add strelka

DESCRIPTION

@@ -34,6 +34,6 @@ Suggests:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 URL: https://github.com/WangLabCSU/blit, https://wanglabcsu.github.io/blit/
 BugReports: https://github.com/WangLabCSU/blit/issues

NAMESPACE

@@ -41,6 +41,7 @@ export(python)
 export(samtools)
 export(seqkit)
 export(snpEff)
+export(strelka)
 export(trust4)
 export(trust4_gene_names)
 export(trust4_imgt_annot)

NEWS.md

@@ -16,6 +16,8 @@
 
 * new command `bedtools`
 
+* new command `strelka`
+
 # blit 0.2.0
 
 ## New features

R/cmd-strelka.R

@@ -0,0 +1,50 @@
+#' Run strelka
+#' 
+#' Strelka is a fast and accurate small variant caller optimized for analysis of germline variation 
+#' in small cohorts and somatic variation in tumor/normal sample pairs. 
+#'
+#' @param script Name of the Strelka script. One of
+#' `r oxford_comma(code_quote(StrelkaScripts))`.
+#' @param ... `r rd_dots("strelka")`.
+#' @param strelka `r rd_cmd("strelka")`.
+#' @seealso 
+#' - <https://github.com/Illumina/strelka>
+#' 
+#' `r rd_seealso()`
+#' @inherit exec return
+#' @family command
+#' @export
+strelka <- make_command(
+  "strelka",
+  function(script, ...) {
+    script <- rlang::arg_match0(script, StrelkaScripts)
+    Strelka$new(
+      script = script,
+      ...
+      )
+  }
+)
+
+Strelka <- R6::R6Class(
+  "Strelka",
+  inherit = Command,
+  private = list(
+    alias = function() "strelka",
+    command_locate = function() {
+      py2 <- Sys.which("python2")
+      if (py2 == "") {
+        stop("Cannot locate python2. Please install it or activate a Conda environment with Python2.")
+      }else{py2}
+    },
+    setup_help_params = function() "--help",
+    setup_command_params = function(script) {
+      script_path <- pkg_extdata("strelka", paste0(script, ".py"))
+      file_executable(script_path)
+      c(script_path, super$combine_params())
+    }
+  )
+)
+
+StrelkaScripts <- c(
+  "configureStrelkaGermlineWorkflow", "configureStrelkaSomaticWorkflow", "runWorkflow"
+)

_pkgdown.yml

@@ -52,6 +52,7 @@ reference:
     - varscan
     - snpEff
     - gistic2
+    - strelka
 
   - title: "Transcriptomic tools"
     desc: "Wrappers for transcriptome sequencing data processing and analysis tools."

