rescue parseCSQToGRanges from ensemblVEP (#12)

* bump x.y.z version to even y prior to creation of RELEASE_3_14 branch * bump x.y.z version to odd y following creation of RELEASE_3_14 branch * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch * bump x.y.z version to even y prior to creation of RELEASE_3_16 branch * bump x.y.z version to odd y following creation of RELEASE_3_16 branch * bump x.y.z version to even y prior to creation of RELEASE_3_17 branch * bump x.y.z version to odd y following creation of RELEASE_3_17 branch * bump x.y.z version to even y prior to creation of RELEASE_3_18 branch * bump x.y.z version to odd y following creation of RELEASE_3_18 branch * bump x.y.z version to even y prior to creation of RELEASE_3_19 branch * bump x.y.z version to odd y following creation of RELEASE_3_19 branch * rescue parseCSQToGRanges from ensemblVEP * fix import, export, and documentation * remove github action --------- Co-authored-by: Nitesh Turaga <[email protected]> Co-authored-by: J Wokaty <[email protected]> Co-authored-by: J Wokaty <[email protected]>
kevinrue · Jul 4, 2024 · 2de7232 · 2de7232
1 parent 45e1709
commit 2de7232
Show file tree

Hide file tree

Showing 12 changed files with 270 additions and 205 deletions.
diff --git a/.github/workflows/build_check_deploy.yaml b/.github/workflows/build_check_deploy.yaml
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.1', bioc: '3.14'}
-          ##- { os: windows-latest, r: '4.1', bioc: '3.14'}
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.20', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.20'}
+          # - { os: windows-latest, r: 'devel', bioc: '3.20'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -79,20 +79,20 @@ jobs:
       ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
       ## If they update their steps, we will also need to update ours.
       - name: Checkout Repository
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       ## R is already included in the Bioconductor docker images
       - name: Setup R from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-r@master
+        uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
 
       ## pandoc is already included in the Bioconductor docker images
       - name: Setup pandoc from r-lib
         if: runner.os != 'Linux'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -102,19 +102,19 @@ jobs:
 
       - name: Restore R package cache
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.1-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
@@ -143,6 +143,9 @@ jobs:
           ## Required for tcltk
           brew install xquartz --cask
 
+          ## Required for terra
+          brew install gdal
+
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
@@ -176,7 +179,7 @@ jobs:
           gha_repos <- if(
               .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
           ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.14/bioc",
+              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.20/bioc",
               BiocManager::repositories()
               ) else BiocManager::repositories()
 
@@ -210,15 +213,15 @@ jobs:
         shell: Rscript {0}
 
       - name: Install covr
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           remotes::install_cran("covr")
         shell: Rscript {0}
 
       - name: Install pkgdown
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          remotes::install_github("r-lib/pkgdown")
+          remotes::install_cran("pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -259,27 +262,28 @@ jobs:
         run: |
           BiocCheck::BiocCheck(
               dir('check', 'tar.gz$', full.names = TRUE),
-              `quit-with-status` = TRUE,
+              `quit-with-status` = FALSE,
               `no-check-R-ver` = TRUE,
               `no-check-bioc-help` = TRUE
           )
         shell: Rscript {0}
 
       - name: Test coverage
-        if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
         run: |
           covr::codecov()
         shell: Rscript {0}
 
       - name: Install package
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: R CMD INSTALL .
 
       - name: Build and deploy pkgdown site
-        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
+          git config --global user.name "$GITHUB_ACTOR"
+          git config --global user.email "[email protected]"
+          git config --global --add safe.directory /__w/kevinrue/TVTB
           Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
         shell: bash {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
@@ -291,7 +295,7 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-devel-r-4.1-results
+          name: ${{ runner.os }}-biocversion-devel-r-devel-results
           path: check
 
