204 lines
12 KiB
Python
Executable File
204 lines
12 KiB
Python
Executable File
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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from gatkConfigParser import *
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import glob
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import itertools
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if __name__ == "__main__":
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usage = """usage: %prog [-c config.cfg]*"""
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parser = OptionParser(usage=usage)
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parser.add_option("-q", "--farm", dest="farmQueue",
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type="string", default=None,
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help="Farm queue to send processing jobs to")
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parser.add_option("-c", "--config", dest="configs",
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action="append", type="string", default=[],
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help="Configuration file")
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parser.add_option("-w", "--wait", dest="initialWaitID",
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type="string", default=None,
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help="If providedm the first job dispatched to LSF will use this id as it ended() prerequisite")
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parser.add_option("", "--dry", dest="dry",
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action='store_true', default=False,
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help="If provided, nothing actually gets run, just a dry run")
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parser.add_option("-i", "--ignoreExistingFiles", dest="ignoreExistingFiles",
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action='store_true', default=False,
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help="Ignores already written files, if present")
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parser.add_option("-d", "--dir", dest="outputdir",
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type="string", default="./",
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help="Output directory")
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(OPTIONS, args) = parser.parse_args()
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if len(args) != 0:
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parser.error("incorrect number of arguments")
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config = gatkConfigParser(OPTIONS.configs)
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if not os.path.exists(OPTIONS.outputdir):
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os.mkdir(OPTIONS.outputdir)
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def outputDir(suffix):
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return os.path.join(OPTIONS.outputdir, suffix)
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intervals_dir = outputDir("intervals")
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cleaner_output = outputDir("cleaner")
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injector_output = outputDir("bams")
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snp_output = outputDir("calls/unfiltered_snps")
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filter_output = outputDir("calls/filtered_snps")
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indel_output = outputDir("calls/indels")
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final_bam_dir = "/humgen/gsa-hphome1/projects/1kg_pilot2/useTheseBamsForAnalyses"
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samples = ["NA12878","NA12891","NA12892","NA19238","NA19239","NA19240"]
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techs = ["SLX"]
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chrs = range(1, 23) + ["X"]
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DoCs = [82,91,70,56,68,86]
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# Official genome-wide Depth of Coverage tables for pilot 2, freeze 5:
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# NA12878 NA12891 NA12892 NA19238 NA19239 NA19240
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# 454: 36 18
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# SLX: 82 91 70 56 68 86
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# SOLID: 37 64
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# 454+SLD: 64 77
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# ALL: 138 150
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for sample, DoC in zip(samples, DoCs):
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#
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# Actually do some work here
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#
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MQs = [100,5,5]
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def finalBam(tech):
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return os.path.join(final_bam_dir, "%s.%s.bam" % ( sample, tech ))
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def outputFileTech(root, tech, name):
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return os.path.join(root, "%s.%s.%s" % ( sample, tech, name ))
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def badSnps( tech ):
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return os.path.join(cleaner_output, "%s.%s.realigner.badsnps" % ( sample, tech ))
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def indelsForFiltering( tech ):
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return outputFileTech(indel_output, tech, "low.calls")
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myTechs = techs
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if sample in ["NA12878", "NA19240"]:
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myTechs = techs + ["SOLID","454"]
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for tech,mappingQuality in zip(myTechs,MQs):
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myChrs = chrs
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if sample in ["NA12891", "NA19239"]:
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myChrs = chrs + ["Y"]
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def badSnpsChr( tech, chr ):
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return os.path.join(cleaner_output, "%s.chr%s.%s.realigner.badsnps" % ( sample, chr, tech ))
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for chr in myChrs:
