more and better python scripts for dealing with calls
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@881 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
parent
a1218ef508
commit
3998085e4b
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@ -10,7 +10,22 @@ import itertools
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gatkPath = "~/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar"
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ref = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"
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analysis = "CombineDuplicates"
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def geli2dbsnpFile(geli):
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root, flowcellDotlane, ext = picard_utils.splitPath(geli)
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return os.path.join(root, flowcellDotlane) + '.dbsnp_matches'
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def bams2geli(bams):
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def call1(bam):
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geli = os.path.splitext(bam)[0] + '.geli'
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jobid = 0
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if not os.path.exists(geli):
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cmd = picard_utils.callGenotypesCmd( bam, geli, options = picard_utils.hybridSelectionExtraArgsForCalling())
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue )
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return geli, jobid
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calls = map(call1, bams)
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return map(lambda x: x[0], calls), map(lambda x: x[1], calls)
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def main():
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global OPTIONS, ROOT
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@ -25,7 +40,7 @@ def main():
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help="minimum lod for calling a variant")
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parser.add_option("-k", "--column", dest="column",
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type="int", default=1,
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help="Column in the file with the geli file path")
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help="Column in the file with the bam or geli file path")
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parser.add_option("-o", "--output", dest="output",
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type="string", default='/dev/stdout',
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help="x")
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@ -35,17 +50,36 @@ def main():
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parser.error("incorrect number of arguments")
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lines = [line.split() for line in open(args[0])]
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nIndividuals = int(args[1])
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gelis = map( lambda x: x[OPTIONS.column-1], lines )
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variantsOut = map( lambda geli: os.path.split(geli)[1] + '.calls', gelis)
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data = map( lambda x: x[OPTIONS.column-1], lines )
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if os.path.splitext(data[0])[1] == '.bam':
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gelis, jobids = bams2geli(data)
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if filter(lambda x: x <> 0, jobids) <> []:
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# there's still work to do
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sys.exit('Stopping. Please rerun this program when the farm jobs are complete: ' + str(jobids))
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print 'gelis', gelis
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print 'jobids', jobids
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else:
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gelis = map( lambda x: x[OPTIONS.column-1], lines )
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jobids = [None] * len(gelis)
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print 'Geli files'
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print gelis
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print variantsOut
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for geli, jobid in zip(gelis, jobids):
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dbsnpFile = geli2dbsnpFile(geli)
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if not os.path.exists(dbsnpFile):
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dbsnpCmd = picard_utils.CollectDbSnpMatchesCmd(geli, dbsnpFile, OPTIONS.lod)
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farm_commands.cmd(dbsnpCmd, OPTIONS.farmQueue, waitID = jobid)
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# read in the dbSNP tracks
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nTotalSnps = 0
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nNovelSnps = 0
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for geli in gelis:
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root, flowcellDotlane, ext = picard_utils.splitPath(geli)
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dbsnp_matches = os.path.join(root, flowcellDotlane) + '.dbsnp_matches'
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#dbsnp_matches = os.path.join(root, flowcellDotlane) + '.dbsnp_matches'
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dbsnp_matches = geli2dbsnpFile(geli)
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print dbsnp_matches
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if os.path.exists(dbsnp_matches):
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TOTAL_SNPS, NOVEL_SNPS, PCT_DBSNP, NUM_IN_DB_SNP = picard_utils.read_dbsnp(dbsnp_matches)
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nTotalSnps += int(TOTAL_SNPS)
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@ -55,7 +89,9 @@ def main():
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print 'DATA: NOVEL SNP CALLS SUMMED ACROSS LANES, NOT ACCOUNT FOR IDENTITY ', nNovelSnps
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print 'DATA: AVERAGE DBSNP RATE ACROSS LANES ', float(nTotalSnps - nNovelSnps) / nTotalSnps
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# convert the geli's to text
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jobid = None
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variantsOut = map( lambda geli: os.path.split(geli)[1] + '.calls', gelis)
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for geli, variantOut in zip(gelis, variantsOut):
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if not os.path.exists(variantOut):
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cmd = ("GeliToText.jar I=%s | awk '$7 > %f' > %s" % ( geli, OPTIONS.lod, variantOut) )
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@ -90,11 +90,11 @@ class MergeFilesSpec:
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sizes = map(greek, sizes)
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return sizes
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def mergeCmd(self, mergeBin = None):
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def mergeCmd(self, mergeBin = None, MSD = False):
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if mergeBin == None:
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mergeBin = MERGE_BIN
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return picard_utils.mergeBAMCmd(self.getMergedBAM(), self.sources(), mergeBin)
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return picard_utils.mergeBAMCmd(self.getMergedBAM(), self.sources(), mergeBin, MSD = MSD)
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def getIndexCmd(self):
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return "samtools index " + self.getMergedBAM()
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@ -34,6 +34,9 @@ by key and spawn merge and index jobs to merge all of the files sharing the same
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parser.add_option("-m", "--mergeBin", dest="mergeBin",
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type="string", default=None,
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help="Path to merge binary")
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parser.add_option("", "--MSD", dest="MSD",
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action='store_true', default=False,
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help="Merge sequence dictionaries?")