inst/extdata/strelka/configureStrelkaGermlineWorkflow.py

@@ -0,0 +1,189 @@
+#!/usr/bin/env python2
+#
+# Strelka - Small Variant Caller
+# Copyright (c) 2009-2018 Illumina, Inc.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+#
+
+"""
+This script configures the strelka germline small variant calling workflow
+"""
+
+import os,sys
+
+if sys.version_info >= (3,0):
+    import platform
+    raise Exception("Strelka does not currently support python3 (version %s detected)" % (platform.python_version()))
+
+if sys.version_info < (2,6):
+    import platform
+    raise Exception("Strelka requires python2 version 2.6+ (version %s detected)" % (platform.python_version()))
+
+
+scriptDir='/home/dingjia/.local/share/R/blit/appmamba/envs/strelka/share/strelka-2.9.10-2/bin'
+scriptName=os.path.basename(__file__)
+workflowDir='/home/dingjia/.local/share/R/blit/appmamba/envs/strelka/share/strelka-2.9.10-2/lib/python'
+
+sys.path.append(workflowDir)
+
+from configBuildTimeInfo import workflowVersion
+from strelkaSharedOptions import StrelkaSharedWorkflowOptionsBase
+from configureUtil import BamSetChecker, groomBamList, joinFile, OptParseException, checkFixTabixIndexedFileOption
+from makeRunScript import makeRunScript
+from strelkaGermlineWorkflow import StrelkaGermlineWorkflow
+from workflowUtil import ensureDir, exeFile
+
+
+
+class StrelkaGermlineWorkflowOptions(StrelkaSharedWorkflowOptionsBase) :
+
+    def workflowDescription(self) :
+        return """Version: %s
+
+This script configures Strelka germline small variant calling.
+You must specify an alignment file (BAM or CRAM) for at least one sample.
+""" % (workflowVersion)
+
+
+    def addWorkflowGroupOptions(self,group) :
+        group.add_option("--bam", type="string",dest="bamList",metavar="FILE", action="append",
+                         help="Sample BAM or CRAM file. May be specified more than once, multiple inputs will be treated as each BAM file representing a different sample. [required] (no default)")
+        group.add_option("--ploidy", type="string", dest="ploidyFilename", metavar="FILE",
+                         help="Provide ploidy file in VCF. The VCF should include one sample column per input sample labeled with the same sample names found in the input BAM/CRAM RG header sections."
+                              " Ploidy should be provided in records using the FORMAT/CN field, which are interpreted to span the range [POS+1, INFO/END]. Any CN value besides 1 or 0 will be treated as 2."
+                              " File must be tabix indexed. (no default)")
+        group.add_option("--noCompress", type="string", dest="noCompressBed", metavar="FILE",
+                         help="Provide BED file of regions where gVCF block compression is not allowed. File must be bgzip-compressed/tabix-indexed. (no default)")
+        group.add_option("--callContinuousVf", type="string", dest="callContinuousVf", metavar="CHROM", action="append",
+                         help="Call variants on CHROM without a ploidy prior assumption, issuing calls with continuous variant frequencies (no default)")
+        group.add_option("--rna", dest="isRNA", action="store_true",
+                         help="Set options for RNA-Seq input.")
+
+        StrelkaSharedWorkflowOptionsBase.addWorkflowGroupOptions(self,group)
+
+
+    def addExtendedGroupOptions(self,group) :
+        # note undocumented library behavior: "dest" is optional, but not including it here will
+        # cause the hidden option to always print
+        group.add_option("--disableSequenceErrorEstimation", dest="isEstimateSequenceError", action="store_false",
+                         help="Disable estimation of sequence error rates from data.")
+        group.add_option("--useAllDataForSequenceErrorEstimation", dest="isErrorEstimationFromAllData", action="store_true",
+                         help="Instead of sampling a subset of data for error estimation, use all data from sufficiently large chromosomes."
+                              " This could greatly increase the workflow's runtime.")
+
+        StrelkaSharedWorkflowOptionsBase.addExtendedGroupOptions(self,group)
+
+
+    def getOptionDefaults(self) :
+
+        self.configScriptDir=scriptDir
+        defaults=StrelkaSharedWorkflowOptionsBase.getOptionDefaults(self)
+
+        libexecDir=defaults["libexecDir"]
+
+        configDir=os.path.abspath(os.path.join(scriptDir,"../share/config"))
+        assert os.path.isdir(configDir)
+
+        defaults.update({
+            'runDir' : 'StrelkaGermlineWorkflow',
+            'strelkaGermlineBin' : joinFile(libexecDir,exeFile("starling2")),
+            'bgzip9Bin' : joinFile(libexecDir, exeFile("bgzip9")),
+            'configDir' : configDir,
+            'germlineSnvScoringModelFile' : joinFile(configDir,'germlineSNVScoringModels.json'),
+            'germlineIndelScoringModelFile' : joinFile(configDir,'germlineIndelScoringModels.json'),
+            'rnaSnvScoringModelFile' : joinFile(configDir,'RNASNVScoringModels.json'),
+            'rnaIndelScoringModelFile' : joinFile(configDir,'RNAIndelScoringModels.json'),
+            'callContinuousVf' : [],
+            'getCountsBin' : joinFile(libexecDir,exeFile("GetSequenceAlleleCounts")),
+            'mergeCountsBin' : joinFile(libexecDir,exeFile("MergeSequenceAlleleCounts")),
+            'estimateVariantErrorRatesBin' : joinFile(libexecDir,exeFile("EstimateVariantErrorRates")),
+            'thetaParamFile' : joinFile(configDir,'theta.json'),
+            'indelErrorRateDefault' : joinFile(configDir,'indelErrorModel.json'),
+            'isEstimateSequenceError' : True,
+            'isErrorEstimationFromAllData' : False
+            })
+        return defaults
+
+
+    def validateAndSanitizeOptions(self,options) :
+
+        StrelkaSharedWorkflowOptionsBase.validateAndSanitizeOptions(self,options)
+
+        options.ploidyFilename = checkFixTabixIndexedFileOption(options.ploidyFilename,"ploidy file")
+        options.noCompressBed = checkFixTabixIndexedFileOption(options.noCompressBed,"no-compress bed")
+        if options.snvScoringModelFile is None :
+            if options.isRNA :
+                options.snvScoringModelFile = options.rnaSnvScoringModelFile
+            else :
+                options.snvScoringModelFile = options.germlineSnvScoringModelFile
+
+        if options.indelScoringModelFile is None :
+            if options.isRNA :
+                options.indelScoringModelFile = options.rnaIndelScoringModelFile
+            else :
+                options.indelScoringModelFile = options.germlineIndelScoringModelFile
+
+        # Disable dynamic error estimation for Exome
+        if options.isExome :
+            options.isEstimateSequenceError = False
+
+        # Disable dynamic error estimation for RNA
+        if options.isRNA :
+            options.isEstimateSequenceError = False
+
+        groomBamList(options.bamList,"input")
+
+        def safeLen(x) :
+            if x is None : return 0
+            return len(x)
+
+        if safeLen(options.bamList) == 0 :
+            raise OptParseException("No input sample alignment files specified")
+
+        bamSetChecker = BamSetChecker()
+        bamSetChecker.appendBams(options.bamList,"Input")
+        bamSetChecker.check(options.htsfileBin, options.referenceFasta)
+
+
+
+def main() :
+
+    primarySectionName="StrelkaGermline"
+    options,iniSections=StrelkaGermlineWorkflowOptions().getRunOptions(primarySectionName, version=workflowVersion)
+
+    # we don't need to instantiate the workflow object during configuration,
+    # but this is done here to trigger additional parameter validation:
+    #
+    StrelkaGermlineWorkflow(options)
+
+    # generate runscript:
+    #
+    ensureDir(options.runDir)
+    workflowScriptPath = os.path.join(options.runDir, options.workflowScriptName)
+
+    makeRunScript(workflowScriptPath,os.path.join(workflowDir,"strelkaGermlineWorkflow.py"),"StrelkaGermlineWorkflow",primarySectionName,iniSections)
+
+    notefp=sys.stdout
+    notefp.write("""
+Successfully created workflow run script.
+To execute the workflow, run the following script and set appropriate options:
+
+%s
+""" % (workflowScriptPath))
+
+
+if __name__ == "__main__" :
+    main()