       - uses: docker/build-push-action@v1

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: TVTB
 Type: Package
 Title: TVTB: The VCF Tool Box
-Version: 1.19.1
-Date: 2021-08-30
+Version: 1.31.1
+Date: 2024-07-04
 Authors@R: person("Kevin", "Rue-Albrecht", role = c("aut", "cre"),
     email = "[email protected]")
 Description: The package provides S4 classes and methods to filter,
@@ -14,20 +14,47 @@ Description: The package provides S4 classes and methods to filter,
     Shiny Variant Explorer (tSVE).
 License: Artistic-2.0
 Depends: R (>= 3.4), methods, utils, stats
-Imports: AnnotationFilter, BiocGenerics (>= 0.25.1), BiocParallel, Biostrings,
-    ensembldb, ensemblVEP, GenomeInfoDb, GenomicRanges, GGally, ggplot2, Gviz,
-    limma, IRanges (>= 2.21.6), reshape2, Rsamtools, S4Vectors (>= 0.25.14),
-    SummarizedExperiment, VariantAnnotation (>= 1.19.9)
+Imports:
+    AnnotationFilter,
+    BiocGenerics (>= 0.25.1),
+    BiocParallel,
+    Biostrings,
+    ensembldb,
+    GenomeInfoDb,
+    GenomicRanges,
+    GGally,
+    ggplot2,
+    Gviz,
+    limma,
+    IRanges (>= 2.21.6),
+    reshape2,
+    Rsamtools,
+    S4Vectors (>= 0.25.14),
+    SummarizedExperiment,
+    VariantAnnotation (>= 1.19.9)
 Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT
     (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12),
     rmarkdown, testthat, covr, pander
-biocViews: Software, Genetics, GeneticVariability, GenomicVariation,
-    DataRepresentation, GUI, Genetics, DNASeq, WholeGenome,
-    Visualization, MultipleComparison, DataImport,
-    VariantAnnotation, Sequencing, Coverage, Alignment,
+biocViews:
+    Software,
+    Genetics,
+    GeneticVariability,
+    GenomicVariation,
+    DataRepresentation,
+    GUI,
+    Genetics,
+    DNASeq,
+    WholeGenome,
+    Visualization,
+    MultipleComparison,
+    DataImport,
+    VariantAnnotation,
+    Sequencing,
+    Coverage,
+    Alignment,
     SequenceMatching
 Collate: utils.R tSVE.R AllClasses.R AllGenerics.R Genotypes-class.R
-    TVTBparam-class.R VcfFilterRules-class.R countGenos-methods.R
+    TVTBparam-class.R VcfFilterRules-class.R parseCSQToGRanges.R countGenos-methods.R
     autodetectGenotypes.R addCountGenos-methods.R addFrequencies-methods.R
     addOverallFrequencies-methods.R
     addPhenoLevelFrequencies-methods.R dropInfo.R readVcf-methods.R
@@ -36,4 +63,3 @@ Collate: utils.R tSVE.R AllClasses.R AllGenerics.R Genotypes-class.R
 VignetteBuilder: knitr
 URL: https://github.com/kevinrue/TVTB
 BugReports: https://github.com/kevinrue/TVTB/issues
-RoxygenNote: 7.1.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -39,7 +39,7 @@ importFrom(
 
 importFrom(
     "stats",
-    "as.formula"
+    "as.formula", "setNames"
 )
 
 # When Source and Version will be possible to add to VCF INFO fields
@@ -71,8 +71,6 @@ importFrom(
     "vcfSamples<-", "vcfWhich<-", "vcfFixed<-", "vcfInfo<-", "vcfGeno<-"
 )
 
-importFrom("ensemblVEP", "parseCSQToGRanges")
-
 importFrom(
     "ggplot2",
     "ggplot", "aes_string", "facet_wrap",
@@ -96,6 +94,12 @@ importFrom(
     "reshape2",
     "melt", "dcast")
 
+importFrom(
+    "GenomeInfoDb",
+    "genome",
+    "genome<-"
+)
+
 #exportPattern("^[[:alpha:]]+")
 
 # runShinyApp.R ----
@@ -142,7 +146,8 @@ exportClasses(
 # Default methods
 export(
     "TVTBparam", "Genotypes",
-    "VcfFixedRules", "VcfInfoRules", "VcfVepRules", "VcfFilterRules"
+    "VcfFixedRules", "VcfInfoRules", "VcfVepRules", "VcfFilterRules",
+    "parseCSQToGRanges"
 )
 
 # Re-export useful methods defined in other packages ----

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -187,3 +187,10 @@ setGeneric(
     function(x, value)
         standardGeneric("svp<-")
 )
+
+# ensemblVEP ----
+
+setGeneric("parseCSQToGRanges", signature = "x",
+  function(x, VCFRowID=TRUE, ...)
+    standardGeneric("parseCSQToGRanges")
+)