Fix URIs matching error in sdrfToNfConf.R (#46)

* Update sdrfToNfConf.R * fix value of 'missing_uri_files', when 'uri_select' is not a data.frame or matrix * rm blank space
ebi-gene-expression-group · May 20, 2024 · ac7bf36 · ac7bf36
1 parent c5b46fc
commit ac7bf36
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/bin/sdrfToNfConf.R b/bin/sdrfToNfConf.R
@@ -162,7 +162,7 @@ for ( n in names(opt) ) {
 }
 
 ################################################################################
-# First round SDRF field checks: before we know about field content 
+# First round SDRF field checks: before we know about field content
 ################################################################################
 
 # Load the SDRF
@@ -1124,14 +1124,14 @@ configs <- lapply(species_list, function(species){
         }else{
 
           # For each library we check if there is a fastq URI that can supply the file
-          uri_select <- apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files)         
+          uri_select <- apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files)
 
           if (is.data.frame(uri_select) || is.matrix(uri_select)) {
             # the following line gives an error: dim(X) must have a positive length
             # if not a matrix or a data.frame
             missing_uri_files <- files[which(! apply(apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files), 1, any))]
           } else {
-            missing_uri_files <- files[which(! apply(as.data.frame( apply(species.protocol.sdrf[,uri_cols], 2, function(x) basename(x) == files) ), 1, any))]
+            missing_uri_files <- files[which(! any(apply(species.protocol.sdrf[, uri_cols], 2, function(x) basename(x) == files))  )]
           }
 
           if (length(missing_uri_files) > 0){

diff --git a/bin/utils.R b/bin/utils.R
@@ -1,5 +1,5 @@
 pinfo <- function(...) {
-    cat(paste0("[INFO ",format(Sys.time(), format="%d/%m-%H:%M"),"] ",...,"\n"))
+    cat(paste0("[INFO ", format(Sys.time(), format="%d/%m-%H:%M"),"] ",...,"\n"))
 }
 
 perror <- function(...) {
@@ -10,14 +10,14 @@ pwarning <- function(...) {
   cat(paste0("[WARNING] ",...,"\n"),file=stderr())
 }
 
-read.tsv <- function(f,header=TRUE, comment.char="", nrows=-1L,fill=FALSE, quote="\"", colClasses=NULL, drop=NULL) {
+read.tsv <- function(f, header=TRUE, comment.char="", nrows=-1L,fill=FALSE, quote="\"", colClasses=NULL, drop=NULL) {
     tsv.data <- NULL
 
     suppressPackageStartupMessages(require(data.table))
 
-    fread(input=f,sep = "\t", nrows=nrows, header=header,check.names=FALSE,data.table=FALSE,fill=fill,drop=drop, quote=quote,colClasses=colClasses)
+    fread(input=f, sep = "\t", nrows=nrows, header=header, check.names=FALSE,data.table=FALSE, fill=fill, drop=drop, quote=quote, colClasses=colClasses)
 }
 
 write.tsv <- function(x, file, header=TRUE){
     fwrite(x,file=file,sep="\t",row.names=FALSE,col.names=header,quote=FALSE,verbose=FALSE)
-}
+}