCATCTTT,15488,3,clonotype3,clonotype3_consensus_1 -AGCGTATCAGTAAGCG-1,True,AGCGTATCAGTAAGCG-1_contig_3,True,698,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,15430,5,clonotype3,None -AGCGTCGTCCAAATGC-1,True,AGCGTCGTCCAAATGC-1_contig_1,True,743,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,10330,3,clonotype9,clonotype9_consensus_1 -AGCGTCGTCCAAATGC-1,True,AGCGTCGTCCAAATGC-1_contig_2,True,514,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,47034,5,clonotype9,clonotype9_consensus_2 -AGCGTCGTCCAAATGC-1,True,AGCGTCGTCCAAATGC-1_contig_3,True,626,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,21384,2,clonotype9,None -AGGGATGGTCTGATTG-1,True,AGGGATGGTCTGATTG-1_contig_1,True,603,TRA,TRAV14D-3-DV8,None,TRAJ45,TRAC,True,True,CAASATGGADRLTF,TGTGCAGCAAGTGCGACAGGAGGTGCAGATAGACTCACCTTT,35678,4,clonotype35,clonotype35_consensus_1 -AGGGATGGTCTGATTG-1,True,AGGGATGGTCTGATTG-1_contig_2,True,528,TRB,TRBV10,None,TRBJ2-4,TRBC2,True,True,CASSLDWGGGNTLYF,TGTGCCAGCAGCTTGGACTGGGGGGGCGGGAACACCTTGTACTTT,41658,4,clonotype35,clonotype35_consensus_2 -AGGGTGAAGATATGCA-1,True,AGGGTGAAGATATGCA-1_contig_1,True,518,TRB,TRBV13-1,None,TRBJ2-1,TRBC2,True,True,CASSLGGRYAEQFF,TGTGCCAGCAGTCTGGGGGGGCGCTATGCTGAGCAGTTCTTC,49874,6,clonotype36,clonotype36_consensus_1 -AGGGTGAAGATATGCA-1,True,AGGGTGAAGATATGCA-1_contig_2,True,337,TRA,TRAV16N,None,TRAJ50,TRAC,True,False,CAMRESASSSFSKLVF,TGTGCTATGAGAGAGTCAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,27728,2,clonotype36,None -AGGTCATAGGATGTAT-1,True,AGGTCATAGGATGTAT-1_contig_1,True,591,TRA,TRAV12-3,None,TRAJ49,TRAC,True,True,CALSDPVTGYQNFYF,TGTGCTTTGAGTGACCCTGTCACGGGTTACCAGAACTTCTATTTT,24622,13,clonotype12,clonotype12_consensus_1 -AGGTCATAGGATGTAT-1,True,AGGTCATAGGATGTAT-1_contig_2,True,578,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASRLGFEQYF,TGTGCCAGCCGACTGGGGTTTGAACAGTACTTC,48318,21,clonotype12,clonotype12_consensus_2 -AGTAGTCAGATCCCGC-1,True,AGTAGTCAGATCCCGC-1_contig_1,True,535,TRA,TRAV6N-7,None,TRAJ17,TRAC,True,True,CALRSTNSAGNKLTF,TGTGCTCTGAGGTCAACTAACAGTGCAGGGAACAAGCTAACTTTT,59814,4,clonotype37,clonotype37_consensus_1 -AGTAGTCAGATCCCGC-1,True,AGTAGTCAGATCCCGC-1_contig_2,True,536,TRB,TRBV20,TRBD2,TRBJ2-3,TRBC2,True,True,CGARDWGGSETLYF,TGTGGTGCTAGGGACTGGGGGGGCTCAGAAACGCTGTATTTT,19018,1,clonotype37,clonotype37_consensus_2 -AGTGAGGTCAACACCA-1,True,AGTGAGGTCAACACCA-1_contig_1,True,588,TRA,TRAV12-3,None,TRAJ15,TRAC,True,True,CALSAYQGGRALIF,TGTGCTTTGAGTGCCTACCAGGGAGGCAGAGCTCTGATATTT,47388,8,clonotype38,clonotype38_consensus_2 -AGTGAGGTCAACACCA-1,True,AGTGAGGTCAACACCA-1_contig_2,True,710,TRB,TRBV19,None,TRBJ1-6,TRBC1,True,True,CASTRTGGGNSPLYF,TGTGCCAGCACCCGGACAGGGGGCGGTAATTCGCCCCTCTACTTT,11320,2,clonotype38,clonotype38_consensus_1 -AGTGAGGTCAACACCA-1,True,AGTGAGGTCAACACCA-1_contig_3,True,630,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,19716,2,clonotype38,None -AGTGTCACAAGCTGAG-1,True,AGTGTCACAAGCTGAG-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,37212,10,clonotype1,clonotype1_consensus_2 -AGTGTCACAAGCTGAG-1,True,AGTGTCACAAGCTGAG-1_contig_2,True,555,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,28976,5,clonotype1,clonotype1_consensus_1 -AGTGTCACAAGCTGAG-1,True,AGTGTCACAAGCTGAG-1_contig_3,True,581,TRA,TRAV5D-4,None,TRAJ50,TRAC,True,False,None,None,9946,3,clonotype1,None -ATAAGAGAGGAATTAC-1,True,ATAAGAGAGGAATTAC-1_contig_1,True,594,TRA,TRAV7D-4,None,TRAJ48,TRAC,True,True,CAASEQGGNEKITF,TGTGCAGCTAGTGAGCAAGGGGGAAATGAGAAAATAACTTTT,35276,6,clonotype39,clonotype39_consensus_2 -ATAAGAGAGGAATTAC-1,True,ATAAGAGAGGAATTAC-1_contig_2,True,575,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGDVRASAETLYF,TGTGCCAGCGGTGATGTCAGGGCTAGTGCAGAAACGCTGTATTTT,39376,7,clonotype39,clonotype39_consensus_1 -ATCCGAACAAGTCTAC-1,True,ATCCGAACAAGTCTAC-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-1,TRBC2,True,True,CASSQGQGDYAEQFF,TGTGCCAGCAGCCAAGGACAGGGGGACTATGCTGAGCAGTTCTTC,38822,11,clonotype40,clonotype40_consensus_2 -ATCCGAACAAGTCTAC-1,True,ATCCGAACAAGTCTAC-1_contig_2,True,725,TRA,TRAV9D-2,None,TRAJ43,TRAC,True,True,CAVGNNNAPRF,TGTGCTGTGGGAAACAACAATGCCCCACGATTT,22560,4,clonotype40,clonotype40_consensus_1 -ATCCGAACAAGTCTAC-1,True,ATCCGAACAAGTCTAC-1_contig_3,True,443,TRA,None,None,TRAJ41,TRAC,False,False,None,None,11790,5,clonotype40,None -ATCGAGTGTGTGTGCC-1,True,ATCGAGTGTGTGTGCC-1_contig_1,True,520,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,9558,1,clonotype1,clonotype1_consensus_1 -ATCGAGTGTGTGTGCC-1,True,ATCGAGTGTGTGTGCC-1_contig_2,True,682,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,56060,5,clonotype1,clonotype1_consensus_2 -ATCGAGTGTGTGTGCC-1,True,ATCGAGTGTGTGTGCC-1_contig_3,True,670,TRA,TRAV5D-4,None,TRAJ50,TRAC,True,False,None,None,11946,1,clonotype1,None -ATCTACTAGGGTTTCT-1,True,ATCTACTAGGGTTTCT-1_contig_1,True,549,TRA,TRAV7-3,None,TRAJ18,TRAC,True,True,CAVDRGSALGRLHF,TGTGCAGTCGATAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,28636,3,clonotype41,clonotype41_consensus_1 -ATCTACTAGGGTTTCT-1,True,ATCTACTAGGGTTTCT-1_contig_2,True,661,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,True,CGATDIYEQYF,TGTGGTGCTACCGACATCTATGAACAGTACTTC,49042,3,clonotype41,clonotype41_consensus_2 -ATCTGCCCAGCTATTG-1,True,ATCTGCCCAGCTATTG-1_contig_1,True,718,TRB,TRBV19,None,TRBJ2-3,TRBC2,True,True,CASSRDWGAETLYF,TGTGCCAGCAGTCGGGACTGGGGGGCTGAAACGCTGTATTTT,59122,9,clonotype42,clonotype42_consensus_1 -ATCTGCCCAGCTATTG-1,True,ATCTGCCCAGCTATTG-1_contig_2,True,538,TRB,TRBV13-1,None,TRBJ2-4,TRBC2,True,False,None,None,11944,4,clonotype42,None -ATGAGGGAGGGCATGT-1,True,ATGAGGGAGGGCATGT-1_contig_1,True,538,TRB,TRBV20,TRBD1,TRBJ2-7,TRBC2,True,True,CGVPRDRGREQYF,TGTGGTGTCCCCCGGGACAGGGGGCGCGAACAGTACTTC,36286,16,clonotype13,clonotype13_consensus_3 -ATGAGGGAGGGCATGT-1,True,ATGAGGGAGGGCATGT-1_contig_2,True,509,TRB,TRBV29,None,TRBJ2-7,TRBC2,True,True,CASSGDRGHEQYF,TGTGCTAGCAGTGGGGACAGGGGTCATGAACAGTACTTC,24636,10,clonotype13,clonotype13_consensus_1 -ATGAGGGAGGGCATGT-1,True,ATGAGGGAGGGCATGT-1_contig_3,True,513,TRA,TRAV13-1,None,TRAJ6,TRAC,True,True,CAMATSGGNYKPTF,TGTGCTATGGCCACCTCAGGAGGAAACTACAAACCTACGTTT,3212,2,clonotype13,clonotype13_consensus_2 -ATGAGGGAGGGCATGT-1,True,ATGAGGGAGGGCATGT-1_contig_4,True,557,TRA,TRAV4-3,None,TRAJ15,TRAC,True,False,None,None,14204,4,clonotype13,None -ATTATCCAGCTCCCAG-1,True,ATTATCCAGCTCCCAG-1_contig_1,True,504,TRA,TRAV21-DV12,None,TRAJ47,TRAC,True,True,CILRRVDYANKMIF,TGTATCCTGAGACGGGTGGACTATGCAAACAAGATGATCTTT,10764,1,clonotype43,clonotype43_consensus_2 -ATTATCCAGCTCCCAG-1,True,ATTATCCAGCTCCCAG-1_contig_2,True,605,TRB,TRBV3,None,TRBJ1-2,TRBC1,True,True,CASSLAGGVNSDYTF,TGTGCCAGCAGCTTAGCAGGGGGAGTAAACTCCGACTACACCTTC,59984,9,clonotype43,clonotype43_consensus_1 -ATTATCCAGGGTATCG-1,True,ATTATCCAGGGTATCG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,34478,13,clonotype4,clonotype4_consensus_2 -ATTATCCAGGGTATCG-1,True,ATTATCCAGGGTATCG-1_contig_2,True,715,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,10472,3,clonotype4,clonotype4_consensus_1 -ATTATCCAGGGTATCG-1,True,ATTATCCAGGGTATCG-1_contig_3,True,354,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,13478,5,clonotype4,None -ATTATCCAGGGTATCG-1,True,ATTATCCAGGGTATCG-1_contig_4,True,344,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,18142,4,clonotype4,None -ATTCTACAGCTAAGAT-1,True,ATTCTACAGCTAAGAT-1_contig_1,True,644,TRA,TRAV7-1,None,TRAJ12,TRAC,True,True,CAVSIGTGGYKVVF,TGTGCAGTGAGCATTGGGACTGGAGGCTATAAAGTGGTCTTT,12214,12,clonotype11,clonotype11_consensus_2 -ATTCTACAGCTAAGAT-1,True,ATTCTACAGCTAAGAT-1_contig_2,True,566,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,54234,19,clonotype11,clonotype11_consensus_1 -ATTCTACGTCCGAGTC-1,True,ATTCTACGTCCGAGTC-1_contig_1,True,543,TRB,TRBV13-2,TRBD2,TRBJ2-4,TRBC2,True,True,CASGDGDWGGATVTLYF,TGTGCCAGCGGTGATGGGGACTGGGGGGGCGCGACGGTCACCTTGTACTTT,52476,9,clonotype44,clonotype44_consensus_2 -ATTCTACGTCCGAGTC-1,True,ATTCTACGTCCGAGTC-1_contig_2,True,567,TRA,TRAV2,None,TRAJ15,TRAC,True,True,CIVTPLQGGRALIF,TGCATTGTGACCCCCCTCCAGGGAGGCAGAGCTCTGATATTT,11354,2,clonotype44,clonotype44_consensus_3 -ATTCTACGTCCGAGTC-1,True,ATTCTACGTCCGAGTC-1_contig_3,True,557,TRA,TRAV5-1,None,TRAJ11,TRAC,True,True,CSASRGDSGYNKLTF,TGCTCAGCAAGTAGAGGGGACTCGGGATACAACAAACTCACTTTT,9888,3,clonotype44,clonotype44_consensus_1 -ATTCTACGTCCGAGTC-1,True,ATTCTACGTCCGAGTC-1_contig_4,True,470,TRB,TRBV19,None,TRBJ2-3,None,True,False,CQQFRGRSAETLYF,TGCCAGCAGTTCAGGGGGCGGTCTGCAGAAACGCTGTATTTT,2528,1,clonotype44,None -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_1,True,569,TRB,TRBV2,None,TRBJ1-1,TRBC1,True,True,CASSQEEGANTEVFF,TGTGCCAGCAGCCAAGAGGAGGGTGCAAACACAGAAGTCTTCTTT,15342,5,clonotype6,clonotype6_consensus_2 -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_2,True,558,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCCGGGCAAATGCTTACAAAGTCATCTTT,9492,4,clonotype6,clonotype6_consensus_1 -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_3,True,308,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,7046,1,clonotype6,None -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_4,True,364,TRB,None,None,TRBJ2-4,TRBC2,False,False,None,None,7616,1,clonotype6,None -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_5,True,320,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,9150,2,clonotype6,None -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_6,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,21360,5,clonotype6,None -ATTGGACAGGACCACA-1,True,ATTGGACAGGACCACA-1_contig_7,True,562,TRA,TRAV8N-2,None,TRAJ52,TRAC,True,False,None,None,7236,3,clonotype6,None -ATTGGACTCGGTTAAC-1,True,ATTGGACTCGGTTAAC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,31014,9,clonotype9,clonotype9_consensus_2 -ATTGGACTCGGTTAAC-1,True,ATTGGACTCGGTTAAC-1_contig_2,True,725,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,15346,4,clonotype9,clonotype9_consensus_1 -ATTGGACTCGGTTAAC-1,True,ATTGGACTCGGTTAAC-1_contig_3,True,339,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,30330,6,clonotype9,None -CAAGGCCCATCCAACA-1,True,CAAGGCCCATCCAACA-1_contig_1,True,727,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,31136,7,clonotype4,clonotype4_consensus_1 -CAAGGCCCATCCAACA-1,True,CAAGGCCCATCCAACA-1_contig_2,True,541,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,17962,4,clonotype4,clonotype4_consensus_2 -CAAGGCCCATCCAACA-1,True,CAAGGCCCATCCAACA-1_contig_3,True,351,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,11324,1,clonotype4,None -CAAGGCCCATCCAACA-1,True,CAAGGCCCATCCAACA-1_contig_4,True,344,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,13736,1,clonotype4,None -CACATAGGTCTCCCTA-1,True,CACATAGGTCTCCCTA-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,33978,10,clonotype1,clonotype1_consensus_2 -CACATAGGTCTCCCTA-1,True,CACATAGGTCTCCCTA-1_contig_2,True,439,TRA,TRAV6-6,None,TRAJ45,None,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,7600,1,clonotype1,clonotype1_consensus_1 -CACATAGGTCTCCCTA-1,True,CACATAGGTCTCCCTA-1_contig_3,True,301,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,26146,6,clonotype1,None -CAGAATCTCTAGAGTC-1,True,CAGAATCTCTAGAGTC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGGAACACAGAAGTCTTCTTT,61260,18,clonotype45,clonotype45_consensus_1 -CAGAATCTCTAGAGTC-1,True,CAGAATCTCTAGAGTC-1_contig_2,True,734,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CALTTSSGQKLVF,TGTGCTCTGACAACTTCAAGTGGCCAGAAGCTGGTTTTT,6418,8,clonotype45,clonotype45_consensus_2 -CAGCAGCAGATGCGAC-1,True,CAGCAGCAGATGCGAC-1_contig_1,True,624,TRB,TRBV2,None,TRBJ2-7,TRBC2,True,True,CASSQDWGVEQYF,TGTGCCAGCAGCCAAGACTGGGGAGTTGAACAGTACTTC,20358,5,clonotype46,clonotype46_consensus_1 -CAGCAGCAGATGCGAC-1,True,CAGCAGCAGATGCGAC-1_contig_2,True,524,TRA,TRAV6-6,None,TRAJ39,TRAC,True,True,CALAPNNNAGAKLTF,TGTGCTCTGGCCCCGAATAATAATGCAGGTGCCAAGCTCACATTC,29680,1,clonotype46,clonotype46_consensus_2 -CAGCAGCAGATGCGAC-1,True,CAGCAGCAGATGCGAC-1_contig_3,True,507,TRA,TRAV6-5,None,TRAJ40,TRAC,True,False,CSGPHTGNYKYVF,TGCTCTGGGCCCCATACAGGAAACTACAAATACGTCTTT,23158,1,clonotype46,None -CAGGTGCCAATCGAAA-1,True,CAGGTGCCAATCGAAA-1_contig_1,True,633,TRB,TRBV2,None,TRBJ1-5,TRBC1,True,True,CASSRPNQAPLF,TGTGCCAGCAGCCGACCCAACCAGGCTCCGCTTTTT,8356,3,clonotype47,clonotype47_consensus_1 -CAGGTGCCAATCGAAA-1,True,CAGGTGCCAATCGAAA-1_contig_2,True,560,Multi,TRDV1,None,TRAJ56,TRAC,True,False,CGGKGGATGGNNKLTF,TGTGGAGGGAAGGGGGGGGCTACTGGAGGCAATAATAAGCTGACTTTT,69802,11,clonotype47,None -CATATGGTCTGTCAAG-1,True,CATATGGTCTGTCAAG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSVGQGNTEVFF,TGTGCCAGCAGCGTCGGACAGGGAAACACAGAAGTCTTCTTT,39634,8,clonotype14,clonotype14_consensus_1 -CATATGGTCTGTCAAG-1,True,CATATGGTCTGTCAAG-1_contig_2,True,726,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CAVSTSSGQKLVF,TGTGCTGTGAGCACTTCAAGTGGCCAGAAGCTGGTTTTT,10456,3,clonotype14,clonotype14_consensus_2 -CATATGGTCTGTCAAG-1,True,CATATGGTCTGTCAAG-1_contig_3,True,522,TRA,TRAV6-6,None,TRAJ45,TRAC,True,False,CTTVLWVPHTGGADRLTF,TGTACTACTGTGCTCTGGGTCCCTCATACAGGAGGTGCAGATAGACTCACCTTT,5504,1,clonotype14,None -CATATGGTCTGTCAAG-1,True,CATATGGTCTGTCAAG-1_contig_4,True,322,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,10720,1,clonotype14,None -CATATGGTCTGTCAAG-1,True,CATATGGTCTGTCAAG-1_contig_5,True,361,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,10152,1,clonotype14,None -CATCGGGAGTCATCCA-1,True,CATCGGGAGTCATCCA-1_contig_1,True,540,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,50402,11,clonotype4,clonotype4_consensus_2 -CATCGGGAGTCATCCA-1,True,CATCGGGAGTCATCCA-1_contig_2,True,697,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,24880,5,clonotype4,clonotype4_consensus_1 -CATGACAAGCGTTCCG-1,True,CATGACAAGCGTTCCG-1_contig_1,True,573,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGDAWGVSAETLYF,TGTGCCAGCGGTGATGCTTGGGGGGTCAGTGCAGAAACGCTGTATTTT,37754,4,clonotype48,clonotype48_consensus_1 -CATGACAAGCGTTCCG-1,True,CATGACAAGCGTTCCG-1_contig_2,True,535,TRA,TRAV6D-3,None,TRAJ49,TRAC,True,True,CAMNPGYQNFYF,TGTGCTATGAATCCGGGTTACCAGAACTTCTATTTT,37322,4,clonotype48,clonotype48_consensus_2 -CATGCCTCAGACTCGC-1,True,CATGCCTCAGACTCGC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,31418,7,clonotype7,clonotype7_consensus_1 -CATGCCTCAGACTCGC-1,True,CATGCCTCAGACTCGC-1_contig_2,True,338,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,35110,6,clonotype7,None -CATGCCTCAGACTCGC-1,True,CATGCCTCAGACTCGC-1_contig_3,True,485,TRA,TRAV9-4,None,TRAJ17,TRAC,True,False,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,6104,4,clonotype7,None -CATGGCGAGAAAGTGG-1,True,CATGGCGAGAAAGTGG-1_contig_1,True,582,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALSVGGADRLTF,TGTGCTCTGAGTGTGGGAGGTGCAGATAGACTCACCTTT,15328,5,clonotype49,clonotype49_consensus_2 -CATGGCGAGAAAGTGG-1,True,CATGGCGAGAAAGTGG-1_contig_2,True,588,TRA,TRAV5D-4,None,TRAJ42,TRAC,True,True,CAAVGGSNAKLTF,TGTGCTGCAGTCGGAGGAAGCAATGCAAAGCTAACCTTC,21978,8,clonotype49,clonotype49_consensus_3 -CATGGCGAGAAAGTGG-1,True,CATGGCGAGAAAGTGG-1_contig_3,True,568,TRB,TRBV1,None,TRBJ2-5,TRBC2,True,True,CTCSAGGGQDTQYF,TGCACCTGCAGTGCAGGGGGAGGCCAAGACACCCAGTACTTT,39582,16,clonotype49,clonotype49_consensus_1 -CCAATCCGTATATGGA-1,True,CCAATCCGTATATGGA-1_contig_1,True,590,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASSAPGLGSYEQYF,TGTGCCAGCAGTGCCCCGGGACTGGGGTCCTATGAACAGTACTTC,17572,2,clonotype15,clonotype15_consensus_2 -CCAATCCGTATATGGA-1,True,CCAATCCGTATATGGA-1_contig_2,True,546,TRA,TRAV7D-3,None,TRAJ26,TRAC,True,True,CAVSLNYAQGLTF,TGTGCAGTGAGCCTCAACTATGCCCAGGGATTAACCTTC,10232,1,clonotype15,clonotype15_consensus_1 -CCAATCCGTATATGGA-1,True,CCAATCCGTATATGGA-1_contig_3,True,647,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,38020,10,clonotype15,None -CCAATCCGTATATGGA-1,True,CCAATCCGTATATGGA-1_contig_4,True,534,TRA,TRAV16N,None,TRAJ38,TRAC,True,False,None,None,10662,3,clonotype15,None -CCACGGAGTGCGATAG-1,True,CCACGGAGTGCGATAG-1_contig_1,True,663,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSIDSAEVFF,TGTGCCAGCAGTATCGACAGCGCAGAAGTCTTCTTT,69598,14,clonotype50,clonotype50_consensus_1 -CCACTACGTTCCATGA-1,True,CCACTACGTTCCATGA-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,45668,14,clonotype1,clonotype1_consensus_2 -CCACTACGTTCCATGA-1,True,CCACTACGTTCCATGA-1_contig_2,True,531,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,15232,7,clonotype1,clonotype1_consensus_1 -CCACTACGTTCCATGA-1,True,CCACTACGTTCCATGA-1_contig_3,True,333,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,6432,1,clonotype1,None -CCACTACGTTCCATGA-1,True,CCACTACGTTCCATGA-1_contig_4,True,391,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,9362,4,clonotype1,None -CCATTCGAGATCTGAA-1,True,CCATTCGAGATCTGAA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCAGGACTGGGGGACTCCTATGAACAGTACTTC,60610,7,clonotype16,clonotype16_consensus_1 -CCATTCGAGATCTGAA-1,True,CCATTCGAGATCTGAA-1_contig_2,True,594,TRA,TRAV7D-4,None,TRAJ40,TRAC,True,True,CAASEGTGNYKYVF,TGTGCAGCTAGTGAAGGTACAGGAAACTACAAATACGTCTTT,8078,2,clonotype16,clonotype16_consensus_2 -CCATTCGCACGCATCG-1,True,CCATTCGCACGCATCG-1_contig_1,True,514,TRB,TRBV13-1,None,TRBJ2-5,TRBC2,True,True,CASSDTTGGQDTQYF,TGTGCCAGCAGTGATACTACTGGGGGCCAAGACACCCAGTACTTT,49954,9,clonotype21,clonotype21_consensus_1 -CCATTCGCACGCATCG-1,True,CCATTCGCACGCATCG-1_contig_2,True,374,TRB,None,None,TRBJ2-4,TRBC2,False,False,None,None,12672,4,clonotype21,None -CCATTCGCACGCATCG-1,True,CCATTCGCACGCATCG-1_contig_3,True,323,TRA,TRAV12-3,None,TRAJ31,TRAC,True,False,None,None,12410,2,clonotype21,None -CCATTCGTCATCTGCC-1,True,CCATTCGTCATCTGCC-1_contig_1,True,512,TRB,TRBV13-1,None,TRBJ2-3,TRBC2,True,True,CASRDSAETLYF,TGTGCCAGCAGGGACAGTGCAGAAACGCTGTATTTT,53134,8,clonotype51,clonotype51_consensus_2 -CCATTCGTCATCTGCC-1,True,CCATTCGTCATCTGCC-1_contig_2,True,522,TRA,TRAV6-6,None,TRAJ26,TRAC,True,True,CALGDHGNYAQGLTF,TGTGCTCTGGGTGATCACGGTAACTATGCCCAGGGATTAACCTTC,24628,3,clonotype51,clonotype51_consensus_1 -CCCTCCTGTTAGGGTG-1,True,CCCTCCTGTTAGGGTG-1_contig_1,True,520,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALSDPAGGADRLTF,TGTGCTCTGAGTGATCCGGCAGGAGGTGCAGATAGACTCACCTTT,44804,9,clonotype52,clonotype52_consensus_1 -CCCTCCTGTTAGGGTG-1,True,CCCTCCTGTTAGGGTG-1_contig_2,True,562,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,False,None,None,5582,1,clonotype52,None -CCCTCCTGTTAGGGTG-1,True,CCCTCCTGTTAGGGTG-1_contig_3,True,753,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,False,CASSIGGNYAEQFF,TGTGCCAGCAGTATTGGGGGGAACTATGCTGAGCAGTTCTTC,9528,2,clonotype52,None -CCCTCCTGTTAGGGTG-1,True,CCCTCCTGTTAGGGTG-1_contig_4,True,355,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,17390,3,clonotype52,None -CCGTTCACATATACGC-1,True,CCGTTCACATATACGC-1_contig_1,True,728,TRA,TRAV9-4,None,TRAJ22,TRAC,True,True,CAVTSSGSWQLIF,TGTGCTGTGACATCTTCTGGCAGCTGGCAACTCATCTTT,1494,1,clonotype3,clonotype3_consensus_1 -CCGTTCACATATACGC-1,True,CCGTTCACATATACGC-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGGAACACAGAAGTCTTCTTT,66676,6,clonotype3,clonotype3_consensus_2 -CCGTTCACATATACGC-1,True,CCGTTCACATATACGC-1_contig_3,True,627,TRA,None,None,TRAJ41,TRAC,False,False,None,None,8524,5,clonotype3,None -CCTAAAGAGAGACGAA-1,True,CCTAAAGAGAGACGAA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,27684,18,clonotype5,clonotype5_consensus_3 -CCTAAAGAGAGACGAA-1,True,CCTAAAGAGAGACGAA-1_contig_2,True,731,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,15062,10,clonotype5,clonotype5_consensus_2 -CCTAAAGAGAGACGAA-1,True,CCTAAAGAGAGACGAA-1_contig_3,True,731,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,12566,8,clonotype5,clonotype5_consensus_1 -CCTAAAGAGAGACGAA-1,True,CCTAAAGAGAGACGAA-1_contig_4,True,368,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,10268,5,clonotype5,None -CCTAAAGAGAGACGAA-1,True,CCTAAAGAGAGACGAA-1_contig_5,True,429,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,4538,2,clonotype5,None -CCTAAAGAGAGACGAA-1,True,CCTAAAGAGAGACGAA-1_contig_6,True,639,TRB,TRBV2,None,TRBJ1-1,TRBC1,True,False,None,None,6442,6,clonotype5,None -CCTAAAGTCGGACAAG-1,True,CCTAAAGTCGGACAAG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,43694,4,clonotype22,clonotype22_consensus_2 -CCTAAAGTCGGACAAG-1,True,CCTAAAGTCGGACAAG-1_contig_2,True,657,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CALSSSSGQKLVF,TGTGCTCTGAGTTCTTCAAGTGGCCAGAAGCTGGTTTTT,30184,6,clonotype22,clonotype22_consensus_1 -CCTAAAGTCGGACAAG-1,True,CCTAAAGTCGGACAAG-1_contig_3,True,800,TRB,None,None,TRBJ1-5,None,False,False,None,None,436,1,clonotype22,None -CCTAAAGTCGGACAAG-1,True,CCTAAAGTCGGACAAG-1_contig_4,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,4072,3,clonotype22,None -CCTACACTCCTACAGA-1,True,CCTACACTCCTACAGA-1_contig_1,True,656,TRB,TRBV19,None,TRBJ2-4,TRBC2,True,True,CASSISGGDSQNTLYF,TGTGCCAGCAGTATCTCTGGGGGGGACAGTCAAAACACCTTGTACTTT,7352,1,clonotype53,clonotype53_consensus_2 -CCTACACTCCTACAGA-1,True,CCTACACTCCTACAGA-1_contig_2,True,521,TRA,TRAV7D-2,None,TRAJ9,TRAC,True,True,CAASKGGNMGYKLTF,TGTGCAGCAAGCAAGGGGGGGAACATGGGCTACAAACTTACCTTC,11346,5,clonotype53,clonotype53_consensus_1 -CCTACACTCCTACAGA-1,True,CCTACACTCCTACAGA-1_contig_3,True,461,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,52554,9,clonotype53,None -CCTACACTCTATGTGG-1,True,CCTACACTCTATGTGG-1_contig_1,True,522,TRB,TRBV17,None,TRBJ2-7,TRBC2,True,True,CASSRDRGHEQYF,TGTGCTAGCAGTAGAGACAGGGGGCATGAACAGTACTTC,69836,22,clonotype54,clonotype54_consensus_1 -CCTACCAGTATGGTTC-1,True,CCTACCAGTATGGTTC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,47968,17,clonotype20,clonotype20_consensus_1 -CCTACCAGTATGGTTC-1,True,CCTACCAGTATGGTTC-1_contig_2,True,333,TRA,TRAV9D-2,None,TRAJ16,TRAC,True,False,CALSSSSGQKLVF,TGTGCTCTGAGTTCTTCAAGTGGCCAGAAGCTGGTTTTT,22470,8,clonotype20,None -CCTACCAGTATGGTTC-1,True,CCTACCAGTATGGTTC-1_contig_3,True,323,TRB,None,None,TRBJ2-2,TRBC2,False,False,None,None,4056,4,clonotype20,None -CCTCAGTAGAATAGGG-1,True,CCTCAGTAGAATAGGG-1_contig_1,True,517,TRB,TRBV14,None,TRBJ1-1,TRBC1,True,True,CASSFGTVTEVFF,TGTGCCAGCAGTTTTGGGACCGTCACAGAAGTCTTCTTT,32852,8,clonotype18,clonotype18_consensus_1 -CCTCAGTAGAATAGGG-1,True,CCTCAGTAGAATAGGG-1_contig_2,True,371,Multi,TRDV1,None,None,TRAC,False,False,None,None,10042,2,clonotype18,None -CCTCAGTAGAATAGGG-1,True,CCTCAGTAGAATAGGG-1_contig_3,True,434,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,33882,5,clonotype18,None -CCTCTGAAGCTAGTCT-1,True,CCTCTGAAGCTAGTCT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,39912,12,clonotype5,clonotype5_consensus_3 -CCTCTGAAGCTAGTCT-1,True,CCTCTGAAGCTAGTCT-1_contig_2,True,514,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,9560,3,clonotype5,clonotype5_consensus_2 -CCTCTGAAGCTAGTCT-1,True,CCTCTGAAGCTAGTCT-1_contig_3,True,514,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,17668,9,clonotype5,clonotype5_consensus_1 -CCTCTGAAGCTAGTCT-1,True,CCTCTGAAGCTAGTCT-1_contig_4,True,357,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,4708,3,clonotype5,None -CCTTCGAAGGCTCTTA-1,True,CCTTCGAAGGCTCTTA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,24430,13,clonotype2,clonotype2_consensus_2 -CCTTCGAAGGCTCTTA-1,True,CCTTCGAAGGCTCTTA-1_contig_2,True,670,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,10456,4,clonotype2,clonotype2_consensus_1 -CCTTCGAAGGCTCTTA-1,True,CCTTCGAAGGCTCTTA-1_contig_3,True,331,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,15272,8,clonotype2,None -CCTTCGAAGGCTCTTA-1,True,CCTTCGAAGGCTCTTA-1_contig_4,True,306,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,23862,8,clonotype2,None -CGACCTTTCGGTCTAA-1,True,CGACCTTTCGGTCTAA-1_contig_1,True,521,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,41796,3,clonotype1,clonotype1_consensus_1 -CGACCTTTCGGTCTAA-1,True,CGACCTTTCGGTCTAA-1_contig_2,True,703,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,34836,3,clonotype1,clonotype1_consensus_2 -CGAGCACAGACTCGGA-1,True,CGAGCACAGACTCGGA-1_contig_1,True,669,TRA,TRAV7-1,None,TRAJ12,TRAC,True,True,CAVSIGTGGYKVVF,TGTGCAGTGAGCATTGGGACTGGAGGCTATAAAGTGGTCTTT,37372,4,clonotype11,clonotype11_consensus_2 -CGAGCACAGACTCGGA-1,True,CGAGCACAGACTCGGA-1_contig_2,True,512,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,29222,5,clonotype11,clonotype11_consensus_1 -CGAGCACAGACTCGGA-1,True,CGAGCACAGACTCGGA-1_contig_3,True,603,TRA,TRAV14N-3,None,TRAJ7,TRAC,True,False,None,None,7188,1,clonotype11,None -CGAGCCACACGTGAGA-1,True,CGAGCCACACGTGAGA-1_contig_1,True,558,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCCGGGCAAATGCTTACAAAGTCATCTTT,53326,10,clonotype23,clonotype23_consensus_1 -CGATCGGCACCGTTGG-1,True,CGATCGGCACCGTTGG-1_contig_1,True,522,TRB,TRBV17,None,TRBJ1-1,TRBC1,True,True,CASSRGSNTEVFF,TGTGCTAGCAGTAGAGGATCAAACACAGAAGTCTTCTTT,55720,8,clonotype55,clonotype55_consensus_1 -CGATCGGCACCGTTGG-1,True,CGATCGGCACCGTTGG-1_contig_2,True,607,TRA,TRAV5D-4,None,TRAJ31,TRAC,True,True,CAASRGNNRIFF,TGTGCTGCAAGTAGGGGCAATAACAGAATCTTCTTT,21432,3,clonotype55,clonotype55_consensus_2 -CGATGTAAGTGTCCCG-1,True,CGATGTAAGTGTCCCG-1_contig_1,True,580,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-1,TRBC2,True,True,CASGEGGADYAEQFF,TGTGCCAGCGGTGAGGGGGGCGCTGACTATGCTGAGCAGTTCTTC,52678,4,clonotype56,clonotype56_consensus_1 -CGATGTAAGTGTCCCG-1,True,CGATGTAAGTGTCCCG-1_contig_2,True,528,TRA,TRAV7D-5,None,TRAJ17,TRAC,True,True,CAVSPRSAGNKLTF,TGTGCAGTGAGCCCAAGGAGTGCAGGGAACAAGCTAACTTTT,25262,4,clonotype56,clonotype56_consensus_2 -CGGACGTAGGACAGCT-1,True,CGGACGTAGGACAGCT-1_contig_1,True,676,TRA,TRAV7-1,None,TRAJ32,TRAC,True,True,CAVDGGSGNKLIF,TGTGCAGTGGATGGGGGCAGTGGCAACAAGCTCATCTTT,22524,4,clonotype57,clonotype57_consensus_1 -CGGACGTAGGACAGCT-1,True,CGGACGTAGGACAGCT-1_contig_2,True,565,TRB,TRBV2,None,TRBJ2-5,TRBC2,True,True,CASSQDWGAQDTQYF,TGTGCCAGCAGCCAAGATTGGGGGGCCCAAGACACCCAGTACTTT,7130,1,clonotype57,clonotype57_consensus_2 -CGGACGTAGGACAGCT-1,True,CGGACGTAGGACAGCT-1_contig_3,True,567,TRA,TRAV6N-7,None,TRAJ6,TRAC,True,False,None,None,26012,2,clonotype57,None -CGGACGTAGGACAGCT-1,True,CGGACGTAGGACAGCT-1_contig_4,True,326,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,14846,1,clonotype57,None -CGGACGTAGGACAGCT-1,True,CGGACGTAGGACAGCT-1_contig_5,True,613,TRB,TRBV13-1,TRBD1,TRBJ2-5,TRBC2,True,False,CQHSGQGADTQYF,TGCCAGCACTCGGGACAGGGGGCCGACACCCAGTACTTT,7738,1,clonotype57,None -CGGAGCTAGACCTTTG-1,True,CGGAGCTAGACCTTTG-1_contig_1,True,591,TRA,TRAV12-3,None,TRAJ49,TRAC,True,True,CALSDPVTGYQNFYF,TGTGCTTTGAGTGACCCTGTCACGGGTTACCAGAACTTCTATTTT,34860,7,clonotype12,clonotype12_consensus_1 -CGGAGCTAGACCTTTG-1,True,CGGAGCTAGACCTTTG-1_contig_2,True,549,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASRLGFEQYF,TGTGCCAGCCGACTGGGGTTTGAACAGTACTTC,43196,6,clonotype12,clonotype12_consensus_2 -CGTAGGCTCTGCCAGG-1,True,CGTAGGCTCTGCCAGG-1_contig_1,True,531,TRA,TRAV6N-7,None,TRAJ33,TRAC,True,True,CALSDRGSNYQLIW,TGTGCTCTGAGTGATCGGGGTAGCAACTATCAGTTGATCTGG,48210,11,clonotype58,clonotype58_consensus_1 -CGTAGGCTCTGCCAGG-1,True,CGTAGGCTCTGCCAGG-1_contig_2,True,701,TRB,TRBV19,None,TRBJ1-5,TRBC1,True,True,CASSIGQGATQAPLF,TGTGCCAGCAGTATCGGACAGGGGGCTACCCAGGCTCCGCTTTTT,11194,5,clonotype58,clonotype58_consensus_2 -CGTAGGCTCTGCCAGG-1,True,CGTAGGCTCTGCCAGG-1_contig_3,True,335,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,19228,11,clonotype58,None -CGTGTAATCTCTTATG-1,True,CGTGTAATCTCTTATG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSLGQGNTEVFF,TGTGCCAGCAGCCTGGGACAGGGGAACACAGAAGTCTTCTTT,50846,6,clonotype59,clonotype59_consensus_1 -CGTGTAATCTCTTATG-1,True,CGTGTAATCTCTTATG-1_contig_2,True,355,TRA,TRAV17,None,TRAJ16,TRAC,True,False,CALSTSSGQKLVF,TGTGCACTGTCAACTTCAAGTGGCCAGAAGCTGGTTTTT,20870,1,clonotype59,None -CGTTAGATCGTGACAT-1,True,CGTTAGATCGTGACAT-1_contig_1,True,537,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,20426,5,clonotype1,clonotype1_consensus_1 -CGTTAGATCGTGACAT-1,True,CGTTAGATCGTGACAT-1_contig_2,True,715,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,43768,10,clonotype1,clonotype1_consensus_2 -CGTTAGATCGTGACAT-1,True,CGTTAGATCGTGACAT-1_contig_3,True,326,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,12494,5,clonotype1,None -CTAACTTTCATGCTCC-1,True,CTAACTTTCATGCTCC-1_contig_1,True,555,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,3880,5,clonotype1,clonotype1_consensus_1 -CTAACTTTCATGCTCC-1,True,CTAACTTTCATGCTCC-1_contig_2,True,715,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,23734,6,clonotype1,clonotype1_consensus_2 -CTAACTTTCATGCTCC-1,True,CTAACTTTCATGCTCC-1_contig_3,True,384,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,31308,5,clonotype1,None -CTAACTTTCATGCTCC-1,True,CTAACTTTCATGCTCC-1_contig_4,True,389,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,16730,4,clonotype1,None -CTACACCTCTCCCTGA-1,True,CTACACCTCTCCCTGA-1_contig_1,True,602,TRA,TRAV5D-4,None,TRAJ33,TRAC,True,True,CAASEVDSNYQLIW,TGTGCTGCAAGTGAGGTGGATAGCAACTATCAGTTGATCTGG,27938,5,clonotype60,clonotype60_consensus_1 -CTACACCTCTCCCTGA-1,True,CTACACCTCTCCCTGA-1_contig_2,True,547,TRB,TRBV10,None,TRBJ1-4,TRBC1,True,True,CASSYGRFSNERLFF,TGTGCCAGCAGCTACGGCAGATTTTCCAACGAAAGATTATTTTTC,38184,4,clonotype60,clonotype60_consensus_2 -CTACACCTCTCCCTGA-1,True,CTACACCTCTCCCTGA-1_contig_3,True,668,TRB,TRBV19,None,TRBJ2-3,TRBC2,True,False,None,None,8734,3,clonotype60,None -CTAGAGTAGAAACCTA-1,True,CTAGAGTAGAAACCTA-1_contig_1,True,597,TRA,TRAV7D-4,None,TRAJ26,TRAC,True,True,CAASDLNNYAQGLTF,TGTGCAGCTAGTGACCTAAATAACTATGCCCAGGGATTAACCTTC,43448,3,clonotype61,clonotype61_consensus_1 -CTAGAGTAGAAACCTA-1,True,CTAGAGTAGAAACCTA-1_contig_2,True,695,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,3602,1,clonotype61,clonotype61_consensus_3 -CTAGAGTAGAAACCTA-1,True,CTAGAGTAGAAACCTA-1_contig_3,True,612,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGDAGGSAETLYF,TGTGCCAGCGGTGATGCGGGGGGTAGTGCAGAAACGCTGTATTTT,5334,4,clonotype61,clonotype61_consensus_2 -CTAGAGTAGAAACCTA-1,True,CTAGAGTAGAAACCTA-1_contig_4,True,533,TRA,TRAV3-3,None,TRAJ21,TRAC,True,False,None,None,19922,6,clonotype61,None -CTAGCCTGTAGCGTAG-1,True,CTAGCCTGTAGCGTAG-1_contig_1,True,552,TRA,TRAV7D-3,None,TRAJ52,TRAC,True,True,CAVSMPGANTGKLTF,TGTGCAGTGAGCATGCCTGGAGCTAACACTGGAAAGCTCACGTTT,15936,2,clonotype62,clonotype62_consensus_2 -CTAGCCTGTAGCGTAG-1,True,CTAGCCTGTAGCGTAG-1_contig_2,True,517,TRB,TRBV14,None,TRBJ2-2,TRBC2,True,True,CASSFDRGAQLYF,TGTGCCAGCAGTTTCGACAGGGGGGCGCAGCTCTACTTT,54180,6,clonotype62,clonotype62_consensus_1 -CTAGCCTGTAGCGTAG-1,True,CTAGCCTGTAGCGTAG-1_contig_3,True,329,TRB,TRBV13-2,None,TRBJ2-7,TRBC2,True,False,None,None,5602,1,clonotype62,None -CTCATTAGTACCTACA-1,True,CTCATTAGTACCTACA-1_contig_1,True,551,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCGGGACAGGGGAACACAGAAGTCTTCTTT,19342,4,clonotype22,clonotype22_consensus_2 -CTCATTAGTACCTACA-1,True,CTCATTAGTACCTACA-1_contig_2,True,716,TRA,TRAV9-4,None,TRAJ16,TRAC,True,True,CALSSSSGQKLVF,TGTGCTCTGAGTTCTTCAAGTGGCCAGAAGCTGGTTTTT,22448,7,clonotype22,clonotype22_consensus_1 -CTCATTAGTACCTACA-1,True,CTCATTAGTACCTACA-1_contig_3,True,355,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,16266,3,clonotype22,None -CTCATTAGTACCTACA-1,True,CTCATTAGTACCTACA-1_contig_4,True,362,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,17176,5,clonotype22,None -CTCCTAGCATGTCTCC-1,True,CTCCTAGCATGTCTCC-1_contig_1,True,594,TRA,TRAV7-4,None,TRAJ7,TRAC,True,True,CAASADYSNNRLTL,TGTGCAGCTAGTGCTGACTACAGCAACAACAGACTTACTTTG,29842,10,clonotype63,clonotype63_consensus_1 -CTCCTAGCATGTCTCC-1,True,CTCCTAGCATGTCTCC-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSSGGGNTEVFF,TGTGCCAGCAGCTCAGGGGGCGGGAACACAGAAGTCTTCTTT,44102,13,clonotype63,clonotype63_consensus_2 -CTCGTACCACATCTTT-1,True,CTCGTACCACATCTTT-1_contig_1,True,514,TRB,TRBV14,None,TRBJ2-3,TRBC2,True,True,CASRLGWETLYF,TGTGCCAGCAGACTGGGGTGGGAAACGCTGTATTTT,47760,10,clonotype64,clonotype64_consensus_1 -CTCGTACCACATCTTT-1,True,CTCGTACCACATCTTT-1_contig_2,True,597,TRA,TRAV7-4,None,TRAJ56,TRAC,True,True,CAASEQGGGNNKLTF,TGTGCAGCTAGTGAGCAAGGGGGAGGCAATAATAAGCTGACTTTT,28812,6,clonotype64,clonotype64_consensus_2 -CTCGTACCACATCTTT-1,True,CTCGTACCACATCTTT-1_contig_3,True,447,TRB,TRBV17,None,TRBJ1-6,None,True,False,CGVQDNSPLYF,TGTGGGGTACAGGATAATTCGCCCCTCTACTTT,4,2,clonotype64,None -CTCTGGTTCCTCCTAG-1,True,CTCTGGTTCCTCCTAG-1_contig_1,True,605,TRA,TRAV5D-4,None,TRAJ32,TRAC,True,True,CAASRGGSGNKLIF,TGTGCTGCAAGTCGTGGGGGCAGTGGCAACAAGCTCATCTTT,33256,5,clonotype65,clonotype65_consensus_1 -CTCTGGTTCCTCCTAG-1,True,CTCTGGTTCCTCCTAG-1_contig_2,True,485,TRB,TRBV10,None,None,TRBC1,False,False,None,None,42132,5,clonotype65,None -CTGATCCTCACGACTA-1,True,CTGATCCTCACGACTA-1_contig_1,True,701,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSMGTISNERLFF,TGTGCCAGCAGTATGGGGACAATTTCCAACGAAAGATTATTTTTC,15726,2,clonotype66,clonotype66_consensus_1 -CTGATCCTCACGACTA-1,True,CTGATCCTCACGACTA-1_contig_2,True,560,TRA,TRAV14D-3-DV8,None,TRAJ48,TRAC,True,True,CAALYGNEKITF,TGTGCAGCCTTGTATGGAAATGAGAAAATAACTTTT,11846,2,clonotype66,clonotype66_consensus_2 -CTGATCCTCACGACTA-1,True,CTGATCCTCACGACTA-1_contig_3,True,617,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,47380,3,clonotype66,None -CTGCGGAAGGTTCCTA-1,True,CTGCGGAAGGTTCCTA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,36602,43,clonotype5,clonotype5_consensus_3 -CTGCGGAAGGTTCCTA-1,True,CTGCGGAAGGTTCCTA-1_contig_2,True,726,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,10474,15,clonotype5,clonotype5_consensus_2 -CTGCGGAAGGTTCCTA-1,True,CTGCGGAAGGTTCCTA-1_contig_3,True,696,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,3052,3,clonotype5,clonotype5_consensus_1 -CTGCGGAAGGTTCCTA-1,True,CTGCGGAAGGTTCCTA-1_contig_4,True,369,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,9190,6,clonotype5,None -CTGCGGAAGGTTCCTA-1,True,CTGCGGAAGGTTCCTA-1_contig_5,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,17006,17,clonotype5,None -CTGCTGTAGTGACATA-1,True,CTGCTGTAGTGACATA-1_contig_1,True,507,TRA,TRAV21-DV12,None,TRAJ39,TRAC,True,True,CILRGNNNAGAKLTF,TGTATCCTGAGAGGGAATAATAATGCAGGTGCCAAGCTCACATTC,12870,2,clonotype67,clonotype67_consensus_1 -CTGCTGTAGTGACATA-1,True,CTGCTGTAGTGACATA-1_contig_2,True,567,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-4,TRBC1,True,True,CASGRDSSNERLFF,TGTGCCAGCGGTCGGGACAGCTCCAACGAAAGATTATTTTTC,13458,2,clonotype67,clonotype67_consensus_2 -CTGCTGTAGTGACATA-1,True,CTGCTGTAGTGACATA-1_contig_3,True,365,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,13706,1,clonotype67,None -CTGCTGTAGTGACATA-1,True,CTGCTGTAGTGACATA-1_contig_4,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,27640,3,clonotype67,None -CTGCTGTAGTGACATA-1,True,CTGCTGTAGTGACATA-1_contig_5,True,595,TRA,TRAV12-3,None,TRAJ52,TRAC,True,False,None,None,9076,4,clonotype67,None -CTGTGCTAGGAATTAC-1,True,CTGTGCTAGGAATTAC-1_contig_1,True,579,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-3,TRBC2,True,True,CASGDRGSSAETLYF,TGTGCCAGCGGTGACCGGGGGTCTAGTGCAGAAACGCTGTATTTT,51086,6,clonotype68,clonotype68_consensus_2 -CTGTGCTAGGAATTAC-1,True,CTGTGCTAGGAATTAC-1_contig_2,True,558,TRA,TRAV16N,None,TRAJ40,TRAC,True,True,CAMREGHTGNYKYVF,TGTGCTATGAGAGAGGGCCATACAGGAAACTACAAATACGTCTTT,24208,4,clonotype68,clonotype68_consensus_1 -CTGTGCTTCTTGGGTA-1,True,CTGTGCTTCTTGGGTA-1_contig_1,True,728,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,10926,3,clonotype2,clonotype2_consensus_1 -CTGTGCTTCTTGGGTA-1,True,CTGTGCTTCTTGGGTA-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,35224,11,clonotype2,clonotype2_consensus_2 -CTGTGCTTCTTGGGTA-1,True,CTGTGCTTCTTGGGTA-1_contig_3,True,777,TRA,TRAV3-1,None,TRAJ22,TRAC,True,False,CAVSIFW,TGCGCAGTCAGCATCTTCTGG,1970,1,clonotype2,None -CTGTGCTTCTTGGGTA-1,True,CTGTGCTTCTTGGGTA-1_contig_4,True,494,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,28460,7,clonotype2,None -CTTAACTCAGCGATCC-1,True,CTTAACTCAGCGATCC-1_contig_1,True,571,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSADQGGSYEQYF,TGCACCTGCAGTGCAGATCAGGGGGGCTCCTATGAACAGTACTTC,38872,5,clonotype69,clonotype69_consensus_1 -CTTAACTCAGCGATCC-1,True,CTTAACTCAGCGATCC-1_contig_2,True,422,TRA,TRAV13-1,None,TRAJ22,TRAC,True,False,CAMDASSGSWQLIF,TGTGCTATGGATGCATCTTCTGGCAGCTGGCAACTCATCTTT,35428,3,clonotype69,None -CTTGGCTAGCAGGTCA-1,True,CTTGGCTAGCAGGTCA-1_contig_1,True,602,TRB,TRBV3,None,TRBJ2-7,TRBC2,True,True,CASSLDGGAYEQYF,TGTGCCAGCAGCTTAGATGGGGGGGCCTATGAACAGTACTTC,37430,2,clonotype70,clonotype70_consensus_1 -CTTGGCTAGCAGGTCA-1,True,CTTGGCTAGCAGGTCA-1_contig_2,True,768,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,1942,13,clonotype70,None -GAACATCAGTCAAGCG-1,True,GAACATCAGTCAAGCG-1_contig_1,True,664,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,43612,11,clonotype17,clonotype17_consensus_1 -GAACATCAGTCAAGCG-1,True,GAACATCAGTCAAGCG-1_contig_2,True,353,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,19258,4,clonotype17,None -GAAGCAGAGGTAGCCA-1,True,GAAGCAGAGGTAGCCA-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-5,TRBC2,True,True,CASSQSGLGGQDTQYF,TGTGCCAGCAGCCAATCGGGACTGGGGGGTCAAGACACCCAGTACTTT,50832,2,clonotype71,clonotype71_consensus_1 -GAAGCAGAGGTAGCCA-1,True,GAAGCAGAGGTAGCCA-1_contig_2,True,534,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,27516,3,clonotype71,None -GAATAAGCACGGCCAT-1,True,GAATAAGCACGGCCAT-1_contig_1,True,573,TRA,TRAV2,None,TRAJ24,TRAC,True,True,CIVTDMTTASLGKLQF,TGCATTGTGACTGACATGACAACTGCCAGTTTGGGGAAACTGCAGTTT,27482,4,clonotype72,clonotype72_consensus_1 -GACAGAGGTCAGAAGC-1,True,GACAGAGGTCAGAAGC-1_contig_1,True,614,TRB,TRBV3,None,TRBJ2-1,TRBC2,True,True,CASSLERQGRDNYAEQFF,TGTGCCAGCAGCTTAGAGAGACAGGGGAGGGATAACTATGCTGAGCAGTTCTTC,73194,9,clonotype73,clonotype73_consensus_1 -GACGTTATCGCCGTGA-1,True,GACGTTATCGCCGTGA-1_contig_1,True,676,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSMGTRDTQYF,TGTGCCAGCAGTATGGGGACAAGGGACACCCAGTACTTT,57920,23,clonotype1,clonotype1_consensus_2 -GACGTTATCGCCGTGA-1,True,GACGTTATCGCCGTGA-1_contig_2,True,522,TRA,TRAV6-6,None,TRAJ45,TRAC,True,True,CALGDPAGGADRLTF,TGTGCTCTGGGTGATCCCGCAGGAGGTGCAGATAGACTCACCTTT,15060,4,clonotype1,clonotype1_consensus_1 -GACGTTATCGCCGTGA-1,True,GACGTTATCGCCGTGA-1_contig_3,True,577,TRA,TRAV5D-4,None,TRAJ50,TRAC,True,False,None,None,4938,2,clonotype1,None -GACTAACCACACTGCG-1,True,GACTAACCACACTGCG-1_contig_1,True,510,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSLGQGNTEVFF,TGTGCCAGCAGCCTGGGACAGGGGAACACAGAAGTCTTCTTT,47902,6,clonotype74,clonotype74_consensus_1 -GACTAACCACACTGCG-1,True,GACTAACCACACTGCG-1_contig_2,True,629,TRA,TRAV17,None,TRAJ16,TRAC,True,True,CALSTSSGQKLVF,TGTGCACTGTCAACTTCAAGTGGCCAGAAGCTGGTTTTT,8046,5,clonotype74,clonotype74_consensus_2 -GACTAACCACACTGCG-1,True,GACTAACCACACTGCG-1_contig_3,True,504,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,19846,6,clonotype74,None -GACTACAGTCGACTAT-1,True,GACTACAGTCGACTAT-1_contig_1,True,580,TRB,TRBV13-3,None,TRBJ2-3,TRBC2,True,True,CASSRDREALYF,TGTGCCAGCAGCCGGGACAGGGAGGCGCTGTATTTT,41272,6,clonotype75,clonotype75_consensus_2 -GACTACAGTCGACTAT-1,True,GACTACAGTCGACTAT-1_contig_2,True,516,TRA,TRAV6-6,None,TRAJ15,TRAC,True,True,CALSELQGGRALIF,TGTGCTCTGAGTGAACTCCAGGGAGGCAGAGCTCTGATATTT,9988,4,clonotype75,clonotype75_consensus_1 -GACTACAGTCGACTAT-1,True,GACTACAGTCGACTAT-1_contig_3,True,545,TRB,TRBV16,None,TRBJ1-2,TRBC1,True,False,CKQLQGNSDYTF,TGCAAGCAGCTTCAGGGAAACTCCGACTACACCTTC,25106,3,clonotype75,None -GACTGCGGTGCCTGCA-1,True,GACTGCGGTGCCTGCA-1_contig_1,True,507,TRA,TRAV21-DV12,None,TRAJ56,TRAC,True,True,CILRGATGGNNKLTF,TGTATCCTGAGGGGGGCTACTGGAGGCAATAATAAGCTGACTTTT,64194,11,clonotype19,clonotype19_consensus_1 -GACTGCGGTGCCTGCA-1,True,GACTGCGGTGCCTGCA-1_contig_2,True,562,TRB,TRBV2,None,TRBJ2-4,TRBC2,True,True,CASSQRQGQNTLYF,TGTGCCAGCAGCCAAAGACAGGGCCAAAACACCTTGTACTTT,9752,3,clonotype19,clonotype19_consensus_2 -GACTGCGGTGCGATAG-1,True,GACTGCGGTGCGATAG-1_contig_1,True,586,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCCGGGCAAATGCTTACAAAGTCATCTTT,43650,5,clonotype23,clonotype23_consensus_1 -GACTGCGGTGCGATAG-1,True,GACTGCGGTGCGATAG-1_contig_2,True,815,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,3804,1,clonotype23,None -GACTGCGGTGCGATAG-1,True,GACTGCGGTGCGATAG-1_contig_3,True,360,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,27412,3,clonotype23,None -GACTGCGGTGCGATAG-1,True,GACTGCGGTGCGATAG-1_contig_4,True,562,TRA,TRAV8N-2,None,TRAJ52,TRAC,True,False,None,None,2818,3,clonotype23,None -GAGGTGAAGACCACGA-1,True,GAGGTGAAGACCACGA-1_contig_1,True,516,TRB,TRBV17,None,TRBJ1-6,TRBC1,True,True,CGVQDNSPLYF,TGTGGGGTACAGGATAATTCGCCCCTCTACTTT,50674,9,clonotype8,clonotype8_consensus_3 -GAGGTGAAGACCACGA-1,True,GAGGTGAAGACCACGA-1_contig_2,True,534,TRB,TRBV13-3,None,TRBJ1-3,TRBC1,True,True,CASSGDRGGNTLYF,TGTGCCAGCAGTGGGGACAGGGGTGGAAATACGCTCTATTTT,20656,5,clonotype8,clonotype8_consensus_1 -GAGGTGAAGACCACGA-1,True,GAGGTGAAGACCACGA-1_contig_3,True,536,TRA,TRAV16N,None,TRAJ56,TRAC,True,True,CAMREGPGGNNKLTF,TGTGCTATGAGAGAGGGACCTGGAGGCAATAATAAGCTGACTTTT,5092,1,clonotype8,clonotype8_consensus_2 -GATTCAGTCAGCAACT-1,True,GATTCAGTCAGCAACT-1_contig_1,True,560,TRA,TRAV3-3,None,TRAJ49,TRAC,True,True,CAVSEGYQNFYF,TGCGCAGTCAGTGAGGGTTACCAGAACTTCTATTTT,36920,9,clonotype76,clonotype76_consensus_2 -GATTCAGTCAGCAACT-1,True,GATTCAGTCAGCAACT-1_contig_2,True,575,TRA,TRAV13-1,None,TRAJ33,TRAC,True,True,CAMERSNYQLIW,TGTGCTATGGAAAGGAGCAACTATCAGTTGATCTGG,31992,7,clonotype76,clonotype76_consensus_1 -GATTCAGTCAGCAACT-1,True,GATTCAGTCAGCAACT-1_contig_3,True,564,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGGTGVYEQYF,TGTGCCAGCGGAGGGACTGGGGTCTATGAACAGTACTTC,8660,3,clonotype76,clonotype76_consensus_3 -GCAGCCATCATCTGTT-1,True,GCAGCCATCATCTGTT-1_contig_1,True,544,TRB,TRBV10,None,TRBJ2-1,TRBC2,True,True,CASSYWGGDAEQFF,TGTGCCAGCAGCTACTGGGGGGGCGATGCTGAGCAGTTCTTC,46684,5,clonotype77,clonotype77_consensus_1 -GCAGCCATCATCTGTT-1,True,GCAGCCATCATCTGTT-1_contig_2,True,386,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,18438,3,clonotype77,None -GCAGCCATCATCTGTT-1,True,GCAGCCATCATCTGTT-1_contig_3,True,569,TRA,TRAV3-4,None,TRAJ48,TRAC,True,False,None,None,11398,4,clonotype77,None -GCATACAAGCTGCAAG-1,True,GCATACAAGCTGCAAG-1_contig_1,True,594,TRA,TRAV7D-4,None,TRAJ40,TRAC,True,True,CAASEGTGNYKYVF,TGTGCAGCTAGTGAAGGTACAGGAAACTACAAATACGTCTTT,60886,9,clonotype78,clonotype78_consensus_1 -GCATACAAGTGTACTC-1,True,GCATACAAGTGTACTC-1_contig_1,True,576,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-2,TRBC2,True,True,CASGGDWGGANTGQLYF,TGTGCCAGCGGCGGGGACTGGGGGGGTGCAAACACCGGGCAGCTCTACTTT,22092,8,clonotype79,clonotype79_consensus_1 -GCATACAGTGGCAAAC-1,True,GCATACAGTGGCAAAC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,6206,1,clonotype2,clonotype2_consensus_2 -GCATACAGTGGCAAAC-1,True,GCATACAGTGGCAAAC-1_contig_2,True,724,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,19092,4,clonotype2,clonotype2_consensus_1 -GCATACAGTGGCAAAC-1,True,GCATACAGTGGCAAAC-1_contig_3,True,369,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,False,CQQYEQGLANTEVFF,TGCCAGCAGTATGAACAGGGGCTTGCAAACACAGAAGTCTTCTTT,16396,2,clonotype2,None -GCATACAGTGGCAAAC-1,True,GCATACAGTGGCAAAC-1_contig_4,True,415,TRA,TRAV3-1,None,TRAJ22,TRAC,True,False,CAVSIFW,TGCGCAGTCAGCATCTTCTGG,9512,1,clonotype2,None -GCATACAGTGGCAAAC-1,True,GCATACAGTGGCAAAC-1_contig_5,True,376,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,26138,3,clonotype2,None -GCATGATCAGTCGTGC-1,True,GCATGATCAGTCGTGC-1_contig_1,True,574,TRA,TRAV13-1,None,TRAJ37,TRAC,True,True,CAMGAGNTRKLIF,TGTGCTATGGGGGCAGGCAATACTAGAAAACTCATCTTT,68190,3,clonotype80,clonotype80_consensus_1 -GCATGCGCATTAGGCT-1,True,GCATGCGCATTAGGCT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,69846,13,clonotype4,clonotype4_consensus_2 -GCATGCGCATTAGGCT-1,True,GCATGCGCATTAGGCT-1_contig_2,True,642,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,3264,1,clonotype4,clonotype4_consensus_1 -GCCAAATGTTAAGATG-1,True,GCCAAATGTTAAGATG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGGAACACAGAAGTCTTCTTT,48640,10,clonotype3,clonotype3_consensus_2 -GCCAAATGTTAAGATG-1,True,GCCAAATGTTAAGATG-1_contig_2,True,726,TRA,TRAV9-4,None,TRAJ22,TRAC,True,True,CAVTSSGSWQLIF,TGTGCTGTGACATCTTCTGGCAGCTGGCAACTCATCTTT,24670,3,clonotype3,clonotype3_consensus_1 -GCGAGAATCCGCAGTG-1,True,GCGAGAATCCGCAGTG-1_contig_1,True,731,TRB,TRBV12-1,None,TRBJ2-1,TRBC2,True,True,CASSVDWGGDAEQFF,TGTGCCAGCTCGGTCGACTGGGGGGGGGATGCTGAGCAGTTCTTC,53110,5,clonotype81,clonotype81_consensus_1 -GCGAGAATCCGCAGTG-1,True,GCGAGAATCCGCAGTG-1_contig_2,True,550,TRA,TRAV3-3,None,TRAJ50,TRAC,True,True,CAVSPLIASSSFSKLVF,TGCGCAGTCAGTCCCCTTATAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,23776,4,clonotype81,clonotype81_consensus_2 -GCGCAGTCACATGGGA-1,True,GCGCAGTCACATGGGA-1_contig_1,True,566,TRB,TRBV29,None,TRBJ2-7,TRBC2,True,True,CASSLRDRGIEQYF,TGTGCTAGCAGTTTAAGGGACAGGGGGATTGAACAGTACTTC,69102,9,clonotype82,clonotype82_consensus_1 -GCGCGATTCACCACCT-1,True,GCGCGATTCACCACCT-1_contig_1,True,528,TRA,TRAV7-3,None,TRAJ40,TRAC,True,True,CAVSMGTGNYKYVF,TGTGCAGTGAGCATGGGTACAGGAAACTACAAATACGTCTTT,13606,3,clonotype83,clonotype83_consensus_1 -GCGCGATTCACCACCT-1,True,GCGCGATTCACCACCT-1_contig_2,True,588,TRA,TRAV13-1,None,TRAJ37,TRAC,True,True,CAMGAGNTRKLIF,TGTGCTATGGGGGCAGGCAATACTAGAAAACTCATCTTT,34312,8,clonotype83,clonotype83_consensus_3 -GCGCGATTCACCACCT-1,True,GCGCGATTCACCACCT-1_contig_3,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGATTCCTATGAACAGTACTTC,26532,10,clonotype83,clonotype83_consensus_2 -GCTTGAATCAATAAGG-1,True,GCTTGAATCAATAAGG-1_contig_1,True,600,TRA,TRAV12D-2,None,TRAJ9,TRAC,True,True,CALSVRNMGYKLTF,TGTGCTCTGAGTGTCAGGAACATGGGCTACAAACTTACCTTC,13062,4,clonotype84,clonotype84_consensus_2 -GCTTGAATCAATAAGG-1,True,GCTTGAATCAATAAGG-1_contig_2,True,647,TRB,TRBV19,None,TRBJ2-5,TRBC2,True,True,CASSILGQDTQYF,TGTGCCAGCAGTATTCTGGGGCAAGACACCCAGTACTTT,55706,12,clonotype84,clonotype84_consensus_1 -GCTTGAATCAATAAGG-1,True,GCTTGAATCAATAAGG-1_contig_3,True,518,TRB,TRBV14,None,TRBJ1-3,TRBC1,True,False,None,None,4580,2,clonotype84,None -GGAACTTGTCGCATAT-1,True,GGAACTTGTCGCATAT-1_contig_1,True,544,TRB,TRBV10,None,TRBJ1-3,TRBC1,True,True,CASSLTGVGNTLYF,TGTGCCAGCAGCTTGACAGGGGTCGGAAATACGCTCTATTTT,7010,4,clonotype85,clonotype85_consensus_1 -GGAACTTGTCGCATAT-1,True,GGAACTTGTCGCATAT-1_contig_2,True,432,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,59918,23,clonotype85,None -GGAGCAATCGCCGTGA-1,True,GGAGCAATCGCCGTGA-1_contig_1,True,510,TRB,TRBV29,None,TRBJ2-7,TRBC2,True,True,CASSGDRGHEQYF,TGTGCTAGCAGTGGGGACAGGGGTCATGAACAGTACTTC,29626,18,clonotype13,clonotype13_consensus_1 -GGAGCAATCGCCGTGA-1,True,GGAGCAATCGCCGTGA-1_contig_2,True,581,TRA,TRAV13-1,None,TRAJ6,TRAC,True,True,CAMATSGGNYKPTF,TGTGCTATGGCCACCTCAGGAGGAAACTACAAACCTACGTTT,18328,10,clonotype13,clonotype13_consensus_2 -GGAGCAATCGCCGTGA-1,True,GGAGCAATCGCCGTGA-1_contig_3,True,532,TRB,TRBV20,TRBD1,TRBJ2-7,TRBC2,True,True,CGVPRDRGREQYF,TGTGGTGTCCCCCGGGACAGGGGGCGCGAACAGTACTTC,22382,15,clonotype13,clonotype13_consensus_3 -GGAGCAATCGCCGTGA-1,True,GGAGCAATCGCCGTGA-1_contig_4,True,557,TRA,TRAV4-3,None,TRAJ15,TRAC,True,False,None,None,7106,5,clonotype13,None -GGGACCTAGAACAATC-1,True,GGGACCTAGAACAATC-1_contig_1,True,600,TRA,TRAV14D-3-DV8,None,TRAJ48,TRAC,True,True,CAATNYGNEKITF,TGTGCAGCAACCAACTATGGAAATGAGAAAATAACTTTT,9386,4,clonotype86,clonotype86_consensus_1 -GGGACCTAGAACAATC-1,True,GGGACCTAGAACAATC-1_contig_2,True,571,TRB,TRBV1,None,TRBJ2-3,TRBC2,True,True,CTCSADTTSAETLYF,TGCACCTGCAGTGCTGACACCACTAGTGCAGAAACGCTGTATTTT,44674,21,clonotype86,clonotype86_consensus_2 -GGGACCTAGAACAATC-1,True,GGGACCTAGAACAATC-1_contig_3,True,331,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,19552,8,clonotype86,None -GGGACCTAGAACAATC-1,True,GGGACCTAGAACAATC-1_contig_4,True,711,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,2282,4,clonotype86,None -GGGACCTGTAATCGTC-1,True,GGGACCTGTAATCGTC-1_contig_1,True,567,TRA,TRAV4D-4,None,TRAJ6,TRAC,True,True,CAALTSGGNYKPTF,TGTGCTGCCCTCACCTCAGGAGGAAACTACAAACCTACGTTT,45458,3,clonotype87,clonotype87_consensus_1 -GGGACCTGTAATCGTC-1,True,GGGACCTGTAATCGTC-1_contig_2,True,502,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSEKYEQYF,TGTGCCAGCAGTGAGAAATATGAACAGTACTTC,27504,4,clonotype87,clonotype87_consensus_2 -GGGACCTGTACGACCC-1,True,GGGACCTGTACGACCC-1_contig_1,True,531,TRB,TRBV13-3,None,TRBJ2-3,TRBC2,True,True,CASSGDRDETLYF,TGTGCCAGCAGTGGAGACAGGGACGAAACGCTGTATTTT,55800,7,clonotype88,clonotype88_consensus_1 -GGGACCTGTACGACCC-1,True,GGGACCTGTACGACCC-1_contig_2,True,641,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,False,None,None,21342,2,clonotype88,None -GGGAGATCATTGGGCC-1,True,GGGAGATCATTGGGCC-1_contig_1,True,564,TRA,TRAV4-4-DV10,None,TRAJ31,TRAC,True,True,CAAEYNNNRIFF,TGTGCTGCTGAGTATAACAATAACAGAATCTTCTTT,25418,11,clonotype89,clonotype89_consensus_1 -GGGAGATCATTGGGCC-1,True,GGGAGATCATTGGGCC-1_contig_2,True,568,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,True,CTCSAGQGAGEVFF,TGCACCTGCAGTGCAGGGCAGGGGGCGGGTGAAGTCTTCTTT,39696,21,clonotype89,clonotype89_consensus_2 -GGGAGATCATTGGGCC-1,True,GGGAGATCATTGGGCC-1_contig_3,True,568,TRA,TRAV14D-1,None,TRAJ38,TRAC,True,True,CAASLLNVGDNSKLIW,TGTGCAGCAAGTCTCCTTAATGTTGGTGACAACAGTAAGCTGATTTGG,12958,6,clonotype89,clonotype89_consensus_3 -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_1,True,565,TRB,TRBV2,None,TRBJ1-1,TRBC1,True,True,CASSQEEGANTEVFF,TGTGCCAGCAGCCAAGAGGAGGGTGCAAACACAGAAGTCTTCTTT,13218,5,clonotype6,clonotype6_consensus_2 -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_2,True,558,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCCGGGCAAATGCTTACAAAGTCATCTTT,22384,6,clonotype6,clonotype6_consensus_1 -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_3,True,369,TRB,None,None,TRBJ2-4,TRBC2,False,False,None,None,3504,1,clonotype6,None -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_4,True,562,TRA,TRAV8N-2,None,TRAJ52,TRAC,True,False,None,None,8320,2,clonotype6,None -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_5,True,303,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,10444,2,clonotype6,None -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_6,True,373,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,12726,3,clonotype6,None -GGTGTTAGTTATCACG-1,True,GGTGTTAGTTATCACG-1_contig_7,True,334,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,7342,1,clonotype6,None -GTAACGTAGTCCGGTC-1,True,GTAACGTAGTCCGGTC-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,13958,11,clonotype90,clonotype90_consensus_3 -GTAACGTAGTCCGGTC-1,True,GTAACGTAGTCCGGTC-1_contig_2,True,568,TRB,TRBV1,None,TRBJ2-5,TRBC2,True,True,CTCSAELGQDTQYF,TGCACCTGCAGTGCAGAGCTGGGGCAAGACACCCAGTACTTT,32178,27,clonotype90,clonotype90_consensus_1 -GTAACGTAGTCCGGTC-1,True,GTAACGTAGTCCGGTC-1_contig_3,True,724,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,3282,4,clonotype90,clonotype90_consensus_2 -GTAACGTAGTCCGGTC-1,True,GTAACGTAGTCCGGTC-1_contig_4,True,475,TRA,TRAV11,None,TRAJ18,TRAC,True,False,None,None,5134,5,clonotype90,None -GTAACGTAGTCCGGTC-1,True,GTAACGTAGTCCGGTC-1_contig_5,True,697,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,10986,8,clonotype90,None -GTAACGTAGTCCGGTC-1,True,GTAACGTAGTCCGGTC-1_contig_6,True,590,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,False,CQQYEQGLANTEVFF,TGCCAGCAGTATGAACAGGGGCTTGCAAACACAGAAGTCTTCTTT,8562,12,clonotype90,None -GTACTTTCAGAGTGTG-1,True,GTACTTTCAGAGTGTG-1_contig_1,True,545,TRB,TRBV29,None,TRBJ2-4,TRBC2,True,True,CASSFDTLYF,TGTGCTAGCAGTTTCGACACCTTGTACTTT,62878,9,clonotype91,clonotype91_consensus_1 -GTACTTTCAGAGTGTG-1,True,GTACTTTCAGAGTGTG-1_contig_2,True,432,TRA,TRAV13-1,None,TRAJ53,TRAC,True,False,None,None,15476,3,clonotype91,None -GTACTTTGTAGGCTGA-1,True,GTACTTTGTAGGCTGA-1_contig_1,True,561,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGSGTNAYKVIF,TGTGCTATGAGAGAGGGCTCAGGGACAAATGCTTACAAAGTCATCTTT,18720,15,clonotype24,clonotype24_consensus_2 -GTACTTTGTAGGCTGA-1,True,GTACTTTGTAGGCTGA-1_contig_2,True,718,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSISRGNTEVFF,TGTGCCAGCAGTATAAGCAGGGGAAACACAGAAGTCTTCTTT,37454,25,clonotype24,clonotype24_consensus_1 -GTACTTTGTAGGCTGA-1,True,GTACTTTGTAGGCTGA-1_contig_3,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,12060,9,clonotype24,None -GTACTTTGTAGGCTGA-1,True,GTACTTTGTAGGCTGA-1_contig_4,True,504,TRA,TRAV9-4,None,TRAJ33,TRAC,True,False,CSERGSNYQLIW,TGCTCTGAGCGCGGGAGCAACTATCAGTTGATCTGG,6764,5,clonotype24,None -GTAGTCACATCGACGC-1,True,GTAGTCACATCGACGC-1_contig_1,True,524,TRA,TRAV6-4,None,TRAJ50,TRAC,True,True,CALVASSSFSKLVF,TGTGCTCTGGTAGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,35970,3,clonotype92,clonotype92_consensus_1 -GTAGTCACATCGACGC-1,True,GTAGTCACATCGACGC-1_contig_2,True,648,TRB,TRBV2,None,TRBJ2-3,TRBC2,True,True,CASSQERGTAETLYF,TGTGCCAGCAGCCAAGAGAGGGGAACGGCAGAAACGCTGTATTTT,40162,4,clonotype92,clonotype92_consensus_2 -GTCGGGTCATTCACTT-1,True,GTCGGGTCATTCACTT-1_contig_1,True,588,TRB,TRBV17,None,TRBJ1-6,TRBC1,True,True,CGVQDNSPLYF,TGTGGGGTACAGGATAATTCGCCCCTCTACTTT,14776,1,clonotype93,clonotype93_consensus_2 -GTCGGGTCATTCACTT-1,True,GTCGGGTCATTCACTT-1_contig_2,True,539,TRB,TRBV13-3,None,TRBJ1-3,TRBC1,True,True,CASSGDRGGNTLYF,TGTGCCAGCAGTGGGGACAGGGGTGGAAATACGCTCTATTTT,34816,3,clonotype93,clonotype93_consensus_1 -GTCGGGTCATTCACTT-1,True,GTCGGGTCATTCACTT-1_contig_3,True,532,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,19374,4,clonotype93,None -GTTTCTACATTTGCTT-1,True,GTTTCTACATTTGCTT-1_contig_1,True,571,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGSGTNAYKVIF,TGTGCTATGAGAGAGGGCTCAGGGACAAATGCTTACAAAGTCATCTTT,36510,10,clonotype24,clonotype24_consensus_2 -GTTTCTACATTTGCTT-1,True,GTTTCTACATTTGCTT-1_contig_2,True,718,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSISRGNTEVFF,TGTGCCAGCAGTATAAGCAGGGGAAACACAGAAGTCTTCTTT,34762,7,clonotype24,clonotype24_consensus_1 -TAAACCGGTGTTAAGA-1,True,TAAACCGGTGTTAAGA-1_contig_1,True,557,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-7,TRBC2,True,True,CASGELGGREQYF,TGTGCCAGCGGTGAACTGGGGGGGCGTGAACAGTACTTC,33990,11,clonotype94,clonotype94_consensus_2 -TAAACCGGTGTTAAGA-1,True,TAAACCGGTGTTAAGA-1_contig_2,True,597,TRA,TRAV5D-4,None,TRAJ49,TRAC,True,True,CAAREAGYQNFYF,TGTGCTGCAAGGGAGGCGGGTTACCAGAACTTCTATTTT,33458,12,clonotype94,clonotype94_consensus_1 -TAAACCGGTGTTAAGA-1,True,TAAACCGGTGTTAAGA-1_contig_3,True,443,TRA,None,None,TRAJ41,TRAC,False,False,None,None,6154,1,clonotype94,None -TAAGCGTCATTCTCAT-1,True,TAAGCGTCATTCTCAT-1_contig_1,True,583,TRA,TRAV12D-2,None,TRAJ17,TRAC,True,True,CDPTNSAGNKLTF,TGTGACCCTACTAACAGTGCAGGGAACAAGCTAACTTTT,9674,2,clonotype95,clonotype95_consensus_2 -TAAGCGTCATTCTCAT-1,True,TAAGCGTCATTCTCAT-1_contig_2,True,521,TRB,TRBV13-1,None,TRBJ2-2,TRBC2,True,True,CASSDAGGDTGQLYF,TGTGCCAGCAGTGATGCAGGGGGTGACACCGGGCAGCTCTACTTT,45494,7,clonotype95,clonotype95_consensus_1 -TAAGCGTCATTCTCAT-1,True,TAAGCGTCATTCTCAT-1_contig_3,True,558,TRA,TRAV5-1,None,TRAJ2,TRAC,True,True,CSASMDTGGLSGKLTF,TGCTCAGCAAGTATGGATACTGGAGGACTAAGTGGTAAATTAACATTC,5894,2,clonotype95,clonotype95_consensus_3 -TAAGCGTCATTCTCAT-1,True,TAAGCGTCATTCTCAT-1_contig_4,True,610,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,14844,2,clonotype95,None -TAAGTGCAGAGTGACC-1,True,TAAGTGCAGAGTGACC-1_contig_1,True,562,TRB,TRBV1,None,TRBJ1-2,TRBC1,True,True,CTCSAGNSDYTF,TGCACCTGCAGTGCAGGGAACTCCGACTACACCTTC,15994,4,clonotype96,clonotype96_consensus_2 -TAAGTGCAGAGTGACC-1,True,TAAGTGCAGAGTGACC-1_contig_2,True,539,TRA,TRAV9-1,None,TRAJ43,TRAC,True,True,CAVLNNNNAPRF,TGTGCTGTCCTCAATAACAACAATGCCCCACGATTT,5778,2,clonotype96,clonotype96_consensus_1 -TAAGTGCAGAGTGACC-1,True,TAAGTGCAGAGTGACC-1_contig_3,True,309,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,41500,7,clonotype96,None -TAAGTGCAGAGTGACC-1,True,TAAGTGCAGAGTGACC-1_contig_4,True,362,TRB,TRBV19,None,TRBJ2-7,TRBC2,True,False,None,None,3896,3,clonotype96,None -TACGGGCTCTTAGAGC-1,True,TACGGGCTCTTAGAGC-1_contig_1,True,521,TRA,TRAV13-1,None,TRAJ6,TRAC,True,True,CAMATSGGNYKPTF,TGTGCTATGGCCACCTCAGGAGGAAACTACAAACCTACGTTT,14060,6,clonotype13,clonotype13_consensus_2 -TACGGGCTCTTAGAGC-1,True,TACGGGCTCTTAGAGC-1_contig_2,True,570,TRB,TRBV20,TRBD1,TRBJ2-7,TRBC2,True,True,CGVPRDRGREQYF,TGTGGTGTCCCCCGGGACAGGGGGCGCGAACAGTACTTC,11780,7,clonotype13,clonotype13_consensus_3 -TACGGGCTCTTAGAGC-1,True,TACGGGCTCTTAGAGC-1_contig_3,True,515,TRB,TRBV29,None,TRBJ2-7,TRBC2,True,True,CASSGDRGHEQYF,TGTGCTAGCAGTGGGGACAGGGGTCATGAACAGTACTTC,41492,18,clonotype13,clonotype13_consensus_1 -TACGGGCTCTTAGAGC-1,True,TACGGGCTCTTAGAGC-1_contig_4,True,557,TRA,TRAV4-3,None,TRAJ15,TRAC,True,False,None,None,11180,5,clonotype13,None -TACTCGCGTGCAGGTA-1,True,TACTCGCGTGCAGGTA-1_contig_1,True,514,TRB,TRBV13-1,None,TRBJ1-3,TRBC1,True,True,CASSDLGNSGNTLYF,TGTGCCAGCAGTGATCTGGGGAATTCTGGAAATACGCTCTATTTT,70978,21,clonotype97,clonotype97_consensus_1 -TAGACCATCCAAACAC-1,True,TAGACCATCCAAACAC-1_contig_1,True,571,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-4,TRBC1,True,True,CASGDAGEANERLFF,TGTGCCAGCGGTGATGCCGGGGAAGCCAACGAAAGATTATTTTTC,54426,8,clonotype98,clonotype98_consensus_1 -TAGACCATCCAAACAC-1,True,TAGACCATCCAAACAC-1_contig_2,True,538,TRA,TRAV11,None,TRAJ18,TRAC,True,True,CVVGDRGSALGRLHF,TGTGTGGTGGGCGATAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,5774,1,clonotype98,clonotype98_consensus_2 -TAGACCATCCAAACAC-1,True,TAGACCATCCAAACAC-1_contig_3,True,510,TRA,TRAV12-1,None,TRAJ21,TRAC,True,False,CPVLLCSESPNYNVLYF,TGCCCTGTACTACTGTGCTCTGAGTCGCCTAATTACAACGTGCTTTACTTC,7552,1,clonotype98,None -TAGGCATAGGCCCTCA-1,True,TAGGCATAGGCCCTCA-1_contig_1,True,660,TRB,TRBV2,None,TRBJ1-1,TRBC1,True,True,CASSQEEGANTEVFF,TGTGCCAGCAGCCAAGAGGAGGGTGCAAACACAGAAGTCTTCTTT,17632,6,clonotype6,clonotype6_consensus_2 -TAGGCATAGGCCCTCA-1,True,TAGGCATAGGCCCTCA-1_contig_2,True,548,TRA,TRAV16N,None,TRAJ30,TRAC,True,True,CAMREGRANAYKVIF,TGTGCTATGAGAGAGGGCCGGGCAAATGCTTACAAAGTCATCTTT,18706,4,clonotype6,clonotype6_consensus_1 -TAGGCATAGGCCCTCA-1,True,TAGGCATAGGCCCTCA-1_contig_3,True,332,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,31648,10,clonotype6,None -TAGGCATAGGCCCTCA-1,True,TAGGCATAGGCCCTCA-1_contig_4,True,388,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,8546,2,clonotype6,None -TCAGATGTCCGGGTGT-1,True,TCAGATGTCCGGGTGT-1_contig_1,True,557,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-2,TRBC1,True,True,CASGDNRDSDYTF,TGTGCCAGCGGTGATAACAGGGACTCCGACTACACCTTC,75410,6,clonotype99,clonotype99_consensus_1 -TCAGGATAGCTAGTCT-1,True,TCAGGATAGCTAGTCT-1_contig_1,True,678,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSIGGASNERLFF,TGTGCCAGCAGTATAGGGGGGGCGTCCAACGAAAGATTATTTTTC,68580,17,clonotype10,clonotype10_consensus_2 -TCAGGATAGCTAGTCT-1,True,TCAGGATAGCTAGTCT-1_contig_2,True,538,TRA,TRAV13-1,None,TRAJ53,TRAC,True,True,CAILSGGSNYKLTF,TGTGCTATCCTCAGTGGAGGCAGCAATTACAAACTGACATTT,5434,3,clonotype10,clonotype10_consensus_1 -TCAGGATGTGCACCAC-1,True,TCAGGATGTGCACCAC-1_contig_1,True,501,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,24670,19,clonotype2,clonotype2_consensus_2 -TCAGGATGTGCACCAC-1,True,TCAGGATGTGCACCAC-1_contig_2,True,715,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,3452,3,clonotype2,clonotype2_consensus_1 -TCAGGATGTGCACCAC-1,True,TCAGGATGTGCACCAC-1_contig_3,True,416,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,5786,3,clonotype2,None -TCAGGATGTGCACCAC-1,True,TCAGGATGTGCACCAC-1_contig_4,True,598,TRA,TRAV3-1,None,TRAJ22,TRAC,True,False,CAVSIFW,TGCGCAGTCAGCATCTTCTGG,2494,5,clonotype2,None -TCAGGATGTGCACCAC-1,True,TCAGGATGTGCACCAC-1_contig_5,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,27044,16,clonotype2,None -TCAGGATGTGCACCAC-1,True,TCAGGATGTGCACCAC-1_contig_6,True,545,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,14192,11,clonotype2,None -TCGGGACGTGACGCCT-1,True,TCGGGACGTGACGCCT-1_contig_1,True,522,TRB,TRBV5,None,TRBJ2-1,TRBC2,True,True,CASSQGQGDYAEQFF,TGTGCCAGCAGCCAAGGACAGGGGGACTATGCTGAGCAGTTCTTC,27158,9,clonotype100,clonotype100_consensus_2 -TCGGGACGTGACGCCT-1,True,TCGGGACGTGACGCCT-1_contig_2,True,699,TRA,TRAV9D-2,None,TRAJ43,TRAC,True,True,CAVGNNNAPRF,TGTGCTGTGGGAAACAACAATGCCCCACGATTT,13382,10,clonotype100,clonotype100_consensus_1 -TCGGGACGTGACGCCT-1,True,TCGGGACGTGACGCCT-1_contig_3,True,507,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,20020,6,clonotype100,clonotype100_consensus_3 -TCGGGACGTGACGCCT-1,True,TCGGGACGTGACGCCT-1_contig_4,True,621,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,15176,4,clonotype100,None -TCGTAGACATTTGCTT-1,True,TCGTAGACATTTGCTT-1_contig_1,True,576,TRB,TRBV13-3,None,TRBJ2-1,TRBC2,True,True,CASSDDWGSYAEQFF,TGTGCCAGCAGTGATGACTGGGGGAGCTATGCTGAGCAGTTCTTC,18000,4,clonotype101,clonotype101_consensus_1 -TCGTAGACATTTGCTT-1,True,TCGTAGACATTTGCTT-1_contig_2,True,526,TRB,TRBV14,None,TRBJ2-2,TRBC2,True,True,CASSPRDRENTGQLYF,TGTGCCAGCAGCCCCCGGGACAGGGAAAACACCGGGCAGCTCTACTTT,31136,8,clonotype101,clonotype101_consensus_2 -TCGTAGACATTTGCTT-1,True,TCGTAGACATTTGCTT-1_contig_3,True,597,TRA,TRAV14D-3-DV8,None,TRAJ57,TRAC,True,True,CAASDQGGSAKLIF,TGTGCAGCAAGTGATCAAGGAGGGTCTGCGAAGCTCATCTTT,2952,1,clonotype101,clonotype101_consensus_4 -TCGTAGACATTTGCTT-1,True,TCGTAGACATTTGCTT-1_contig_4,True,538,TRA,TRAV19,None,TRAJ56,TRAC,True,True,CAAGGATGGNNKLTF,TGCGCAGCAGGGGGGGCTACTGGAGGCAATAATAAGCTGACTTTT,12826,2,clonotype101,clonotype101_consensus_3 -TCGTAGACATTTGCTT-1,True,TCGTAGACATTTGCTT-1_contig_5,True,320,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,4568,1,clonotype101,None -TCGTAGACATTTGCTT-1,True,TCGTAGACATTTGCTT-1_contig_6,True,609,TRB,TRBV5,None,TRBJ1-4,TRBC1,True,False,None,None,6856,2,clonotype101,None -TCTGGAACACAACGTT-1,True,TCTGGAACACAACGTT-1_contig_1,True,572,TRA,TRAV14D-3-DV8,None,TRAJ26,TRAC,True,True,CAASYYAQGLTF,TGTGCAGCAAGTTACTATGCCCAGGGATTAACCTTC,1044,1,clonotype102,clonotype102_consensus_2 -TCTGGAACACAACGTT-1,True,TCTGGAACACAACGTT-1_contig_2,True,710,TRB,TRBV19,None,TRBJ1-6,TRBC1,True,True,CASSLRDRENSPLYF,TGTGCCAGCAGTCTCCGGGACAGGGAGAATTCGCCCCTCTACTTT,10986,7,clonotype102,clonotype102_consensus_1 -TCTGGAACACAACGTT-1,True,TCTGGAACACAACGTT-1_contig_3,True,308,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,56808,21,clonotype102,None -TCTGGAACACAACGTT-1,True,TCTGGAACACAACGTT-1_contig_4,True,353,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,2144,1,clonotype102,None -TCTGGAACACAACGTT-1,True,TCTGGAACACAACGTT-1_contig_5,True,448,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,2392,1,clonotype102,None -TGACAACCAACTGGCC-1,True,TGACAACCAACTGGCC-1_contig_1,True,599,TRA,TRAV13-1,None,TRAJ53,TRAC,True,True,CAILSGGSNYKLTF,TGTGCTATCCTCAGTGGAGGCAGCAATTACAAACTGACATTT,35056,10,clonotype10,clonotype10_consensus_1 -TGACAACCAACTGGCC-1,True,TGACAACCAACTGGCC-1_contig_2,True,721,TRB,TRBV19,None,TRBJ1-4,TRBC1,True,True,CASSIGGASNERLFF,TGTGCCAGCAGTATAGGGGGGGCGTCCAACGAAAGATTATTTTTC,9738,5,clonotype10,clonotype10_consensus_2 -TGACAACCAACTGGCC-1,True,TGACAACCAACTGGCC-1_contig_3,True,443,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,19092,2,clonotype10,None -TGACAACCAACTGGCC-1,True,TGACAACCAACTGGCC-1_contig_4,True,306,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,13086,2,clonotype10,None -TGACAACTCGTCTGAA-1,True,TGACAACTCGTCTGAA-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,19898,5,clonotype5,clonotype5_consensus_3 -TGACAACTCGTCTGAA-1,True,TGACAACTCGTCTGAA-1_contig_2,True,721,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,12844,3,clonotype5,clonotype5_consensus_2 -TGACAACTCGTCTGAA-1,True,TGACAACTCGTCTGAA-1_contig_3,True,725,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,3646,2,clonotype5,clonotype5_consensus_1 -TGACAACTCGTCTGAA-1,True,TGACAACTCGTCTGAA-1_contig_4,True,334,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,17314,3,clonotype5,None -TGACAACTCGTCTGAA-1,True,TGACAACTCGTCTGAA-1_contig_5,True,407,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,22012,6,clonotype5,None -TGACTAGGTTCCCGAG-1,True,TGACTAGGTTCCCGAG-1_contig_1,True,549,TRA,TRAV7-3,None,TRAJ12,TRAC,True,True,CAVSRGTGGYKVVF,TGTGCAGTGAGCAGGGGGACTGGAGGCTATAAAGTGGTCTTT,22548,7,clonotype103,clonotype103_consensus_2 -TGACTAGGTTCCCGAG-1,True,TGACTAGGTTCCCGAG-1_contig_2,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCCGGACTGGGGGACTCCTATGAACAGTACTTC,13088,8,clonotype103,clonotype103_consensus_1 -TGACTAGGTTCCCGAG-1,True,TGACTAGGTTCCCGAG-1_contig_3,True,496,TRA,TRAV6-5,None,TRAJ23,TRAC,True,False,None,None,5144,2,clonotype103,None -TGACTAGGTTCCCGAG-1,True,TGACTAGGTTCCCGAG-1_contig_4,True,341,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,36830,8,clonotype103,None -TGAGAGGCAGCTGTGC-1,True,TGAGAGGCAGCTGTGC-1_contig_1,True,628,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSIGGNYAEQFF,TGTGCCAGCAGTATTGGGGGGAACTATGCTGAGCAGTTCTTC,75546,7,clonotype104,clonotype104_consensus_1 -TGATTTCTCATCGCTC-1,True,TGATTTCTCATCGCTC-1_contig_1,True,697,TRA,TRAV9-4,None,TRAJ22,TRAC,True,True,CAVTSSGSWQLIF,TGTGCTGTGACATCTTCTGGCAGCTGGCAACTCATCTTT,59824,9,clonotype3,clonotype3_consensus_1 -TGATTTCTCATCGCTC-1,True,TGATTTCTCATCGCTC-1_contig_2,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGGAACACAGAAGTCTTCTTT,16172,2,clonotype3,clonotype3_consensus_2 -TGATTTCTCATCGCTC-1,True,TGATTTCTCATCGCTC-1_contig_3,True,566,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,1008,1,clonotype3,None -TGCTACCCAGGATTGG-1,True,TGCTACCCAGGATTGG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,49016,8,clonotype4,clonotype4_consensus_2 -TGCTACCCAGGATTGG-1,True,TGCTACCCAGGATTGG-1_contig_2,True,728,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,19014,5,clonotype4,clonotype4_consensus_1 -TGCTACCCAGGATTGG-1,True,TGCTACCCAGGATTGG-1_contig_3,True,498,TRB,TRBV2,None,TRBJ1-1,TRBC1,True,False,None,None,9264,3,clonotype4,None -TGGACGCAGCGATTCT-1,True,TGGACGCAGCGATTCT-1_contig_1,True,518,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASRLGFEQYF,TGTGCCAGCCGACTGGGGTTTGAACAGTACTTC,46518,23,clonotype12,clonotype12_consensus_2 -TGGACGCAGCGATTCT-1,True,TGGACGCAGCGATTCT-1_contig_2,True,591,TRA,TRAV12-3,None,TRAJ49,TRAC,True,True,CALSDPVTGYQNFYF,TGTGCTTTGAGTGACCCTGTCACGGGTTACCAGAACTTCTATTTT,21126,10,clonotype12,clonotype12_consensus_1 -TGGACGCAGCGATTCT-1,True,TGGACGCAGCGATTCT-1_contig_3,True,588,TRA,TRAV12D-1,None,TRAJ57,TRAC,True,False,CALSD,TGTGCTTTGAGTGAT,4362,2,clonotype12,None -TGGACGCAGCGATTCT-1,True,TGGACGCAGCGATTCT-1_contig_4,True,401,TRA,None,None,TRAJ39,TRAC,False,False,None,None,4402,1,clonotype12,None -TGGCGCAAGGACATTA-1,True,TGGCGCAAGGACATTA-1_contig_1,True,518,TRB,TRBV13-1,None,TRBJ1-2,TRBC1,True,True,CASSVTGANSDYTF,TGTGCCAGCAGTGTGACAGGGGCAAACTCCGACTACACCTTC,7886,1,clonotype105,clonotype105_consensus_2 -TGGCGCAAGGACATTA-1,True,TGGCGCAAGGACATTA-1_contig_2,True,537,TRB,TRBV20,None,TRBJ1-1,TRBC1,True,True,CGARGEGTNTEVFF,TGTGGTGCTAGGGGGGAAGGGACAAACACAGAAGTCTTCTTT,11320,2,clonotype105,clonotype105_consensus_1 -TGGCGCAAGGACATTA-1,True,TGGCGCAAGGACATTA-1_contig_3,True,336,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,45198,3,clonotype105,None -TGGCGCAAGGACATTA-1,True,TGGCGCAAGGACATTA-1_contig_4,True,543,TRA,TRAV7D-3,None,TRAJ35,TRAC,False,False,CAVTGFASALTF,TGTGCAGTGACAGGCTTTGCAAGTGCGCTGACATTT,10160,1,clonotype105,None -TGGTTAGCATGGTAGG-1,True,TGGTTAGCATGGTAGG-1_contig_1,True,528,TRB,TRBV17,None,TRBJ1-3,TRBC1,True,True,CASSSWQNSGNTLYF,TGTGCTAGCAGTAGCTGGCAGAATTCTGGAAATACGCTCTATTTT,65000,26,clonotype106,clonotype106_consensus_1 -TGGTTAGCATGGTAGG-1,True,TGGTTAGCATGGTAGG-1_contig_2,True,594,TRA,TRAV7-4,None,TRAJ45,TRAC,True,True,CAASDTGGADRLTF,TGTGCAGCTAGTGATACAGGAGGTGCAGATAGACTCACCTTT,4518,2,clonotype106,clonotype106_consensus_2 -TGGTTAGCATGGTAGG-1,True,TGGTTAGCATGGTAGG-1_contig_3,True,748,Multi,TRDV5,None,TRAJ33,TRAC,True,False,CASGRDSNYQLIW,TGTGCCTCGGGGAGGGATAGCAACTATCAGTTGATCTGG,2930,3,clonotype106,None -TGTGTTTTCGTAGGAG-1,True,TGTGTTTTCGTAGGAG-1_contig_1,True,639,TRA,TRAV7D-2,None,TRAJ32,TRAC,True,True,CAASMGGGSGNKLIF,TGTGCAGCAAGCATGGGGGGGGGCAGTGGCAACAAGCTCATCTTT,42862,4,clonotype107,clonotype107_consensus_2 -TGTGTTTTCGTAGGAG-1,True,TGTGTTTTCGTAGGAG-1_contig_2,True,522,TRB,TRBV31,None,TRBJ2-3,TRBC2,True,True,CAWTGGPAETLYF,TGTGCCTGGACTGGGGGTCCTGCAGAAACGCTGTATTTT,33678,4,clonotype107,clonotype107_consensus_1 -TGTGTTTTCTGTTGAG-1,True,TGTGTTTTCTGTTGAG-1_contig_1,True,516,TRB,TRBV17,None,TRBJ1-6,TRBC1,True,True,CGVQDNSPLYF,TGTGGGGTACAGGATAATTCGCCCCTCTACTTT,66006,3,clonotype108,clonotype108_consensus_1 -TGTGTTTTCTTCCTTC-1,True,TGTGTTTTCTTCCTTC-1_contig_1,True,518,TRB,TRBV13-1,None,TRBJ1-3,TRBC1,True,True,CASSDGGVGNTLYF,TGTGCCAGCAGTGATGGAGGGGTTGGAAATACGCTCTATTTT,30748,2,clonotype109,clonotype109_consensus_1 -TGTGTTTTCTTCCTTC-1,True,TGTGTTTTCTTCCTTC-1_contig_2,True,358,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,21780,1,clonotype109,None -TGTGTTTTCTTCCTTC-1,True,TGTGTTTTCTTCCTTC-1_contig_3,True,330,TRB,None,None,TRBJ1-4,TRBC1,False,False,None,None,25022,5,clonotype109,None -TGTTCCGCAGCGTTCG-1,True,TGTTCCGCAGCGTTCG-1_contig_1,True,521,TRB,TRBV13-1,None,TRBJ2-5,TRBC2,True,True,CASSDTTGGQDTQYF,TGTGCCAGCAGTGATACTACTGGGGGCCAAGACACCCAGTACTTT,78230,8,clonotype21,clonotype21_consensus_1 -TTAGGCAGTATTAGCC-1,True,TTAGGCAGTATTAGCC-1_contig_1,True,516,TRB,TRBV17,None,TRBJ1-6,TRBC1,True,True,CGVQDNSPLYF,TGTGGGGTACAGGATAATTCGCCCCTCTACTTT,60222,60,clonotype8,clonotype8_consensus_3 -TTAGGCAGTATTAGCC-1,True,TTAGGCAGTATTAGCC-1_contig_2,True,558,TRA,TRAV16N,None,TRAJ56,TRAC,True,True,CAMREGPGGNNKLTF,TGTGCTATGAGAGAGGGACCTGGAGGCAATAATAAGCTGACTTTT,3228,3,clonotype8,clonotype8_consensus_2 -TTAGGCAGTATTAGCC-1,True,TTAGGCAGTATTAGCC-1_contig_3,True,555,TRB,TRBV13-3,None,TRBJ1-3,TRBC1,True,True,CASSGDRGGNTLYF,TGTGCCAGCAGTGGGGACAGGGGTGGAAATACGCTCTATTTT,10918,10,clonotype8,clonotype8_consensus_1 -TTATGCTGTAGGCATG-1,True,TTATGCTGTAGGCATG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGGAACACAGAAGTCTTCTTT,41148,4,clonotype3,clonotype3_consensus_2 -TTATGCTGTAGGCATG-1,True,TTATGCTGTAGGCATG-1_contig_2,True,665,TRA,TRAV9-4,None,TRAJ22,TRAC,True,True,CAVTSSGSWQLIF,TGTGCTGTGACATCTTCTGGCAGCTGGCAACTCATCTTT,35314,8,clonotype3,clonotype3_consensus_1 -TTCGAAGTCTCTAAGG-1,True,TTCGAAGTCTCTAAGG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCAGGGACAGGGAACACAGAAGTCTTCTTT,48614,15,clonotype5,clonotype5_consensus_3 -TTCGAAGTCTCTAAGG-1,True,TTCGAAGTCTCTAAGG-1_contig_2,True,726,TRA,TRAV9-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTGACTAACAGTGCAGGGAACAAGCTAACTTTT,5956,3,clonotype5,clonotype5_consensus_2 -TTCGAAGTCTCTAAGG-1,True,TTCGAAGTCTCTAAGG-1_contig_3,True,726,TRA,TRAV9-4,None,TRAJ7,TRAC,True,True,CAVRDYSNNRLTL,TGTGCTGTGAGGGACTACAGCAACAACAGACTTACTTTG,5176,2,clonotype5,clonotype5_consensus_1 -TTCGAAGTCTCTAAGG-1,True,TTCGAAGTCTCTAAGG-1_contig_4,True,365,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,17558,3,clonotype5,None -TTTATGCAGCGTGAGT-1,True,TTTATGCAGCGTGAGT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCCGGACAGGGGAACACAGAAGTCTTCTTT,64736,9,clonotype110,clonotype110_consensus_1 -TTTATGCAGCGTGAGT-1,True,TTTATGCAGCGTGAGT-1_contig_2,True,429,TRA,TRAV9-4,None,TRAJ17,TRAC,True,False,CALTNSAGNKLTF,TGTGCTCTTACTAACAGTGCAGGGAACAAGCTAACTTTT,13444,1,clonotype110,None diff --git a/tests/testthat/fixtures/Chariou/h5files/SCAF1717_5_1_filtered_contig_annotations.csv b/tests/testthat/fixtures/Chariou/h5files/SCAF1717_5_1_filtered_contig_annotations.csv deleted file mode 100644 index 1a08201..0000000 --- a/tests/testthat/fixtures/Chariou/h5files/SCAF1717_5_1_filtered_contig_annotations.csv +++ /dev/null @@ -1,186 +0,0 @@ -barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id -AAAGCAAAGCTGCCCA-1,True,AAAGCAAAGCTGCCCA-1_contig_1,True,568,TRB,TRBV1,None,TRBJ1-5,TRBC1,True,True,CTCSGRDNNQAPLF,TGCACCTGCAGTGGCCGGGACAACAACCAGGCTCCGCTTTTT,69996,9,clonotype2,clonotype2_consensus_1 -AAAGCAAAGCTGCCCA-1,True,AAAGCAAAGCTGCCCA-1_contig_2,True,543,TRA,TRAV7D-2,None,TRAJ49,TRAC,True,True,CADTGYQNFYF,TGTGCAGACACGGGTTACCAGAACTTCTATTTT,9170,2,clonotype2,clonotype2_consensus_2 -AAAGCAACATATGAGA-1,True,AAAGCAACATATGAGA-1_contig_1,True,562,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSADRYEQYF,TGCACCTGCAGTGCAGACAGGTATGAACAGTACTTC,43352,3,clonotype3,clonotype3_consensus_1 -AAAGCAACATATGAGA-1,True,AAAGCAACATATGAGA-1_contig_2,True,391,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,32230,3,clonotype3,None -AAAGTAGGTATTCGTG-1,True,AAAGTAGGTATTCGTG-1_contig_1,True,714,TRB,TRBV2,None,TRBJ1-5,TRBC1,True,True,CASSQERGRHQAPLF,TGTGCCAGCAGCCAAGAGAGGGGAAGGCACCAGGCTCCGCTTTTT,39804,3,clonotype4,clonotype4_consensus_1 -AAAGTAGGTATTCGTG-1,True,AAAGTAGGTATTCGTG-1_contig_2,True,322,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,20470,3,clonotype4,None -AACTGGTCAAGCGTAG-1,True,AACTGGTCAAGCGTAG-1_contig_1,True,523,TRA,TRAV7D-2,None,TRAJ21,TRAC,True,True,CAASRGYNVLYF,TGTGCAGCAAGCAGAGGATACAACGTGCTTTACTTC,168,2,clonotype5,clonotype5_consensus_1 -AACTGGTCAAGCGTAG-1,True,AACTGGTCAAGCGTAG-1_contig_2,True,558,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGDEWVQDTQYF,TGTGCCAGCGGTGATGAGTGGGTCCAAGACACCCAGTACTTT,674,6,clonotype5,clonotype5_consensus_2 -ACACCGGTCAGCGACC-1,True,ACACCGGTCAGCGACC-1_contig_1,True,528,TRA,TRAV6N-7,None,TRAJ39,TRAC,True,True,CALGDNAGAKLTF,TGTGCTCTGGGTGATAATGCAGGTGCCAAGCTCACATTC,61284,5,clonotype6,clonotype6_consensus_1 -ACACTGAAGGGTCTCC-1,True,ACACTGAAGGGTCTCC-1_contig_1,True,564,TRB,TRBV20,TRBD1,TRBJ1-4,TRBC1,True,True,CGAGTGGVNERLFF,TGTGGTGCCGGGACAGGGGGCGTCAACGAAAGATTATTTTTC,31858,2,clonotype7,clonotype7_consensus_2 -ACACTGAAGGGTCTCC-1,True,ACACTGAAGGGTCTCC-1_contig_2,True,588,TRA,TRAV7-4,None,TRAJ49,TRAC,True,True,CAENTGYQNFYF,TGTGCAGAGAACACGGGTTACCAGAACTTCTATTTT,21568,2,clonotype7,clonotype7_consensus_1 -ACACTGAAGGGTCTCC-1,True,ACACTGAAGGGTCTCC-1_contig_3,True,362,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,23310,3,clonotype7,None -ACACTGAAGTGTTGAA-1,True,ACACTGAAGTGTTGAA-1_contig_1,True,518,TRA,TRAV6-4,None,TRAJ17,TRAC,True,True,CAQNSAGNKLTF,TGTGCTCAGAACAGTGCAGGGAACAAGCTAACTTTT,16502,5,clonotype8,clonotype8_consensus_2 -ACACTGAAGTGTTGAA-1,True,ACACTGAAGTGTTGAA-1_contig_2,True,568,TRB,TRBV1,None,TRBJ2-2,TRBC2,True,True,CTCSAQGDTGQLYF,TGCACCTGCAGTGCACAGGGGGACACCGGGCAGCTCTACTTT,54500,12,clonotype8,clonotype8_consensus_1 -ACACTGAAGTGTTGAA-1,True,ACACTGAAGTGTTGAA-1_contig_3,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,6724,1,clonotype8,None -ACATCAGAGAGGGATA-1,True,ACATCAGAGAGGGATA-1_contig_1,True,571,TRB,TRBV1,None,TRBJ2-5,TRBC2,True,True,CTCSARDRVKDTQYF,TGCACCTGCAGTGCCCGGGACAGGGTTAAAGACACCCAGTACTTT,802,8,clonotype9,clonotype9_consensus_1 -ACATCAGAGAGGGATA-1,True,ACATCAGAGAGGGATA-1_contig_2,True,419,TRA,None,None,TRAJ32,TRAC,False,False,None,None,84,1,clonotype9,None -ACATCAGAGAGGGATA-1,True,ACATCAGAGAGGGATA-1_contig_3,True,570,Multi,TRDV1,None,TRAJ50,TRAC,True,False,CGGKAFASSSFSKLVF,TGTGGAGGGAAAGCTTTCGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,326,5,clonotype9,None -ACCTTTAAGCCAGTAG-1,True,ACCTTTAAGCCAGTAG-1_contig_1,True,570,TRB,TRBV13-3,None,TRBJ2-2,TRBC2,True,True,CASSDAGTGVLNTGQLYF,TGTGCCAGCAGTGATGCGGGGACTGGGGTCCTAAACACCGGGCAGCTCTACTTT,30230,4,clonotype10,clonotype10_consensus_2 -ACCTTTAAGCCAGTAG-1,True,ACCTTTAAGCCAGTAG-1_contig_2,True,580,TRA,TRAV12D-2,None,TRAJ43,TRAC,True,True,CALSNNNNAPRF,TGTGCTCTGAGCAATAACAACAATGCCCCACGATTT,45238,6,clonotype10,clonotype10_consensus_1 -ACCTTTAAGCCAGTAG-1,True,ACCTTTAAGCCAGTAG-1_contig_3,True,518,TRB,TRBV31,None,TRBJ2-4,None,True,False,CAWPGLGGRTLYF,TGTGCCTGGCCGGGACTGGGGGGCAGAACGCTGTATTTT,182,2,clonotype10,None -ACGGGTCCATGTAGTC-1,True,ACGGGTCCATGTAGTC-1_contig_1,True,531,TRA,TRAV6N-7,None,TRAJ32,TRAC,True,True,CALRGRGSGNKLIF,TGTGCTCTGAGAGGCCGGGGCAGTGGCAACAAGCTCATCTTT,41034,3,clonotype11,clonotype11_consensus_2 -ACGGGTCCATGTAGTC-1,True,ACGGGTCCATGTAGTC-1_contig_2,True,516,TRB,TRBV5,None,TRBJ2-2,TRBC2,True,True,CASSHPGLGDTGQLYF,TGTGCCAGCAGCCACCCGGGACTGGGTGACACCGGGCAGCTCTACTTT,21822,2,clonotype11,clonotype11_consensus_1 -ACGGGTCCATGTAGTC-1,True,ACGGGTCCATGTAGTC-1_contig_3,True,306,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,15706,1,clonotype11,None -ACTGAACGTAAGAGAG-1,True,ACTGAACGTAAGAGAG-1_contig_1,True,516,TRB,TRBV5,None,TRBJ2-2,TRBC2,True,True,CASSQDLGQYTGQLYF,TGTGCCAGCAGCCAAGATCTGGGACAGTACACCGGGCAGCTCTACTTT,29054,3,clonotype12,clonotype12_consensus_1 -ACTGAACGTAAGAGAG-1,True,ACTGAACGTAAGAGAG-1_contig_2,True,348,TRB,TRBV31,None,TRBJ1-3,TRBC1,True,False,CLESSGNNSGNTLYF,TGCCTGGAGTCATCAGGGAACAATTCTGGAAATACGCTCTATTTT,9634,5,clonotype12,None -AGAGTGGTCCGATATG-1,True,AGAGTGGTCCGATATG-1_contig_1,True,512,TRB,TRBV13-1,None,TRBJ2-7,TRBC2,True,True,CASSDVGGGQYF,TGTGCCAGCAGTGATGTTGGGGGAGGGCAGTACTTC,49024,3,clonotype13,clonotype13_consensus_1 -AGCATACGTACTTCTT-1,True,AGCATACGTACTTCTT-1_contig_1,True,568,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,True,CTCSAGGEGTEVFF,TGCACCTGCAGTGCAGGGGGCGAAGGCACAGAAGTCTTCTTT,64036,16,clonotype14,clonotype14_consensus_1 -AGCATACGTACTTCTT-1,True,AGCATACGTACTTCTT-1_contig_2,True,528,TRA,TRAV6-3,None,TRAJ31,TRAC,True,True,CAMRDNNNRIFF,TGTGCTATGAGAGATAACAATAACAGAATCTTCTTT,11970,3,clonotype14,clonotype14_consensus_2 -AGGGTGAAGCCACCTG-1,True,AGGGTGAAGCCACCTG-1_contig_1,True,540,TRA,TRAV15-1-DV6-1,None,TRAJ12,TRAC,True,True,CALWELAPGGYKVVF,TGTGCTCTCTGGGAGCTGGCTCCTGGAGGCTATAAAGTGGTCTTT,41732,5,clonotype15,clonotype15_consensus_1 -AGGTCATCATGCTAGT-1,True,AGGTCATCATGCTAGT-1_contig_1,True,526,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASSLWGASSYEQYF,TGTGCCAGCAGCCTCTGGGGGGCAAGCTCCTATGAACAGTACTTC,50532,5,clonotype16,clonotype16_consensus_2 -AGGTCATCATGCTAGT-1,True,AGGTCATCATGCTAGT-1_contig_2,True,543,TRA,TRAV6N-7,None,TRAJ27,TRAC,True,True,CALSLNTNTGKLTF,TGTGCTCTGAGTCTTAACACCAATACAGGCAAATTAACCTTT,26362,2,clonotype16,clonotype16_consensus_1 -AGTCTTTGTCCAGTGC-1,True,AGTCTTTGTCCAGTGC-1_contig_1,True,525,TRA,TRAV6-3,None,TRAJ11,TRAC,True,True,CPDSGYNKLTF,TGCCCTGACTCGGGATACAACAAACTCACTTTT,66516,4,clonotype17,clonotype17_consensus_1 -AGTCTTTGTCCAGTGC-1,True,AGTCTTTGTCCAGTGC-1_contig_2,True,353,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,66,1,clonotype17,None -AGTGGGACAATGGATA-1,True,AGTGGGACAATGGATA-1_contig_1,True,518,TRA,TRAV7D-5,None,TRAJ48,TRAC,True,True,CAMKDHGNEKITF,TGTGCAATGAAGGACCATGGAAATGAGAAAATAACTTTT,41990,12,clonotype18,clonotype18_consensus_1 -AGTGGGACAATGGATA-1,True,AGTGGGACAATGGATA-1_contig_2,True,510,TRB,TRBV29,None,TRBJ2-7,TRBC2,True,True,CASSFRIEQYF,TGTGCTAGCAGTTTTCGGATTGAACAGTACTTC,33948,7,clonotype18,clonotype18_consensus_2 -ATCTACTCACATTTCT-1,True,ATCTACTCACATTTCT-1_contig_1,True,524,TRB,TRBV13-1,None,TRBJ2-4,TRBC2,True,True,CASSDAGRGSQNTLYF,TGTGCCAGCAGTGATGCGGGGAGAGGGAGTCAAAACACCTTGTACTTT,43816,6,clonotype19,clonotype19_consensus_1 -ATCTACTCACATTTCT-1,True,ATCTACTCACATTTCT-1_contig_2,True,579,TRA,TRAV12D-2,None,TRAJ18,TRAC,True,True,CALSDRGSALGRLHF,TGTGCTTTGAGTGACAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,22094,22,clonotype19,clonotype19_consensus_2 -ATTGGTGAGTCCGGTC-1,True,ATTGGTGAGTCCGGTC-1_contig_1,True,524,TRB,TRBV13-1,None,TRBJ2-2,TRBC2,True,True,CASSDARDRNTGQLYF,TGTGCCAGCAGTGATGCCCGGGACAGAAACACCGGGCAGCTCTACTTT,17392,2,clonotype1,clonotype1_consensus_1 -ATTGGTGAGTCCGGTC-1,True,ATTGGTGAGTCCGGTC-1_contig_2,True,406,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,28482,3,clonotype1,None -ATTGGTGAGTCCGGTC-1,True,ATTGGTGAGTCCGGTC-1_contig_3,True,333,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,13790,1,clonotype1,None -ATTGGTGAGTCCGGTC-1,True,ATTGGTGAGTCCGGTC-1_contig_4,True,577,TRA,TRAV16N,None,TRAJ13,TRAC,True,False,None,None,18974,3,clonotype1,None -ATTGGTGGTCCGTGAC-1,True,ATTGGTGGTCCGTGAC-1_contig_1,True,523,TRB,TRBV13-3,None,TRBJ2-1,TRBC2,True,True,CASSIRENYAEQFF,TGTGCCAGCAGCATCCGGGAGAACTATGCTGAGCAGTTCTTC,77200,8,clonotype20,clonotype20_consensus_1 -CAAGAAACACGGATAG-1,True,CAAGAAACACGGATAG-1_contig_1,True,516,TRB,TRBV31,None,TRBJ2-5,TRBC2,True,True,CAWTLTGGQDTQYF,TGTGCCTGGACCCTGACAGGGGGCCAAGACACCCAGTACTTT,61808,5,clonotype21,clonotype21_consensus_2 -CAAGAAACACGGATAG-1,True,CAAGAAACACGGATAG-1_contig_2,True,561,TRA,TRAV15D-1-DV6D-1,None,TRAJ16,TRAC,True,True,CALWELECTSSGQKLVF,TGTGCTCTCTGGGAGCTAGAGTGCACTTCAAGTGGCCAGAAGCTGGTTTTT,16838,2,clonotype21,clonotype21_consensus_1 -CACACTCAGATGGGTC-1,True,CACACTCAGATGGGTC-1_contig_1,True,671,TRB,TRBV3,None,TRBJ1-4,TRBC1,True,True,CASSFRANERLFF,TGTGCCAGCAGCTTCAGGGCCAACGAAAGATTATTTTTC,67836,4,clonotype22,clonotype22_consensus_1 -CACACTCAGATGGGTC-1,True,CACACTCAGATGGGTC-1_contig_2,True,402,TRA,TRAV11,None,TRAJ18,TRAC,True,False,CVVGDRGSALGRLHF,TGTGTGGTGGGAGATAGAGGTTCAGCCTTAGGGAGGCTGCATTTT,6492,3,clonotype22,None -CACAGGCCATCGTCGG-1,True,CACAGGCCATCGTCGG-1_contig_1,True,507,TRA,TRAV21-DV12,None,TRAJ39,TRAC,True,True,CILRVFNNAGAKLTF,TGTATCCTGAGAGTCTTTAATAATGCAGGTGCCAAGCTCACATTC,28504,12,clonotype23,clonotype23_consensus_2 -CACAGGCCATCGTCGG-1,True,CACAGGCCATCGTCGG-1_contig_2,True,568,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSADRWGLEQYF,TGCACCTGCAGTGCAGATCGTTGGGGGCTTGAACAGTACTTC,49776,27,clonotype23,clonotype23_consensus_1 -CAGAATCAGACAGGCT-1,True,CAGAATCAGACAGGCT-1_contig_1,True,566,TRA,TRAV16N,None,TRAJ39,TRAC,True,True,CAMREGGNAGAKLTF,TGTGCTATGAGAGAGGGCGGTAATGCAGGTGCCAAGCTCACATTC,9304,2,clonotype24,clonotype24_consensus_2 -CAGAATCAGACAGGCT-1,True,CAGAATCAGACAGGCT-1_contig_2,True,594,TRB,TRBV5,None,TRBJ1-4,TRBC1,True,True,CASSQDWASNERLFF,TGTGCCAGCAGCCAAGATTGGGCTTCCAACGAAAGATTATTTTTC,65952,9,clonotype24,clonotype24_consensus_1 -CAGCAGCGTGGTACAG-1,True,CAGCAGCGTGGTACAG-1_contig_1,True,562,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSADSYEQYF,TGCACCTGCAGTGCAGACTCCTATGAACAGTACTTC,63176,5,clonotype25,clonotype25_consensus_1 -CAGTCCTAGCCACGCT-1,True,CAGTCCTAGCCACGCT-1_contig_1,True,591,TRA,TRAV7-4,None,TRAJ27,TRAC,True,True,CAASGPNTGKLTF,TGTGCAGCTAGTGGCCCCAATACAGGCAAATTAACCTTT,38924,4,clonotype26,clonotype26_consensus_1 -CAGTCCTAGCCACGCT-1,True,CAGTCCTAGCCACGCT-1_contig_2,True,710,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSIAGANYAEQFF,TGTGCCAGCAGTATAGCCGGGGCGAACTATGCTGAGCAGTTCTTC,37564,5,clonotype26,clonotype26_consensus_2 -CAGTCCTGTTCACCTC-1,True,CAGTCCTGTTCACCTC-1_contig_1,True,591,TRA,TRAV7D-4,None,TRAJ45,TRAC,True,True,CAAITGGADRLTF,TGTGCAGCTATTACAGGAGGTGCAGATAGACTCACCTTT,28056,2,clonotype27,clonotype27_consensus_1 -CAGTCCTGTTCACCTC-1,True,CAGTCCTGTTCACCTC-1_contig_2,True,522,TRB,TRBV5,None,TRBJ2-3,TRBC2,True,True,CASSRDWNSAETLYF,TGTGCCAGCAGCCGAGACTGGAATAGTGCAGAAACGCTGTATTTT,22652,3,clonotype27,clonotype27_consensus_2 -CAGTCCTGTTCACCTC-1,True,CAGTCCTGTTCACCTC-1_contig_3,True,511,TRA,TRAV6-5,None,TRAJ42,TRAC,True,False,CTTVLWVIGGSNAKLTF,TGTACTACTGTGCTCTGGGTGATAGGAGGAAGCAATGCAAAGCTAACCTTC,24982,2,clonotype27,None -CCCAGTTTCTGGCGTG-1,True,CCCAGTTTCTGGCGTG-1_contig_1,True,524,TRB,TRBV13-1,None,TRBJ2-2,TRBC2,True,True,CASSDARDRNTGQLYF,TGTGCCAGCAGTGATGCCCGGGACAGAAACACCGGGCAGCTCTACTTT,21512,4,clonotype1,clonotype1_consensus_1 -CCCAGTTTCTGGCGTG-1,True,CCCAGTTTCTGGCGTG-1_contig_2,True,422,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,44672,8,clonotype1,None -CCCAGTTTCTGGCGTG-1,True,CCCAGTTTCTGGCGTG-1_contig_3,True,357,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,9012,2,clonotype1,None -CCGGTAGCATTCTCAT-1,True,CCGGTAGCATTCTCAT-1_contig_1,True,715,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSRRTGDKQFF,TGTGCCAGCAGTAGGAGGACAGGGGATAAGCAGTTCTTC,65424,3,clonotype28,clonotype28_consensus_2 -CCGGTAGCATTCTCAT-1,True,CCGGTAGCATTCTCAT-1_contig_2,True,548,TRA,TRAV9-1,None,TRAJ50,TRAC,True,True,CAASKGSSSFSKLVF,TGTGCTGCGAGCAAGGGATCCTCCTCCTTCAGCAAGCTGGTGTTT,5644,1,clonotype28,clonotype28_consensus_1 -CCGGTAGCATTCTCAT-1,True,CCGGTAGCATTCTCAT-1_contig_3,True,558,TRA,TRAV12-1,None,TRAJ45,TRAC,True,False,CPVLLCSYTGGADRLTF,TGCCCTGTACTACTGTGCTCTTATACAGGAGGTGCAGATAGACTCACCTTT,5816,2,clonotype28,None -CCGTGGATCGGTTAAC-1,True,CCGTGGATCGGTTAAC-1_contig_1,True,701,TRB,TRBV19,None,TRBJ2-3,TRBC2,True,True,CASRTQGIGAETLYF,TGTGCCAGCAGGACTCAGGGGATCGGTGCAGAAACGCTGTATTTT,43996,4,clonotype29,clonotype29_consensus_1 -CCGTGGATCGGTTAAC-1,True,CCGTGGATCGGTTAAC-1_contig_2,True,533,TRA,TRAV6N-7,None,TRAJ53,TRAC,True,True,CALGGGGSNYKLTF,TGTGCTCTGGGTGGAGGAGGCAGCAATTACAAACTGACATTT,14968,1,clonotype29,clonotype29_consensus_2 -CCGTGGATCGGTTAAC-1,True,CCGTGGATCGGTTAAC-1_contig_3,True,432,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,20256,1,clonotype29,None -CGATCGGGTCCAGTTA-1,True,CGATCGGGTCCAGTTA-1_contig_1,True,513,TRA,TRAV7-3,None,TRAJ2,TRAC,True,True,CAVSTGGLSGKLTF,TGTGCAGTGAGTACTGGAGGACTAAGTGGTAAATTAACATTC,7642,3,clonotype30,clonotype30_consensus_2 -CGATCGGGTCCAGTTA-1,True,CGATCGGGTCCAGTTA-1_contig_2,True,698,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASSIWGSNTEVFF,TGTGCCAGCAGTATTTGGGGGTCAAACACAGAAGTCTTCTTT,41092,8,clonotype30,clonotype30_consensus_1 -CGATCGGGTCCAGTTA-1,True,CGATCGGGTCCAGTTA-1_contig_3,True,717,TRB,None,None,TRBJ2-4,TRBC2,False,False,None,None,29892,7,clonotype30,None -CGATTGAGTGTTGAGG-1,True,CGATTGAGTGTTGAGG-1_contig_1,True,618,TRB,TRBV20,None,TRBJ1-1,TRBC1,True,True,CGARAGANTEVFF,TGTGGTGCTAGGGCCGGTGCAAACACAGAAGTCTTCTTT,63236,3,clonotype31,clonotype31_consensus_1 -CGCGTTTCATTACCTT-1,True,CGCGTTTCATTACCTT-1_contig_1,True,573,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-5,TRBC1,True,True,CASGDQGRNQAPLF,TGTGCCAGCGGTGATCAGGGGAGGAACCAGGCTCCGCTTTTT,57028,11,clonotype32,clonotype32_consensus_1 -CGCGTTTCATTACCTT-1,True,CGCGTTTCATTACCTT-1_contig_2,True,588,TRA,TRAV12-3,None,TRAJ39,TRAC,True,True,CALRNNNAGAKLTF,TGTGCTTTGAGGAATAATAATGCAGGTGCCAAGCTCACATTC,10140,2,clonotype32,clonotype32_consensus_2 -CGTCAGGAGCGAAGGG-1,True,CGTCAGGAGCGAAGGG-1_contig_1,True,556,TRB,TRBV20,None,TRBJ1-1,TRBC1,True,True,CGARGGAPEVFF,TGTGGTGCTAGGGGGGGGGCCCCAGAAGTCTTCTTT,27938,3,clonotype33,clonotype33_consensus_2 -CGTCAGGAGCGAAGGG-1,True,CGTCAGGAGCGAAGGG-1_contig_2,True,509,TRB,TRBV26,None,TRBJ1-1,TRBC1,True,True,CARGINTEVFF,TGTGCCAGAGGGATTAACACAGAAGTCTTCTTT,48616,4,clonotype33,clonotype33_consensus_1 -CGTTCTGTCTCAAACG-1,True,CGTTCTGTCTCAAACG-1_contig_1,True,555,TRA,TRAV7D-5,None,TRAJ48,TRAC,True,True,CAMTDGNEKITF,TGTGCAATGACGGATGGAAATGAGAAAATAACTTTT,34094,8,clonotype34,clonotype34_consensus_2 -CGTTCTGTCTCAAACG-1,True,CGTTCTGTCTCAAACG-1_contig_2,True,520,TRB,TRBV31,None,TRBJ1-1,TRBC1,True,True,CAWSLDNANTEVFF,TGTGCCTGGAGTCTCGACAATGCAAACACAGAAGTCTTCTTT,23288,3,clonotype34,clonotype34_consensus_1 -CGTTCTGTCTCAAACG-1,True,CGTTCTGTCTCAAACG-1_contig_3,True,551,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,16480,4,clonotype34,None -CTAAGACCATCCCATC-1,True,CTAAGACCATCCCATC-1_contig_1,True,558,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASSDNWGYEQYF,TGTGCCAGCAGTGATAACTGGGGTTATGAACAGTACTTC,27436,2,clonotype35,clonotype35_consensus_1 -CTAAGACCATCCCATC-1,True,CTAAGACCATCCCATC-1_contig_2,True,519,TRA,TRAV7D-5,None,TRAJ52,TRAC,True,True,CAITGANTGKLTF,TGTGCAATCACTGGAGCTAACACTGGAAAGCTCACGTTT,13208,1,clonotype35,clonotype35_consensus_2 -CTAAGACCATCCCATC-1,True,CTAAGACCATCCCATC-1_contig_3,True,711,TRB,None,None,TRBJ1-2,TRBC1,False,False,None,None,14742,1,clonotype35,None -CTAAGACCATCCCATC-1,True,CTAAGACCATCCCATC-1_contig_4,True,598,TRA,TRAV7-4,None,TRAJ49,TRAC,True,False,None,None,15182,3,clonotype35,None -CTCCTAGAGTTAGCGG-1,True,CTCCTAGAGTTAGCGG-1_contig_1,True,558,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSDRRGRGGERLFF,TGTGCCAGCAGTGATCGCAGGGGGCGCGGGGGCGAAAGATTATTTTTC,16314,3,clonotype36,clonotype36_consensus_1 -CTCCTAGAGTTAGCGG-1,True,CTCCTAGAGTTAGCGG-1_contig_2,True,414,TRB,None,None,TRBJ1-3,TRBC1,False,False,None,None,16062,2,clonotype36,None -CTCCTAGAGTTAGCGG-1,True,CTCCTAGAGTTAGCGG-1_contig_3,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,20872,3,clonotype36,None -CTCCTAGAGTTAGCGG-1,True,CTCCTAGAGTTAGCGG-1_contig_4,True,498,TRA,TRAV19,None,TRAJ56,TRAC,True,False,CAAGDLLE,TGCGCAGCAGGTGACCTACTGGAG,21474,3,clonotype36,None -CTCGAAAAGCCACTAT-1,True,CTCGAAAAGCCACTAT-1_contig_1,True,542,TRA,TRAV9-1,None,TRAJ27,TRAC,True,True,CAVRNTNTGKLTF,TGTGCTGTGAGGAACACCAATACAGGCAAATTAACCTTT,63534,9,clonotype37,clonotype37_consensus_1 -CTGATCCAGTCAAGCG-1,True,CTGATCCAGTCAAGCG-1_contig_1,True,541,TRB,TRBV10,None,TRBJ1-6,TRBC1,True,True,CASSRGGNSPLYF,TGTGCCAGCTCAAGGGGGGGGAATTCGCCCCTCTACTTT,18922,1,clonotype38,clonotype38_consensus_1 -CTGATCCAGTCAAGCG-1,True,CTGATCCAGTCAAGCG-1_contig_2,True,623,TRA,TRAV5D-4,None,TRAJ56,TRAC,True,True,CAASRTGGNNKLTF,TGTGCTGCAAGTAGGACTGGAGGCAATAATAAGCTGACTTTT,58300,4,clonotype38,clonotype38_consensus_2 -CTGGTCTAGTACGACG-1,True,CTGGTCTAGTACGACG-1_contig_1,True,530,TRA,TRAV6N-7,None,TRAJ50,TRAC,True,True,CALGEPSSFSKLVF,TGTGCTCTGGGTGAACCCTCCTCCTTCAGCAAGCTGGTGTTT,47632,5,clonotype39,clonotype39_consensus_2 -CTGGTCTAGTACGACG-1,True,CTGGTCTAGTACGACG-1_contig_2,True,547,TRB,TRBV10,None,TRBJ1-4,TRBC1,True,True,CASSTGQFSNERLFF,TGTGCCAGCAGCACGGGACAGTTTTCCAACGAAAGATTATTTTTC,29094,4,clonotype39,clonotype39_consensus_1 -CTTAACTAGTGTACCT-1,True,CTTAACTAGTGTACCT-1_contig_1,True,562,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGASQDTQYF,TGTGCCAGCGGTGCCTCTCAAGACACCCAGTACTTT,56152,8,clonotype40,clonotype40_consensus_1 -CTTAACTAGTGTACCT-1,True,CTTAACTAGTGTACCT-1_contig_2,True,562,TRA,TRAV4-4-DV10,None,TRAJ52,TRAC,True,True,CAAANTGANTGKLTF,TGTGCTGCTGCAAACACTGGAGCTAACACTGGAAAGCTCACGTTT,7032,1,clonotype40,clonotype40_consensus_2 -CTTAACTAGTGTACCT-1,True,CTTAACTAGTGTACCT-1_contig_3,True,690,TRA,TRAV13-4-DV7,None,TRAJ49,TRAC,True,False,None,None,11962,1,clonotype40,None -CTTTGCGCAACAACCT-1,True,CTTTGCGCAACAACCT-1_contig_1,True,524,TRA,TRAV6D-4,None,TRAJ22,TRAC,True,True,CALVESSGSWQLIF,TGTGCTCTGGTTGAGTCTTCTGGCAGCTGGCAACTCATCTTT,19270,3,clonotype41,clonotype41_consensus_2 -CTTTGCGCAACAACCT-1,True,CTTTGCGCAACAACCT-1_contig_2,True,657,TRB,TRBV2,None,TRBJ2-7,TRBC2,True,True,CASSQEGQGRNEQYF,TGTGCCAGCAGCCAAGAGGGACAGGGGAGGAATGAACAGTACTTC,23990,3,clonotype41,clonotype41_consensus_1 -CTTTGCGCAACAACCT-1,True,CTTTGCGCAACAACCT-1_contig_3,True,510,TRB,None,None,TRBJ1-6,TRBC1,False,False,None,None,33468,3,clonotype41,None -GAAATGAGTTTGACAC-1,True,GAAATGAGTTTGACAC-1_contig_1,True,660,TRA,TRAV5D-4,None,TRAJ45,TRAC,True,True,CAAINTGGADRLTF,TGTGCTGCGATCAATACAGGAGGTGCAGATAGACTCACCTTT,47380,5,clonotype42,clonotype42_consensus_2 -GAAATGAGTTTGACAC-1,True,GAAATGAGTTTGACAC-1_contig_2,True,519,TRB,TRBV5,None,TRBJ2-4,TRBC2,True,True,CASSHWASQNTLYF,TGTGCCAGCAGCCACTGGGCTAGTCAAAACACCTTGTACTTT,31490,2,clonotype42,clonotype42_consensus_1 -GACGCGTCAGACGCAA-1,True,GACGCGTCAGACGCAA-1_contig_1,True,530,TRA,TRAV16N,None,TRAJ27,TRAC,True,True,CAMREGNTNTGKLTF,TGTGCTATGAGAGAGGGCAACACCAATACAGGCAAATTAACCTTT,19732,1,clonotype43,clonotype43_consensus_1 -GACGCGTCAGACGCAA-1,True,GACGCGTCAGACGCAA-1_contig_2,True,640,TRB,TRBV1,None,TRBJ1-2,TRBC1,True,True,CTCSALASNSDYTF,TGCACCTGCAGTGCCCTGGCATCAAACTCCGACTACACCTTC,16296,2,clonotype43,clonotype43_consensus_2 -GACGCGTCAGACGCAA-1,True,GACGCGTCAGACGCAA-1_contig_3,True,559,TRA,TRAV11,None,TRAJ27,TRAC,True,True,CVVVLNTNTGKLTF,TGTGTGGTGGTCCTTAACACCAATACAGGCAAATTAACCTTT,20348,1,clonotype43,clonotype43_consensus_3 -GACGCGTCAGACGCAA-1,True,GACGCGTCAGACGCAA-1_contig_4,True,718,TRB,None,None,TRBJ2-5,TRBC2,False,False,None,None,22412,2,clonotype43,None -GATCGATTCTTGACGA-1,True,GATCGATTCTTGACGA-1_contig_1,True,518,TRA,TRAV6D-4,None,TRAJ31,TRAC,True,True,CALAPNNNRIFF,TGTGCTCTGGCCCCAAACAATAACAGAATCTTCTTT,25480,3,clonotype44,clonotype44_consensus_1 -GATCGATTCTTGACGA-1,True,GATCGATTCTTGACGA-1_contig_2,True,527,TRB,TRBV5,None,TRBJ1-4,TRBC1,True,True,CASSQDPGQTNERLFF,TGTGCCAGCAGCCAAGATCCGGGACAAACCAACGAAAGATTATTTTTC,12156,2,clonotype44,clonotype44_consensus_2 -GATCGATTCTTGACGA-1,True,GATCGATTCTTGACGA-1_contig_3,True,397,TRA,TRAV6D-7,None,TRAJ44,TRAC,True,False,CALSDLWQWWKTHF,TGTGCTCTGAGTGATCTCTGGCAGTGGTGGAAAACTCACTTT,15256,2,clonotype44,None -GATCGATTCTTGACGA-1,True,GATCGATTCTTGACGA-1_contig_4,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,13294,2,clonotype44,None -GATCGATTCTTGACGA-1,True,GATCGATTCTTGACGA-1_contig_5,True,359,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,12566,1,clonotype44,None -GATCGTAAGAAACCGC-1,True,GATCGTAAGAAACCGC-1_contig_1,True,562,TRA,TRAV7-4,None,TRAJ27,TRAC,True,True,CAASNTNTGKLTF,TGTGCAGCTAGTAACACCAATACAGGCAAATTAACCTTT,33696,6,clonotype45,clonotype45_consensus_1 -GATCGTAAGAAACCGC-1,True,GATCGTAAGAAACCGC-1_contig_2,True,525,TRB,TRBV5,None,TRBJ2-2,TRBC2,True,True,CASSQEGLGNTGQLYF,TGTGCCAGCAGCCAAGAGGGACTGGGAAACACCGGGCAGCTCTACTTT,29574,4,clonotype45,clonotype45_consensus_2 -GCATACACACCCTATC-1,True,GCATACACACCCTATC-1_contig_1,True,601,TRA,TRAV12D-2,None,TRAJ52,TRAC,True,True,CALRGSNTGANTGKLTF,TGTGCTCTGAGGGGTTCTAACACTGGAGCTAACACTGGAAAGCTCACGTTT,34778,5,clonotype46,clonotype46_consensus_2 -GCATACACACCCTATC-1,True,GCATACACACCCTATC-1_contig_2,True,603,TRA,TRAV5D-4,None,TRAJ52,TRAC,True,True,CAARGDTGANTGKLTF,TGTGCTGCAAGAGGGGACACTGGAGCTAACACTGGAAAGCTCACGTTT,24028,4,clonotype46,clonotype46_consensus_3 -GCATACACACCCTATC-1,True,GCATACACACCCTATC-1_contig_3,True,513,TRB,TRBV31,None,TRBJ2-3,TRBC2,True,True,CAWSPRWAGAETLYF,TGTGCCTGGAGTCCCAGGTGGGCCGGGGCAGAAACGCTGTATTTT,15500,2,clonotype46,clonotype46_consensus_1 -GCATACACACCCTATC-1,True,GCATACACACCCTATC-1_contig_4,True,446,TRA,None,None,TRAJ41,TRAC,False,False,None,None,2126,2,clonotype46,None -GCTGGGTGTTACGTCA-1,True,GCTGGGTGTTACGTCA-1_contig_1,True,534,TRB,TRBV17,None,TRBJ1-2,TRBC1,True,True,CASSRESPGTPNSDYTF,TGTGCTAGCAGTAGAGAGAGCCCCGGGACACCAAACTCCGACTACACCTTC,52408,4,clonotype47,clonotype47_consensus_1 -GCTGGGTGTTACGTCA-1,True,GCTGGGTGTTACGTCA-1_contig_2,True,489,TRA,TRAV7-4,None,TRAJ42,TRAC,True,False,CAASEHDSGGSNAKLTF,TGTGCAGCTAGTGAGCATGATTCTGGAGGAAGCAATGCAAAGCTAACCTTC,24862,1,clonotype47,None -GGCGTGTTCACATGCA-1,True,GGCGTGTTCACATGCA-1_contig_1,True,605,TRA,TRAV14D-2,None,TRAJ49,TRAC,True,True,CAANTGYQNFYF,TGTGCAGCAAACACGGGTTACCAGAACTTCTATTTT,14622,3,clonotype48,clonotype48_consensus_2 -GGCGTGTTCACATGCA-1,True,GGCGTGTTCACATGCA-1_contig_2,True,519,TRB,TRBV31,None,TRBJ2-4,TRBC2,True,True,CAWRSSQNTLYF,TGTGCCTGGAGAAGTAGTCAAAACACCTTGTACTTT,64470,11,clonotype48,clonotype48_consensus_1 -GTCATTTGTATGAAAC-1,True,GTCATTTGTATGAAAC-1_contig_1,True,568,TRB,TRBV1,None,TRBJ2-7,TRBC2,True,True,CTCSADRGLYEQYF,TGCACCTGCAGTGCAGACAGGGGGTTATATGAACAGTACTTC,55520,8,clonotype49,clonotype49_consensus_1 -GTCATTTGTATGAAAC-1,True,GTCATTTGTATGAAAC-1_contig_2,True,560,Multi,TRDV2-2,None,TRAJ57,TRAC,True,False,CALMERGWHISEGYELRQGGSAKLIF,TGTGCTCTCATGGAGCGCGGGTGGCACATATCGGAGGGATACGAGCTGCGGCAAGGAGGGTCTGCGAAGCTCATCTTT,19164,3,clonotype49,None -GTCCTCAGTTTACTCT-1,True,GTCCTCAGTTTACTCT-1_contig_1,True,586,TRA,TRAV4-4-DV10,None,TRAJ50,TRAC,True,True,CAAEAASSSFSKLVF,TGTGCTGCTGAGGCCGCATCCTCCTCCTTCAGCAAGCTGGTGTTT,826,13,clonotype50,clonotype50_consensus_2 -GTCCTCAGTTTACTCT-1,True,GTCCTCAGTTTACTCT-1_contig_2,True,519,TRB,TRBV5,TRBD1,TRBJ2-7,TRBC2,True,True,CASSHRDRGLEQYF,TGTGCCAGCAGCCACCGGGACAGGGGGCTTGAACAGTACTTC,228,3,clonotype50,clonotype50_consensus_1 -GTCCTCAGTTTACTCT-1,True,GTCCTCAGTTTACTCT-1_contig_3,True,423,TRB,None,None,TRBJ2-3,TRBC2,False,False,None,None,2030,14,clonotype50,None -GTCTTCGTCCAGATCA-1,True,GTCTTCGTCCAGATCA-1_contig_1,True,568,TRB,TRBV1,None,TRBJ2-1,TRBC2,True,True,CTCSAQVNYAEQFF,TGCACCTGCAGTGCTCAGGTCAACTATGCTGAGCAGTTCTTC,64024,23,clonotype51,clonotype51_consensus_2 -GTCTTCGTCCAGATCA-1,True,GTCTTCGTCCAGATCA-1_contig_2,True,512,TRA,TRAV6D-4,None,TRAJ34,TRAC,True,True,CALDTDKVVF,TGTGCTCTGGATACCGACAAAGTCGTCTTT,11410,4,clonotype51,clonotype51_consensus_1 -GTGCAGCCACAAGACG-1,True,GTGCAGCCACAAGACG-1_contig_1,True,518,TRA,TRAV7D-2,None,TRAJ2,TRAC,True,True,CAASTGGLSGKLTF,TGTGCAGCAAGCACGGGAGGACTAAGTGGTAAATTAACATTC,67990,12,clonotype52,clonotype52_consensus_2 -GTGCAGCCACAAGACG-1,True,GTGCAGCCACAAGACG-1_contig_2,True,572,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGDAGGGDTQYF,TGTGCCAGCGGTGATGCAGGGGGCGGAGACACCCAGTACTTT,11072,2,clonotype52,clonotype52_consensus_1 -GTTACAGAGAGGTACC-1,True,GTTACAGAGAGGTACC-1_contig_1,True,520,TRB,TRBV13-3,None,TRBJ1-2,TRBC1,True,True,CASSERQNSDYTF,TGTGCCAGCAGTGAGAGACAGAACTCCGACTACACCTTC,54776,6,clonotype53,clonotype53_consensus_1 -GTTACAGAGAGGTACC-1,True,GTTACAGAGAGGTACC-1_contig_2,True,579,TRA,TRAV12D-2,None,TRAJ15,TRAC,True,True,CALSDYQGGRALIF,TGTGCTTTGAGTGACTACCAGGGAGGCAGAGCTCTGATATTT,11142,2,clonotype53,clonotype53_consensus_2 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_1,True,512,TRA,TRAV6-5,None,TRAJ5,TRAC,True,True,CALGDTQVVGQLTF,TGTGCTCTGGGTGACACACAGGTTGTGGGGCAGCTCACTTTC,364,10,clonotype54,clonotype54_consensus_1 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_2,True,513,TRB,TRBV31,None,TRBJ1-3,TRBC1,True,True,CAWRGGGGNTLYF,TGTGCCTGGCGGGGGGGGGGAGGAAATACGCTCTATTTT,3084,42,clonotype54,clonotype54_consensus_2 -GTTACAGCATTCGACA-1,True,GTTACAGCATTCGACA-1_contig_3,True,502,TRA,TRAV12-1,None,TRAJ11,TRAC,True,False,CPVLLCSNSGYNKLTF,TGCCCTGTACTACTGTGCTCTAACTCGGGATACAACAAACTCACTTTT,122,2,clonotype54,None -GTTCATTAGGATGTAT-1,True,GTTCATTAGGATGTAT-1_contig_1,True,503,TRA,TRAV6-6,None,TRAJ31,TRAC,True,True,CALGERNRIFF,TGTGCTCTGGGTGAGAGGAACAGAATCTTCTTT,38208,6,clonotype55,clonotype55_consensus_2 -GTTCATTAGGATGTAT-1,True,GTTCATTAGGATGTAT-1_contig_2,True,541,TRB,TRBV12-2+TRBV13-2,None,TRBJ2-5,TRBC2,True,True,CASGGLAQDTQYF,TGTGCCAGCGGGGGACTGGCCCAAGACACCCAGTACTTT,8032,2,clonotype55,clonotype55_consensus_1 -GTTCATTAGGATGTAT-1,True,GTTCATTAGGATGTAT-1_contig_3,True,546,TRA,TRAV6-6,None,TRAJ17,TRAC,True,True,CALSGPNSAGNKLTF,TGTGCTCTGAGTGGACCTAACAGTGCAGGGAACAAGCTAACTTTT,29782,6,clonotype55,clonotype55_consensus_3 -TAAGAGACACCGCTAG-1,True,TAAGAGACACCGCTAG-1_contig_1,True,524,TRA,TRAV6D-4,None,TRAJ26,TRAC,True,True,CALVDYNYAQGLTF,TGTGCTCTGGTTGATTATAACTATGCCCAGGGATTAACCTTC,10508,5,clonotype56,clonotype56_consensus_2 -TAAGAGACACCGCTAG-1,True,TAAGAGACACCGCTAG-1_contig_2,True,565,TRB,TRBV1,None,TRBJ1-1,TRBC1,True,True,CTCSAGEGTEVFF,TGCACCTGCAGTGCCGGGGAAGGCACAGAAGTCTTCTTT,56976,20,clonotype56,clonotype56_consensus_1 -TAAGAGACACCGCTAG-1,True,TAAGAGACACCGCTAG-1_contig_3,True,630,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,9350,5,clonotype56,None -TAAGTGCCAACTGCTA-1,True,TAAGTGCCAACTGCTA-1_contig_1,True,582,TRB,TRBV12-2+TRBV13-2,None,TRBJ1-6,TRBC1,True,True,CASGDEGAHSYNSPLYF,TGTGCCAGCGGTGATGAGGGGGCCCATTCCTATAATTCGCCCCTCTACTTT,58758,8,clonotype57,clonotype57_consensus_1 -TAAGTGCCAACTGCTA-1,True,TAAGTGCCAACTGCTA-1_contig_2,True,903,TRB,TRBV20,None,TRBJ2-7,TRBC2,True,False,None,None,12106,2,clonotype57,None -TACTCATCAGACGCTC-1,True,TACTCATCAGACGCTC-1_contig_1,True,522,TRB,TRBV17,None,TRBJ2-1,TRBC2,True,True,CASRRQGYAEQFF,TGTGCTAGCAGGAGACAGGGCTATGCTGAGCAGTTCTTC,45272,6,clonotype58,clonotype58_consensus_1 -TACTCATCAGACGCTC-1,True,TACTCATCAGACGCTC-1_contig_2,True,531,TRA,TRAV6-3,None,TRAJ33,TRAC,True,True,CAMRDRSNYQLIW,TGTGCTATGAGAGATAGGAGCAACTATCAGTTGATCTGG,32794,4,clonotype58,clonotype58_consensus_2 -TACTTACGTAGCCTCG-1,True,TACTTACGTAGCCTCG-1_contig_1,True,511,TRA,TRAV4-2,None,TRAJ40,TRAC,True,True,CAAYTGNYKYVF,TGTGCTGCTTATACAGGAAACTACAAATACGTCTTT,42280,4,clonotype59,clonotype59_consensus_1 -TACTTACGTAGCCTCG-1,True,TACTTACGTAGCCTCG-1_contig_2,True,370,TRB,TRBV13-2,None,TRBJ2-3,TRBC2,True,False,CASGSGTGAAETLYF,TGTGCCAGCGGGTCCGGGACAGGGGCAGCAGAAACGCTGTATTTT,34624,1,clonotype59,None -TAGCCGGGTTGGTGGA-1,True,TAGCCGGGTTGGTGGA-1_contig_1,True,534,TRB,TRBV13-3,None,TRBJ2-7,TRBC2,True,True,CASSDWTGKTYEQYF,TGTGCCAGCAGTGATTGGACAGGGAAGACCTATGAACAGTACTTC,61316,4,clonotype60,clonotype60_consensus_2 -TAGCCGGGTTGGTGGA-1,True,TAGCCGGGTTGGTGGA-1_contig_2,True,527,TRA,TRAV6-4,None,TRAJ52,TRAC,True,True,CALVDRGANTGKLTF,TGTGCTCTGGTTGATCGGGGAGCTAACACTGGAAAGCTCACGTTT,17816,1,clonotype60,clonotype60_consensus_1 -TAGTTGGAGTGTACCT-1,True,TAGTTGGAGTGTACCT-1_contig_1,True,672,TRB,TRBV19,None,TRBJ1-1,TRBC1,True,True,CASRTGVNTEVFF,TGTGCCAGCAGGACAGGGGTAAACACAGAAGTCTTCTTT,31254,2,clonotype61,clonotype61_consensus_1 -TAGTTGGAGTGTACCT-1,True,TAGTTGGAGTGTACCT-1_contig_2,True,333,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,47520,2,clonotype61,None -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_1,True,543,TRA,TRAV15-1-DV6-1,None,TRAJ33,TRAC,True,True,CALWEPYMDSNYQLIW,TGTGCTCTCTGGGAGCCCTACATGGATAGCAACTATCAGTTGATCTGG,156,2,clonotype62,clonotype62_consensus_1 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_2,True,522,TRB,TRBV5,None,TRBJ2-7,TRBC2,True,True,CASSPGLGDSYEQYF,TGTGCCAGCAGCCCGGGACTGGGGGACTCCTATGAACAGTACTTC,744,7,clonotype62,clonotype62_consensus_2 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_3,True,602,TRA,TRAV14D-2,None,TRAJ33,TRAC,True,False,CALWEPYMDSNYQLIW,TGTGCTCTCTGGGAGCCCTACATGGATAGCAACTATCAGTTGATCTGG,190,3,clonotype62,clonotype62_consensus_1 -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_4,True,309,TRA,None,None,TRAJ11,TRAC,False,False,None,None,164,1,clonotype62,None -TAGTTGGTCCCAAGTA-1,True,TAGTTGGTCCCAAGTA-1_contig_5,True,305,TRA,None,None,TRAJ34,TRAC,False,False,None,None,350,5,clonotype62,None -TATTACCTCCACTCCA-1,True,TATTACCTCCACTCCA-1_contig_1,True,603,TRB,TRBV13-3,None,TRBJ1-4,TRBC1,True,True,CASSDKGRFNERLFF,TGTGCCAGCAGTGATAAGGGGCGTTTCAACGAAAGATTATTTTTC,56988,6,clonotype63,clonotype63_consensus_2 -TATTACCTCCACTCCA-1,True,TATTACCTCCACTCCA-1_contig_2,True,559,TRA,TRAV14D-1,None,TRAJ33,TRAC,True,True,CAASLDSNYQLIW,TGTGCAGCAAGTCTGGATAGCAACTATCAGTTGATCTGG,16764,5,clonotype63,clonotype63_consensus_1 -TCGTAGATCACGCGGT-1,True,TCGTAGATCACGCGGT-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGQGNTEVFF,TGTGCCAGCAGCCCCGGACAGGGGAACACAGAAGTCTTCTTT,1344,12,clonotype64,clonotype64_consensus_1 -TCGTAGATCACGCGGT-1,True,TCGTAGATCACGCGGT-1_contig_2,True,527,TRA,TRAV6N-7,None,TRAJ34,TRAC,True,False,CTTVLFNTDKVVF,TGTACTACTGTGCTCTTCAATACCGACAAAGTCGTCTTT,86,1,clonotype64,None -TCTCTAAAGCCCAACC-1,True,TCTCTAAAGCCCAACC-1_contig_1,True,519,TRB,TRBV17,None,TRBJ2-2,TRBC2,True,True,CASSRQTGQLYF,TGTGCTAGCAGTAGACAAACCGGGCAGCTCTACTTT,49942,8,clonotype65,clonotype65_consensus_1 -TCTCTAAAGCCCAACC-1,True,TCTCTAAAGCCCAACC-1_contig_2,True,635,TRA,TRAV9-4,None,TRAJ32,TRAC,True,False,None,None,28410,3,clonotype65,None -TCTGAGAGTGACAAAT-1,True,TCTGAGAGTGACAAAT-1_contig_1,True,695,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSKTGGAEQFF,TGTGCCAGCAGTAAGACAGGGGGAGCTGAGCAGTTCTTC,55050,9,clonotype66,clonotype66_consensus_1 -TCTGAGAGTGACAAAT-1,True,TCTGAGAGTGACAAAT-1_contig_2,True,564,TRA,TRAV16N,None,TRAJ22,TRAC,True,True,CAMREESSGSWQLIF,TGTGCTATGAGAGAGGAATCTTCTGGCAGCTGGCAACTCATCTTT,22510,2,clonotype66,clonotype66_consensus_2 -TGAAAGAGTGTTGGGA-1,True,TGAAAGAGTGTTGGGA-1_contig_1,True,518,TRA,TRAV7D-5,None,TRAJ52,TRAC,True,True,CAITGANTGKLTF,TGTGCAATCACTGGAGCTAACACTGGAAAGCTCACGTTT,36010,6,clonotype67,clonotype67_consensus_1 -TGACTAGTCGAGAACG-1,True,TGACTAGTCGAGAACG-1_contig_1,True,550,TRA,TRAV10D,None,TRAJ45,TRAC,True,True,CAAGAGGADRLTF,TGTGCAGCTGGGGCAGGAGGTGCAGATAGACTCACCTTT,214,3,clonotype68,clonotype68_consensus_2 -TGACTAGTCGAGAACG-1,True,TGACTAGTCGAGAACG-1_contig_2,True,571,TRB,TRBV1,None,TRBJ2-3,TRBC2,True,True,CTCSADLVSAETLYF,TGCACCTGCAGTGCAGATCTAGTTAGTGCAGAAACGCTGTATTTT,2478,22,clonotype68,clonotype68_consensus_1 -TGAGCCGAGCAGGTCA-1,True,TGAGCCGAGCAGGTCA-1_contig_1,True,508,TRA,TRAV6-5,None,TRAJ49,TRAC,True,True,CALSDPGYQNFYF,TGTGCTCTGAGTGATCCGGGTTACCAGAACTTCTATTTT,41972,6,clonotype69,clonotype69_consensus_1 -TGAGCCGCAGTAAGCG-1,True,TGAGCCGCAGTAAGCG-1_contig_1,True,519,TRB,TRBV5,None,TRBJ1-1,TRBC1,True,True,CASSPGTGNTEVFF,TGTGCCAGCAGCCCCGGGACAGGAAACACAGAAGTCTTCTTT,196,2,clonotype70,clonotype70_consensus_1 -TGAGCCGCAGTAAGCG-1,True,TGAGCCGCAGTAAGCG-1_contig_2,True,666,TRB,None,None,TRBJ2-7,TRBC2,False,False,None,None,838,6,clonotype70,None -TGAGCCGCAGTAAGCG-1,True,TGAGCCGCAGTAAGCG-1_contig_3,True,491,TRA,TRAV12D-2,None,TRAJ17,TRAC,True,False,None,None,186,3,clonotype70,None -TGCCCTACACTTAAGC-1,True,TGCCCTACACTTAAGC-1_contig_1,True,521,TRB,TRBV13-1,None,TRBJ2-2,TRBC2,True,True,CASSDDGADTGQLYF,TGTGCCAGCAGTGATGATGGGGCGGACACCGGGCAGCTCTACTTT,44330,5,clonotype71,clonotype71_consensus_1 -TGCCCTACACTTAAGC-1,True,TGCCCTACACTTAAGC-1_contig_2,True,525,TRA,TRAV6-3,None,TRAJ11,TRAC,True,True,CPDSGYNKLTF,TGCCCTGACTCGGGATACAACAAACTCACTTTT,26432,3,clonotype71,clonotype71_consensus_2 -TGCGGGTGTGACAAAT-1,True,TGCGGGTGTGACAAAT-1_contig_1,True,651,TRB,TRBV19,None,TRBJ2-3,TRBC2,True,True,CASSLGSAETLYF,TGTGCCAGCAGCCTCGGTAGTGCAGAAACGCTGTATTTT,23746,2,clonotype72,clonotype72_consensus_1 -TGCGGGTGTGACAAAT-1,True,TGCGGGTGTGACAAAT-1_contig_2,True,575,TRA,TRAV4-4-DV10,None,TRAJ32,TRAC,True,True,CAAEGYGGSGNKLIF,TGTGCTGCTGAGGGGTATGGGGGCAGTGGCAACAAGCTCATCTTT,35200,3,clonotype72,clonotype72_consensus_2 -TGCGGGTGTGACAAAT-1,True,TGCGGGTGTGACAAAT-1_contig_3,True,356,TRB,None,None,TRBJ2-1,TRBC2,False,False,None,None,17744,1,clonotype72,None -TGGACGCTCGCGTAGC-1,True,TGGACGCTCGCGTAGC-1_contig_1,True,549,TRB,TRBV16,None,TRBJ1-1,TRBC1,True,True,CASSLDGEITEVFF,TGTGCAAGCAGCTTAGACGGGGAGATCACAGAAGTCTTCTTT,75518,5,clonotype73,clonotype73_consensus_1 -TGGCCAGCATGCATGT-1,True,TGGCCAGCATGCATGT-1_contig_1,True,568,TRB,TRBV1,None,TRBJ2-1,TRBC2,True,True,CTCSAQGAYAEQFF,TGCACCTGCAGTGCTCAGGGGGCCTATGCTGAGCAGTTCTTC,68510,12,clonotype74,clonotype74_consensus_1 -TGGCCAGCATGCATGT-1,True,TGGCCAGCATGCATGT-1_contig_2,True,521,TRA,TRAV6D-4,None,TRAJ17,TRAC,True,True,CALTNSAGNKLTF,TGTGCTCTCACTAACAGTGCAGGGAACAAGCTAACTTTT,10388,2,clonotype74,clonotype74_consensus_2 -TGGCTGGAGCGATAGC-1,True,TGGCTGGAGCGATAGC-1_contig_1,True,518,TRB,TRBV13-1,None,TRBJ2-1,TRBC2,True,True,CASSLGQGIAEQFF,TGTGCCAGCAGTCTCGGACAGGGGATTGCTGAGCAGTTCTTC,48066,4,clonotype75,clonotype75_consensus_2 -TGGCTGGAGCGATAGC-1,True,TGGCTGGAGCGATAGC-1_contig_2,True,504,TRA,TRAV21-DV12,None,TRAJ49,TRAC,True,True,CILRVAGGYQNFYF,TGTATCCTGAGAGTAGCGGGGGGTTACCAGAACTTCTATTTT,29136,3,clonotype75,clonotype75_consensus_1 -TGTGGTAGTATAGGGC-1,True,TGTGGTAGTATAGGGC-1_contig_1,True,524,TRB,TRBV13-3,None,TRBJ2-1,TRBC2,True,True,CASSAQNYAEQFF,TGTGCCAGCAGTGCCCAGAACTATGCTGAGCAGTTCTTC,49408,4,clonotype76,clonotype76_consensus_1 -TGTTCCGGTTAAGAAC-1,True,TGTTCCGGTTAAGAAC-1_contig_1,True,504,TRA,TRAV21-DV12,None,TRAJ32,TRAC,True,True,CILNYGGSGNKLIF,TGTATCCTGAATTATGGGGGCAGTGGCAACAAGCTCATCTTT,29102,4,clonotype77,clonotype77_consensus_1 -TGTTCCGGTTAAGAAC-1,True,TGTTCCGGTTAAGAAC-1_contig_2,True,524,TRB,TRBV31,None,TRBJ2-3,TRBC2,True,True,CAWPGLGGRTLYF,TGTGCCTGGCCGGGACTGGGGGGCAGAACGCTGTATTTT,15834,1,clonotype77,clonotype77_consensus_2 -TGTTCCGGTTAAGAAC-1,True,TGTTCCGGTTAAGAAC-1_contig_3,True,1009,TRB,TRBV12-2,None,TRBJ2-5,TRBC2,True,False,None,None,15210,2,clonotype77,None -TGTTCCGGTTAAGAAC-1,True,TGTTCCGGTTAAGAAC-1_contig_4,True,510,TRA,TRAV4-4-DV10,None,TRAJ53,TRAC,True,False,None,None,18228,1,clonotype77,None -TTAGGACAGTACGACG-1,True,TTAGGACAGTACGACG-1_contig_1,True,576,TRA,TRAV12D-1,None,TRAJ13,TRAC,True,True,CALRPSGTYQRF,TGTGCTTTGAGGCCTTCTGGGACTTACCAGAGGTTT,27106,9,clonotype78,clonotype78_consensus_1 -TTAGGCAAGAAACGAG-1,True,TTAGGCAAGAAACGAG-1_contig_1,True,630,TRB,TRBV19,None,TRBJ2-1,TRBC2,True,True,CASSKTGGAEQFF,TGTGCCAGCAGTAAGACAGGGGGAGCTGAGCAGTTCTTC,46832,4,clonotype79,clonotype79_consensus_1 -TTAGTTCCAATTCCTT-1,True,TTAGTTCCAATTCCTT-1_contig_1,True,558,TRB,TRBV13-3,None,TRBJ2-3,TRBC2,True,True,CASSEPGGRAETLYF,TGTGCCAGCAGTGAGCCTGGGGGGCGTGCAGAAACGCTGTATTTT,73908,8,clonotype80,clonotype80_consensus_1 diff --git a/tests/testthat/fixtures/NSCLC_Multi/NSCLC_Multi_Filtered_SO_downsample.rds b/tests/testthat/fixtures/NSCLC_Multi/NSCLC_Multi_Filtered_SO_downsample.rds old mode 100644 new mode 100755 index d3fd8c1..df9f769 Binary files 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a/tests/testthat/fixtures/PBMC_Single/PBMCsingle_Combine_and_Renormalize_SO_downsample.rds and /dev/null differ diff --git a/tests/testthat/fixtures/TEC/TEC_CellTypesSingleR_SO_downsample.rds b/tests/testthat/fixtures/TEC/TEC_CellTypesSingleR_SO_downsample.rds deleted file mode 100644 index d84fb18..0000000 Binary files a/tests/testthat/fixtures/TEC/TEC_CellTypesSingleR_SO_downsample.rds and /dev/null differ diff --git a/tests/testthat/fixtures/TEC/TEC_Filtered_PCA_Norm_SO_downsample.rds b/tests/testthat/fixtures/TEC/TEC_Filtered_PCA_Norm_SO_downsample.rds deleted file mode 100755 index 502f0ff..0000000 Binary files a/tests/testthat/fixtures/TEC/TEC_Filtered_PCA_Norm_SO_downsample.rds and /dev/null differ diff --git a/tests/testthat/helper-Combine_and_Normalize.R b/tests/testthat/helper-Combine_and_Normalize.R index 5edd902..040459a 100755 --- a/tests/testthat/helper-Combine_and_Normalize.R +++ b/tests/testthat/helper-Combine_and_Normalize.R @@ -6,7 +6,7 @@ getParamCN <- function(data){ object=object npcs = 30 - vars.to.regress = c() + vars.to.regress = NULL clust.res.low=0.2 clust.res.high = 1.2 only.var.genes = FALSE @@ -24,12 +24,12 @@ getParamCN <- function(data){ only.var.genes = FALSE - } else if (data == "PBMC_Single") { + } else if (data == "NSCLC_Single") { object <- readRDS(test_path( - paste0("fixtures/",data), paste0(data,'_Filtered_SO_downsample.rds'))) + paste0("fixtures/",data), paste0('NSCLCsingle','_Filtered_SO_downsample.rds'))) npcs = 30 - vars.to.regress = c() + vars.to.regress = NULL clust.res.low=0.2 clust.res.high = 1.2 only.var.genes = FALSE @@ -37,11 +37,11 @@ getParamCN <- function(data){ } else if (data == "NSCLC_Multi") { object <- readRDS(test_path( - paste0("fixtures/",data), paste0(data,'_Filtered_SO_downsample.rds'))) + paste0("fixtures/",data), paste0('NSCLCmulti','_Filtered_SO_downsample.rds'))) object=object npcs = 30 - vars.to.regress = c() + vars.to.regress = NULL clust.res.low=0.2 clust.res.high = 1.2 only.var.genes = FALSE @@ -49,11 +49,11 @@ getParamCN <- function(data){ } else if (data == "BRCA") { object <- readRDS(test_path( - paste0("fixtures/",data), paste0(data,'_Filtered_SO_downsample.rds'))) + paste0("fixtures/",data), paste0('NSCLCmulti','_Filtered_SO_downsample.rds'))) object=object npcs = 30 - vars.to.regress = c() + vars.to.regress = NULL clust.res.low=0.2 clust.res.high = 1.2 only.var.genes = TRUE @@ -67,3 +67,17 @@ getParamCN <- function(data){ "clust.res.high" = clust.res.high, "only.var.genes" = only.var.genes )) } + + + +.drawFig <- function(x, width = 10, height = 10){ + path <- tempfile(fileext = ".png") + ggsave(path, x, width = 10, height = 10) + print(path) +} +.saveSO <- function(x, width = 10, height = 10){ + path <- tempfile(fileext = ".rds") + saveRDS(x, file = path) + print(path) +} + diff --git a/tests/testthat/helper-Dual_Labeling.R b/tests/testthat/helper-Dual_Labeling.R index 0d16285..761f56e 100755 --- a/tests/testthat/helper-Dual_Labeling.R +++ b/tests/testthat/helper-Dual_Labeling.R @@ -17,7 +17,6 @@ getParamDL <- function(data){ data.reduction = "tsne" filter.data = TRUE filter.condition = TRUE - density.heatmap = TRUE display.unscaled.values = TRUE } else if (data == "Chariou") { object <- selectCRObject("Chariou") @@ -34,7 +33,6 @@ getParamDL <- function(data){ apply.filter.2 = TRUE filter.data = FALSE filter.condition = TRUE - density.heatmap = TRUE display.unscaled.values = TRUE } else if (data == "pbmc-single") { object <- selectCRObject("pbmc-single") @@ -51,7 +49,6 @@ getParamDL <- function(data){ filter.condition = TRUE filter.data = TRUE data.reduction = "tsne" - density.heatmap = TRUE display.unscaled.values = TRUE } else if (data == "nsclc-multi") { object <- selectCRObject("nsclc-multi") @@ -68,7 +65,6 @@ getParamDL <- function(data){ apply.filter.2 = TRUE filter.condition = FALSE data.reduction = "tsne" - density.heatmap = TRUE display.unscaled.values = TRUE } else if (data == "BRCA") { object <- selectCRObject("BRCA") @@ -85,7 +81,6 @@ getParamDL <- function(data){ apply.filter.2 = FALSE filter.condition = TRUE data.reduction = "tsne" - density.heatmap = TRUE display.unscaled.values = TRUE } @@ -96,7 +91,6 @@ getParamDL <- function(data){ "marker.2" = marker.2, "marker.2.type" = marker.2.type, "data.reduction" = data.reduction, - "density.heatmap" = density.heatmap, "display.unscaled.values" = display.unscaled.values, "filter.data" = filter.data, "filter.condition" = filter.condition, diff --git a/tests/testthat/helper-Filter_QC.R b/tests/testthat/helper-Filter_QC.R index 25584c8..72d5bd5 100644 --- a/tests/testthat/helper-Filter_QC.R +++ b/tests/testthat/helper-Filter_QC.R @@ -27,7 +27,7 @@ getParamFQ <- function(data){ } else if (data == "NSCLC_Multi") { object=readRDS(test_path( - paste0("fixtures/",data), paste0(data,'_ProcessRaw_SO_downsample.rds'))) + paste0("fixtures/",data), paste0('NSCLCmulti','_ProcessRaw_SO_downsample.rds'))) mad.mitoch.limits=c(NA,3) mitoch.limits = c(NA,25) @@ -47,3 +47,17 @@ getParamFQ <- function(data){ "mad.mitoch.limits" = mad.mitoch.limits, "mitoch.limits" = mitoch.limits)) } + + +.drawFig <- function(x, width = 10, height = 10){ + path <- tempfile(fileext = ".png") + ggsave(path, x, width = 10, height = 10) + print(path) +} +.saveSO <- function(x, width = 10, height = 10){ + path <- tempfile(fileext = ".rds") + saveRDS(x, file = path) + print(path) +} + + diff --git a/tests/testthat/helper-Process_Raw_Data.R b/tests/testthat/helper-Process_Raw_Data.R index b16d3fb..65d2174 100755 --- a/tests/testthat/helper-Process_Raw_Data.R +++ b/tests/testthat/helper-Process_Raw_Data.R @@ -140,3 +140,15 @@ getParamRaw <- function(data){ )) } + +.drawFig <- function(x, width = 10, height = 10){ + path <- tempfile(fileext = ".png") + ggsave(path, x, width = 10, height = 10) + print(path) +} +.saveSO <- function(x, width = 10, height = 10){ + path <- tempfile(fileext = ".rds") + saveRDS(x, file = path) + print(path) +} + diff --git a/tests/testthat/test-Combine_and_Normalize.R b/tests/testthat/test-Combine_and_Normalize.R index bcc9622..fd1e18d 100755 --- a/tests/testthat/test-Combine_and_Normalize.R +++ b/tests/testthat/test-Combine_and_Normalize.R @@ -1,44 +1,97 @@ -for (data in c('TEC','Chariou','PBMC_Single','NSCLC_Multi')) { +for (data in c('TEC','Chariou','NSCLC_Single')) { + + test_that( + paste0("Test Combine & Renormalize - Standard (",data," dataset)"), { + + + data.run <- getParamCN(data) + if(length(data.run$object)>2){ + data.run$object=data.run$object[c(1,2)]} + combine.renormalize.out <- do.call(combineNormalize, data.run) + + + # create output + expected.elements = c("object","plots") + expect_setequal(names(combine.renormalize.out), expected.elements) + # figure slot is a grob + expect_equal(class(combine.renormalize.out$plots$TSNE)[3], 'ggplot') + # SO slot contains data + expect( nrow(combine.renormalize.out$object@assays$RNA@counts),'> 0' ) + # plot slot contains data + expect( object.size(combine.renormalize.out$plot),'> 0' ) + + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_Standard_TSNE.png") + ) + ## Identical test runs returns different rds files + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_Standard.rds") + # ) + + + }) +} + + +for (data in c('NSCLC_Multi')) { test_that( paste0("Test Combine & Renormalize - Standard (",data," dataset)"), { data.run <- getParamCN(data) - + data.run$object=data.run$object[1:2] combine.renormalize.out <- do.call(combineNormalize, data.run) # create output expected.elements = c("object","plots") expect_setequal(names(combine.renormalize.out), expected.elements) + # Data contains Protein Slot + expect_setequal(names(combine.renormalize.out$object@assays), + c("RNA","Protein","SCT")) # figure slot is a grob expect_equal(class(combine.renormalize.out$plots$TSNE)[3], 'ggplot') # SO slot contains data expect( nrow(combine.renormalize.out$object@assays$RNA@counts),'> 0' ) # plot slot contains data expect( object.size(combine.renormalize.out$plot),'> 0' ) + expect( object.size(combine.renormalize.out$plot$`CITEseq UMAP`),'> 0' ) + + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_Standard_TSNE.png") + ) + ## Identical test runs returns