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parser.add_option("", "--keyCol", dest="keyCol",
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type=int, default=1,
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help="Column in the list file holding the key")
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@ -69,7 +72,7 @@ by key and spawn merge and index jobs to merge all of the files sharing the same
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if len(spec.sources()) == 1 and OPTIONS.link:
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cmd = 'ln -s ' + spec.sources()[0] + ' ' + spec.getMergedBAM()
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else:
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cmd = spec.mergeCmd(OPTIONS.mergeBin)
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cmd = spec.mergeCmd(OPTIONS.mergeBin, MSD = OPTIONS.MSD)
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print cmd
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, output, just_print_commands = OPTIONS.dry)
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@ -46,5 +46,5 @@ def cmd(cmd_str_from_user, farm_queue=False, output_head=None, just_print_comman
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status = os.system(cmd_str)
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if not farm_queue:
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print "<<< Exit code:", status,"\n"
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return status
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return int(status)
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@ -21,6 +21,9 @@ analysis = "CombineDuplicates"
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MERGE_BIN = '/seq/software/picard/current/bin/MergeSamFiles.jar'
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CALL_GENOTYPES_BIN = '/seq/software/picard/current/bin/CallGenotypes.jar'
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def CollectDbSnpMatchesCmd(inputGeli, outputFile, lod):
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return 'CollectDbSnpMatches.jar INPUT=%s OUTPUT=%s DBSNP=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.dbsnp MINIMUM_LOD=%f' % (inputGeli, outputFile, lod)
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def unique(l):
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return list(set(l))
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@ -140,10 +143,14 @@ def aggregateGeliCalls( sortedGeliCalls ):
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#return [[loc, list(sharedCallsGroup)] for (loc, sharedCallsGroup) in itertools.groupby(sortedGeliCalls, call2loc)]
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return [[loc, list(sharedCallsGroup)] for (loc, sharedCallsGroup) in itertools.groupby(sortedGeliCalls, call2loc)]
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def mergeBAMCmd( output_filename, inputFiles, mergeBin = MERGE_BIN ):
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def mergeBAMCmd( output_filename, inputFiles, mergeBin = MERGE_BIN, MSD = True ):
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if type(inputFiles) <> list:
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inputFiles = list(inputFiles)
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return 'java -Xmx4096m -jar ' + mergeBin + ' MSD=true AS=true SO=coordinate O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(inputFiles))
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MSDStr = ''
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if MSD: MSDStr = 'MSD=true'
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return 'java -Xmx4096m -jar ' + mergeBin + ' ' + MSDStr + ' AS=true SO=coordinate O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(inputFiles))
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#return 'java -Xmx4096m -jar ' + mergeBin + ' AS=true SO=coordinate O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(inputFiles))
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def getPicardPath(lane, picardRoot = '/seq/picard/'):
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@ -165,8 +172,11 @@ def getReferenceGenotypeFileFromConcordanceFile(concordFile):
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return match.group(1)
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return None
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def hybridSelectionExtraArgsForCalling():
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return "TARGET_INTERVALS=/seq/references/HybSelOligos/thousand_genomes_alpha_redesign/thousand_genomes_alpha_redesign.targets.interval_list CALL_ZERO_COVERAGE_LOCI=true"
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def callGenotypesCmd( inputBam, outputFilename, callGenotypesBin = CALL_GENOTYPES_BIN, options = ''):
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return "java -jar %s INPUT=%s OUTPUT=%s CALLER_ALGORITHM=QUALITY_SCORE PRIOR_MODEL=SNP_FREQUENCY %s" % ( callGenotypesBin, inputBam, outputFilename, options)
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return "java -jar %s INPUT=%s OUTPUT=%s REFERENCE_SEQUENCE=%s CALLER_ALGORITHM=QUALITY_SCORE PRIOR_MODEL=SNP_FREQUENCY %s" % ( callGenotypesBin, inputBam, outputFilename, ref, options)
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def concord(options, geli, output, genotypeFile):
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return ("java -jar /seq/software/picard/current/bin/CollectGenotypeConcordanceStatistics.jar OPTIONS_FILE=%s INPUT=%s OUTPUT=%s REFERENCE_GENOTYPES=%s MINIMUM_LOD=5.0" % ( options, geli, output, genotypeFile ) )
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