Better validation scripts and data
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@562 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
7de5da7065
commit
30218ee31a
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@ -2,6 +2,7 @@ import farm_commands
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import os.path
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import sys
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from optparse import OptionParser
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import string
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defaultCommands = ['CountReads', 'Pileup']
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@ -9,6 +10,72 @@ def indexBAM(reads):
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cmd = "samtools index " + reads
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farm_commands.cmd(cmd, None, None)
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def readIntervalFile(file):
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def notHeaderP(line):
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return line[0][0] <> '@'
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lines = filter(notHeaderP, map( string.split, [line for line in open(file)]))
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byContig = {}
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for entry in lines:
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elt = [int(entry[1]), int(entry[2])]
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if entry[0] in byContig:
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byContig[entry[0]].append(elt)
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else:
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byContig[entry[0]] = [elt]
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#print byContig
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return byContig
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def isIntervalFile(filename):
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return os.path.splitext(filename)[1] == '.interval_list'
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def filterByInterval(intervalMap, unfilteredPileupFile, filteredPileupFile):
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print 'Intervals', intervalMap
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def maybeWrite1(line, offsetMap, out):
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debug = False
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parts = line.split()
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contig = parts[0]
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pos = int(parts[1])
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if debug: print 'pileup', contig, pos, line,
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if contig in intervalMap:
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intervals = intervalMap[contig]
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while (offsetMap[contig] < len(intervals)):
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offset = offsetMap[contig]
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#print intervals[offset]
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curStart, curStop = intervals[offset][0:2]
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if debug: print contig, pos, curStart, curStop
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if pos >= curStart:
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if pos <= curStop:
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#print line,
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print >> out, line,
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break
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else:
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if debug: print 'Progressing', contig, pos, curStart, curStop
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offsetMap[contig] += 1
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else:
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break
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return offsetMap
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def allDone( offsetMap, intervalMap ):
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def oneDone( contig ):
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return offsetMap[contig] >= len(intervalMap[contig])
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return all( map(oneDone, offsetMap.iterkeys()) )
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i = 0
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offsetMap = dict([(key, 0) for key in intervalMap.keys()])
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out = open(filteredPileupFile, 'w')
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for line in open(unfilteredPileupFile):
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offsetMap = maybeWrite1(line, offsetMap, out)
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i += 1
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if i % 10000 == 0 and allDone(offsetMap, intervalMap):
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break
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out.close()
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def main():
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global OPTIONS, ROOT
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@ -32,6 +99,15 @@ def main():
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parser.add_option("-a", "--rebuildAllFiles", dest="rebuildAllFiles",
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action='store_true', default=False,
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help="If provided, all intermediate files (BAM and pileups) will be regenerated")
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parser.add_option("-n", "--dontValidate", dest="dontValidate",
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action='store_true', default=False,
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help="If provided, won't try to validate, just make sure the validation data files are ready")
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parser.add_option("-g", "--gatk", dest="gatkPath",
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type="string", default="~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar",
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help="Path to the gatk")
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parser.add_option("-x", "--args", dest="extraArgs",
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type="string", default="",
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help="Extra args to pass to the GATK")
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parser.add_option("-p", "--justPrint", dest="justPrint",
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action='store_true', default=False,
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help="Don't actually run GATK, just setup data files")
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@ -65,7 +141,7 @@ def main():
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originalReads = os.path.expanduser(originalReads)
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ref = os.path.expanduser(ref)
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if not os.path.exists(originalReads) or not os.path.exists(ref):
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print 'Input files do not exist!', originalReads, ref
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sys.exit(1)
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@ -87,22 +163,39 @@ def main():
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indexBAM(reads)
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if not os.path.exists(subBAM) or OPTIONS.rebuildAllFiles:
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if region == '*':
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if region == '*' or isIntervalFile(region):
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farm_commands.cmd("ln -s " + os.path.abspath(reads) + " " + subBAM)
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farm_commands.cmd("ln -s " + os.path.abspath(readsIndex) + " " + subBAM+'.bai')
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else:
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cmd = "samtools view -b " + reads + " " + region + " > " + subBAM
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farm_commands.cmd(cmd, None, None)
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subBAMIndex = subBAM+'.bai'
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if not os.path.exists(subBAMIndex) or OPTIONS.rebuildAllFiles:
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if region == '*' or isIntervalFile(region):
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farm_commands.cmd("ln -s " + os.path.abspath(readsIndex) + " " + subBAMIndex)
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else:
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indexBAM(subBAM)
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if not os.path.exists(pileup) or OPTIONS.rebuildAllFiles:
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cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + pileup
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farm_commands.cmd(cmd, None, None)
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if isIntervalFile(region):
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filteredPileup = pileup + ".unfiltered"
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if not os.path.exists(filteredPileup) or OPTIONS.rebuildAllFiles:
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cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + filteredPileup
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#farm_commands.cmd(cmd, None, None)
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filterByInterval(readIntervalFile(region), filteredPileup, pileup)
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else:
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cmd = "samtools pileup -cf " + ref + " " + subBAM + " > " + pileup
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farm_commands.cmd(cmd, None, None)
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if not os.path.exists(validationOutput) or OPTIONS.ignoreExistingFiles:
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if not OPTIONS.dontValidate and (not os.path.exists(validationOutput) or OPTIONS.ignoreExistingFiles):
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print validationOutput, 'does not exist'
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analysis = "ValidatingPileup"
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cmd = "java -ea -Xmx1024m -jar ~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar -T " + analysis + " -I " + subBAM + " -R " + ref + " -l INFO -S SILENT -U -B pileup SAMPileup " + pileup
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cmd = "java -ea -Xmx1024m -jar " + OPTIONS.gatkPath + " -T " + analysis + " -I " + subBAM + " -R " + ref + " -l INFO -S SILENT -U " + OPTIONS.extraArgs
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if isIntervalFile(region):
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cmd += " --intervals_file " + region
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cmd += " -B pileup SAMPileup " + pileup
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print cmd
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farm_commands.cmd(cmd, OPTIONS.farmQueue, outputFile=validationOutput, just_print_commands=OPTIONS.justPrint)
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@ -21,6 +21,9 @@
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# samtools import /seq/references/Homo_sapiens_assembly17/v0/Homo_sapiens_assembly17.bam.ref_list /seq/dirseq/aphilipp/combo/sequences/hs/samfiles/30CLA.5.clean.sam 30CLA.5.clean.bam
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/humgen/gsa-scr1/GATK_Data/Validation_Data/30CLA.5.clean.bam /humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta *
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# whole exom interval-based analysis for cancer
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/humgen/gsa-scr1/GATK_Data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta /humgen/gsa-scr1/GATK_Data/Validation_Data/TCGA-06-0188.interval_list
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# WGS tumor -- figure it out
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#/broad/1KG/pilot3/sams/NA12892.bam /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta *
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