different rds files + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_Standard.rds") + # ) + }) } - for (data in c('TEC')) { - + test_that( paste0("Test Combine & Renormalize - only.var.genes (",data," dataset)"), { - - + + data.run <- getParamCN(data) - + data.run$object=data.run$object[c(2,3)] data.run$only.var.genes = TRUE combine.renormalize.out <- do.call(combineNormalize, data.run) - - + + # create output expected.elements = c("object","plots") expect_setequal(names(combine.renormalize.out), expected.elements) @@ -48,9 +101,19 @@ for (data in c('TEC')) { expect( nrow(combine.renormalize.out$object@assays$RNA@counts),'> 0' ) # plot slot contains data expect( object.size(combine.renormalize.out$plot),'> 0' ) - + + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_only.var.genes_TSNE.png") + ) + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_only.var.genes.rds") + # ) + }) -} +} @@ -61,7 +124,7 @@ for (data in c('TEC')) { data.run <- getParamCN(data) - + data.run$object=data.run$object[c(2,3)] data.run$SCT.level = 'Sample' data.run$object = data.run$object combine.renormalize.out <- do.call(combineNormalize, data.run) @@ -77,6 +140,16 @@ for (data in c('TEC')) { # plot slot contains data expect( object.size(combine.renormalize.out$plot),'> 0' ) + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_SCTlevel_TSNE.png") + ) + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_SCTlevel.rds") + # ) + }) } @@ -87,7 +160,7 @@ for (data in c('TEC')) { paste0("Test Combine & Renormalize - exclude.sample (",data," dataset)"), { data.run <- getParamCN(data) - # data.run$input=data.run$input[c(1,2)] + data.run$object=data.run$object[c(2,3)] data.run$exclude.sample=data.run$object[1]%>%names combine.renormalize.out <- do.call(combineNormalize, data.run) @@ -107,6 +180,16 @@ for (data in c('TEC')) { unique(combine.renormalize.out$object@meta.data$orig.ident) ) + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_exclude.sample_TSNE.png") + ) + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_exclude.sample.rds") + # ) + # }) } @@ -119,6 +202,7 @@ for (data in c('TEC')) { data.run <- getParamCN(data) + data.run$object=data.run$object[c(2,3)] data.run$selection.method = "mean.var.plot" combine.renormalize.out <- do.call(combineNormalize, data.run) @@ -133,10 +217,82 @@ for (data in c('TEC')) { # plot slot contains data expect( object.size(combine.renormalize.out$plot),'> 0' ) + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_selection.method_TSNE.png") + ) + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_selection.method.rds") + # ) + }) } +for (data in c('TEC')) { + + test_that( + paste0("Test Combine & Renormalize - Select PCs plots"), { + + + data.run <- getParamCN(data) + data.run$object=data.run$object[c(2,3)] + data.run$methods.pca = c('Elbow','Marchenko-Pastur') + data.run$pca.reg.plot=T + data.run$vars.to.regress = c("percent.mt") + data.run$jackstraw = T + data.run$jackstraw.dims=2 + + combine.renormalize.out <- do.call(combineNormalize, data.run) + + + # create output + expected.elements = c("object","plots") + expect_setequal(names(combine.renormalize.out), expected.elements) + # figure slot is a grob + expect_equal( + class(combine.renormalize.out$plots$TSNE)[3], 'ggplot') + # SO slot contains data + expect( + nrow(combine.renormalize.out$object@assays$RNA@counts),'> 0' ) + # plot slot contains data + expect( + object.size(combine.renormalize.out$plots$TSNE),'> 0' ) + expect( + object.size(combine.renormalize.out$plots$UMAP),'> 0' ) + expect( + object.size(combine.renormalize.out$plot$`Elbow Plot`),'> 0' ) + expect( object.size( + combine.renormalize.out$plot$`Regression Plots`[[1]]),'> 0' ) + expect( + object.size(combine.renormalize.out$plot$JackStraw),'> 0' ) + + skip_on_ci() + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$TSNE), + paste0(data,"_SelectPCsPlot_TSNE.png") + ) + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$`Elbow Plot`), + paste0(data,"_SelectPCsPlot_Elbow.png") + ) + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$JackStraw), + paste0(data,"_SelectPCsPlot_JackStraw.png") + ) + expect_snapshot_file( + .drawFig(combine.renormalize.out$plots$`Regression Plots`[[1]]), + paste0(data,"_SelectPCsPlot_PCAreg.png") + ) + # expect_snapshot_file( + # .saveSO(combine.renormalize.out$object), + # paste0(data,"_selection.method.rds") + # ) + + }) +} diff --git a/tests/testthat/test-Dual_Labeling.R b/tests/testthat/test-Dual_Labeling.R index 1e477ab..472d1b8 100755 --- a/tests/testthat/test-Dual_Labeling.R +++ b/tests/testthat/test-Dual_Labeling.R @@ -2,9 +2,9 @@ test_that("Test Dual labeling TEC Data", { CRObject <- getParamDL("TEC") output <- do.call(dualLabeling, CRObject) - expected.elements = c("object", "plot","plot2") + expected.elements = c("object", "plot","plot_densityHM","plot_table") expect_setequal(names(output), expected.elements) - expect_length(output$plot$grobs, 7) + expect_length(output$plot$grobs, 6) skip_on_ci() expect_snapshot_file( @@ -12,7 +12,11 @@ test_that("Test Dual labeling TEC Data", { "TEC_duallabel.png" ) expect_snapshot_file( - .drawdualtable(output$plot2), + .drawdualplot(output$plot_densityHM), + "TEC_duallabelDensity.png" + ) + expect_snapshot_file( + .drawdualtable(output$plot_table), "TEC_dualtable.png" ) }) @@ -29,9 +33,9 @@ test_that("Dual labeling with umap", { CRObject$data.reduction = "umap" output <- do.call(dualLabeling, CRObject) - expected.elements = c("object", "plot", "plot2") + expected.elements = c("object", "plot","plot_densityHM","plot_table") expect_setequal(names(output), expected.elements) - expect_length(output$plot$grobs, 7) + expect_length(output$plot$grobs, 6) skip_on_ci() expect_snapshot_file( @@ -40,26 +44,14 @@ test_that("Dual labeling with umap", { ) }) -test_that("Dual labeling without density heatmap", { - CRObject <- getParamDL("TEC") - CRObject$density.heatmap = FALSE - output <- do.call(dualLabeling, CRObject) - expect_length(output$plot$grobs, 6) - - skip_on_ci() - expect_snapshot_file( - .drawdualplot(output$plot), - "nodensity_duallabel.png" - ) -}) test_that("Test Dual labeling Chariou Data", { CRObject <- getParamDL("Chariou") output <- do.call(dualLabeling, CRObject) - expected.elements = c("object", "plot", "plot2") + expected.elements = c("object", "plot","plot_densityHM","plot_table") expect_setequal(names(output), expected.elements) - expect_length(output$plot$grobs, 7) + expect_length(output$plot$grobs, 6) skip_on_ci() expect_snapshot_file( @@ -67,7 +59,11 @@ test_that("Test Dual labeling Chariou Data", { "chariou_duallabel.png" ) expect_snapshot_file( - .drawdualtable(output$plot2), + .drawdualplot(output$plot_densityHM), + "chariou_duallabelDensity.png" + ) + expect_snapshot_file( + .drawdualtable(output$plot_table), "chariou_dualtable.png" ) }) @@ -76,9 +72,9 @@ test_that("Test Dual labeling PBMC-single Data", { CRObject <- getParamDL("pbmc-single") output <- do.call(dualLabeling, CRObject) - expected.elements = c("object", "plot", "plot2") + expected.elements = c("object", "plot","plot_densityHM","plot_table") expect_setequal(names(output), expected.elements) - expect_length(output$plot$grobs, 7) + expect_length(output$plot$grobs, 6) skip_on_ci() expect_snapshot_file( @@ -86,7 +82,11 @@ test_that("Test Dual labeling PBMC-single Data", { "pbmc-single_duallabel.png" ) expect_snapshot_file( - .drawdualtable(output$plot2), + .drawdualplot(output$plot_densityHM), + "pbmc-single_duallabelDensity.png" + ) + expect_snapshot_file( + .drawdualtable(output$plot_table), "pbmc_dualtable.png" ) }) @@ -95,9 +95,9 @@ test_that("Test Dual labeling NSCLC-multi Data", { CRObject <- getParamDL("nsclc-multi") output <- do.call(dualLabeling, CRObject) - expected.elements = c("object", "plot", "plot2") + expected.elements = c("object", "plot","plot_densityHM","plot_table") expect_setequal(names(output), expected.elements) - expect_length(output$plot$grobs, 7) + expect_length(output$plot$grobs, 6) skip_on_ci() expect_snapshot_file( @@ -105,8 +105,12 @@ test_that("Test Dual labeling NSCLC-multi Data", { "nsclc-multi_duallabel.png" ) expect_snapshot_file( - .drawdualtable(output$plot2), - "nsclc_dualtable.png" + .drawdualplot(output$plot_densityHM), + "nsclc-multi_duallabelDensity.png" + ) + expect_snapshot_file( + .drawdualtable(output$plot_table), + "nsclc-multi_dualtable.png" ) }) @@ -114,9 +118,9 @@ test_that("Test Dual labeling BRCA Data", { CRObject <- getParamDL("BRCA") output <- do.call(dualLabeling, CRObject) - expected.elements = c("object", "plot", "plot2") + expected.elements = c("object", "plot","plot_densityHM","plot_table") expect_setequal(names(output), expected.elements) - expect_length(output$plot$grobs, 7) + expect_length(output$plot$grobs, 6) skip_on_ci() expect_snapshot_file( @@ -124,7 +128,11 @@ test_that("Test Dual labeling BRCA Data", { "brca_duallabel.png" ) expect_snapshot_file( - .drawdualtable(output$plot2), + .drawdualplot(output$plot_densityHM), + "brca_duallabelDensity.png" + ) + expect_snapshot_file( + .drawdualtable(output$plot_table), "brca_dualtable.png" ) }) diff --git a/tests/testthat/test-Filter_QC.R b/tests/testthat/test-Filter_QC.R index 62e8eda..ec133b1 100755 --- a/tests/testthat/test-Filter_QC.R +++ b/tests/testthat/test-Filter_QC.R @@ -1,11 +1,11 @@ for (data in c('TEC','Chariou','PBMC_Single','NSCLC_Multi')) { - + test_that(paste0("Test Filter and QC - Standard (",data," dataset)"), { - + data.run <- getParamFQ(data) filter.qc.out <- do.call(filterQC, data.run) - - + filter.qc.out$object + # create output expected.elements = c("object","FilteringMeta","plots") expect_setequal(names(filter.qc.out), expected.elements) @@ -17,43 +17,26 @@ for (data in c('TEC','Chariou','PBMC_Single','NSCLC_Multi')) { expect( object.size(filter.qc.out$object[[1]]@assays$RNA@counts),'> 0' ) # plot slot contains data expect( object.size(filter.qc.out$plots),'> 0' ) - - }) - -} -################################################################ + skip_on_ci() + expect_snapshot_file( + .drawFig(filter.qc.out$plots$PostFilterCombined), + paste0(data,"_Standard_combFig.png") + ) + expect_snapshot_file( + .saveSO(filter.qc.out$object), + paste0(data,"_Standard.rds") + ) -# for (data in c('TEC','Chariou','pbmc-single','nsclc-multi')) { -# -# test_that(paste0("Test Filter and QC - plot.histogram (",data," dataset)"),{ -# -# -# data.run <- getParamFQ(data) -# data.run$plot.histogram <- "TRUE" -# filter.qc.out <- do.call(filterQC, data.run) -# -# -# # create output -# expected.elements = c("object","FilteringMeta","plots") -# expect_setequal(names(filter.qc.out), expected.elements) -# # SO contains object same length as input -# expect_equal(length(filter.qc.out$object),length(data.run$object)) -# # figure slot is a grob -# expect_equal(class(filter.qc.out$plots$PostFilterCombined)[2], 'ggplot') -# # SO slot contains data -# expect( object.size(filter.qc.out$object[[1]]@assays$RNA@counts),'> 0' ) -# # plot slot contains data -# expect( object.size(filter.qc.out$plots),'> 0' ) -# -# }) -# -# } + + }) + +} ################################################################ -for (data in c('TEC')) { +for (data in c('Chariou')) { # data=' } else if (data == "pbmc-single' test_that(paste0("Test Filter and QC - filter.vdj.genes (",data," dataset)"), { @@ -74,6 +57,22 @@ for (data in c('TEC')) { expect( object.size(filter.qc.out$object[[1]]@assays$RNA@counts),'> 0' ) # plot slot contains data expect( object.size(filter.qc.out$plots),'> 0' ) + # Check if VDJ genes are removed + # expect( + # sum(filter.qc.out$FilteringMeta[[1]]$`VDJ Genes Removed`>0), + # '==5') + + + skip_on_ci() + expect_snapshot_file( + .drawFig(filter.qc.out$plots$PostFilterCombined), + paste0(data,"_filter.vdj.genes_combFig.png") + ) + expect_snapshot_file( + .saveSO(filter.qc.out$object), + paste0(data,"_filter.vdj.genes.rds") + ) + }) diff --git a/tests/testthat/test-Name_Clusters_by_Enriched_Cell_Type.R b/tests/testthat/test-Name_Clusters_by_Enriched_Cell_Type.R index 01d4c64..bfbf20c 100644 --- a/tests/testthat/test-Name_Clusters_by_Enriched_Cell_Type.R +++ b/tests/testthat/test-Name_Clusters_by_Enriched_Cell_Type.R @@ -24,10 +24,10 @@ test_that("Run Name clusters with interactive plot", { output <- do.call(nameClusters, input) expect_equal(class(output$plot), c("plotly", "htmlwidget")) - expect_snapshot_file( - .drawplot(output$plot), - "TEC_clusters2.png" - ) + # expect_snapshot_file( + # .drawplot(output$plot), + # "TEC_clusters2.png" + # ) }) test_that("Run Name clusters with ordering celltypes", { diff --git a/tests/testthat/test-Process_Raw_Data.R b/tests/testthat/test-Process_Raw_Data.R index 9a8cbab..9bee9af 100755 --- a/tests/testthat/test-Process_Raw_Data.R +++ b/tests/testthat/test-Process_Raw_Data.R @@ -1,53 +1,82 @@ -for (data in c('TEC','NSCLC_Multi')) {#,'PBMC_Single')) { - +for (data in c('TEC','Chariou','NSCLC_Multi')) {#,'PBMC_Single')) { + test_that(paste0("Test Filter and QC - Standard (",data," dataset)"), { - - - data.run <- getParamRaw(data) - Raw.out <- do.call(processRawData, data.run) - # create output - expected.elements = c("object","plots") - expect_setequal(names(Raw.out), expected.elements) - # SO contains object same length as input - expect_equal(length(Raw.out$object),length(data.run$input)) - # figure slot is a ggplot - expect_equal(class(Raw.out$plots[[1]])[2], 'ggplot') - # SO slot contains data - expect( object.size(Raw.out$object[[1]]@assays$RNA@counts),'> 0' ) - # plot slot contains data - expect( object.size(Raw.out$plots),'= 0' ) - - }) - -} -for (data in c('BRCA')) { - - test_that(paste0("Test Split h5 (",data," dataset)"), { - - data.run <- getParamRaw(data) Raw.out <- do.call(processRawData, data.run) - + + + # create output expected.elements = c("object","plots") expect_setequal(names(Raw.out), expected.elements) # SO contains object same length as input - expect_false(isTRUE(all.equal(length(Raw.out$object), - length(data.run$input)))) + expect_equal(length(Raw.out$object),length(grep('.csv',data.run$input, + invert = T,value = T))) # figure slot is a ggplot expect_equal(class(Raw.out$plots[[1]])[2], 'ggplot') # SO slot contains data expect( object.size(Raw.out$object[[1]]@assays$RNA@counts),'> 0' ) # plot slot contains data expect( object.size(Raw.out$plots),'= 0' ) - + + + skip_on_ci() + expect_snapshot_file( + .drawFig(Raw.out$plots$CombinedQC), + paste0(data,"_Standard_combFig.png") + ) + # expect_snapshot_file( # Test failed each run with no changes + # .saveSO(Raw.out$object), + # paste0(data,"_Standard.rds") + # ) + }) - + } + +# for (data in c('BRCA')) { +# +# test_that(paste0("Test Split h5 (",data," dataset)"), { +# +# +# data.run <- getParamRaw(data) +# Raw.out <- do.call(processRawData, data.run) +# +# # create output +# expected.elements = c("object","plots") +# expect_setequal(names(Raw.out), expected.elements) +# # SO is split into multiple samples +# expect_false(isTRUE(all.equal(length(Raw.out$object), +# length(data.run$input)))) +# # figure slot is a ggplot +# expect_equal(class(Raw.out$plots[[1]])[2], 'ggplot') +# # SO slot contains data +# expect( object.size(Raw.out$object[[1]]@assays$RNA@counts),'> 0' ) +# # plot slot contains data +# expect( object.size(Raw.out$plots),'= 0' ) +# +# skip_on_ci() +# expect_snapshot_file( +# .drawFig(Raw.out$plots$CombinedQC), +# paste0(data,"_Standard_combFig.png") +# ) +# # expect_snapshot_file( # Test failed each run with no changes +# # .saveSO(Raw.out$object), +# # paste0(data,"_Standard.rds") +# # ) +# +# +# }) +# +# } + + + + ################################################################ ################################################################ @@ -121,7 +150,8 @@ for (data in c('TEC')) { expected.elements = c("object","plots") expect_setequal(names(Raw.out), expected.elements) # SO contains object same length as input - expect_equal(length(Raw.out$object),2) + expect_false(length(Raw.out$object)==length(data.run$input)) + # figure slot is a ggplot expect_equal(class(Raw.out$plots[[1]])[2], 'ggplot') # SO slot contains data @@ -129,6 +159,17 @@ for (data in c('TEC')) { # plot slot contains data expect( object.size(Raw.out$plots),'>0' ) + skip_on_ci() + expect_snapshot_file( + .drawFig(Raw.out$plots$CombinedQC), + paste0(data,"_Regex_combFig.png") + ) + # expect_snapshot_file( + # .saveSO(Raw.out$object), + # paste0(data,"_Regex.rds") + # ) + + }) }