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bam = "/broad/1KG/DCC/ftp/pilot_data/%s/alignment/%s.chrom%s.%s.SRP000032.2009_07.bam" % ( sample, sample, chr, tech )
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def outputFile(root, name):
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return os.path.join(root, "%s.chr%s.%s.%s" % ( sample, chr, tech, name ))
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def MismatchIntervals(bam, outputFile, intervals):
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return config.gatkCmd('MismatchIntervals') + " -o " + outputFile + " -L " + intervals + " -I " + bam
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def IndelIntervals(bam, outputFile, intervals):
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return config.gatkCmd('IndelIntervals') + " -o " + outputFile + " -L " + intervals + " -I " + bam
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def MergeIntervals(bam, files, outputFile, intervals):
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return config.gatkCmd('MergeIntervals') + " -o " + outputFile + " ".join(map( lambda x: " -intervals " + x, files )) + " -L " + intervals + " -I " + bam
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def CleanIntervals(bam, outputFile, intervals, snpfile):
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return config.gatkCmd('IntervalCleaner') + " -O " + outputFile + " -L " + intervals + " -I " + bam
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def Injector(bam, outputFile, intervals, inputfile):
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return config.gatkCmd('CleanedReadInjector') + " --output_bam " + outputFile + " -L " + intervals + " -I " + bam + " --cleaned_reads " + inputfile
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jobid = None
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mergeid = None
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bamToCallFrom = finalBam(tech)
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if ( tech != "454" ):
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mismatchIntervalsFile = outputFile(intervals_dir, "mismatches.intervals")
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cmd = MismatchIntervals(bam, mismatchIntervalsFile, str(chr))
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, mismatchIntervalsFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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indelIntervalsFile = outputFile(intervals_dir, "indels.intervals")
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cmd = IndelIntervals(bam, indelIntervalsFile, str(chr))
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelIntervalsFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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mergedIntervalsFile = outputFile(intervals_dir, "merged.intervals")
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cmd = MergeIntervals(bam, [mismatchIntervalsFile, indelIntervalsFile], mergedIntervalsFile, str(chr))
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, mergedIntervalsFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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cleanedFile = outputFile(cleaner_output, "bam")
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badsnpsFile = badSnpsChr(tech, str(chr))
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cmd = CleanIntervals(bam, cleanedFile, mergedIntervalsFile, badsnpsFile)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, cleanedFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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injectedFile = outputFile(injector_output, "bam")
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cmd = Injector(bam, injectedFile, str(chr), cleanedFile)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, injectedFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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# HOW DO I CALL MergeBAMBatch FROM HERE?
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# def MergeBams():
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# return "MergeBAMBatch.py -d " + final_bam_dir + " -q " + OPTIONS.farmQueue + " -s '" + bamToCallFrom + "\t" + os.path.join(injector_output, "%s.chr*.%s.bam" % ( sample, tech )) + "'"
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# cmd = MergeBams()
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# jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, bamToCallFrom, just_print_commands = OPTIONS.dry, waitID = jobid)
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mergeid = jobid
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cmd = "cat "
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for chr in myChrs:
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cmd = cmd + " " + badSnpsChr(tech, chr)
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cmd = cmd + " > " + badSnps(tech)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, badSnps(tech), just_print_commands = OPTIONS.dry, waitID = mergeid)
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def IndelCaller(bam, outputFile, fraction):
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return config.gatkCmd('IndelGenotyper') + " -O " + outputFile + " -I " + bam + " -minFraction " + fraction
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def SnpCaller(bam, outputFile):
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return config.gatkCmd('SingleSampleGenotyper') + " -o " + outputFile + " -I " + bam
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def VarFiltration(bam, outputHead, snpcalls, badsnps, indelcalls, depth, mq):
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return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -I " + bam + " -B variant,Variants," + snpcalls + ",cleaned,CleanedOutSnp," + badsnps + ",indels,SimpleIndel," + indelcalls + " -X DepthOfCoverage:max=" + depth + " -X MappingQualityZero:max=" + mq
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def VarFiltration454(bam, outputHead, snpcalls, depth, mq):
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return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -I " + bam + " -B variant,Variants," + snpcalls + " -X DepthOfCoverage:max=" + depth + " -X MappingQualityZero:max=" + mq
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indelsFileHigh = outputFileTech(indel_output, tech, "high.calls")
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cmd = IndelCaller(bamToCallFrom, indelsFileHigh, "0.3")
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelsFileHigh, just_print_commands = OPTIONS.dry, waitID = mergeid)
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indelsFileLow = indelsForFiltering(tech)
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cmd = IndelCaller(bamToCallFrom, indelsFileLow, "0.1")
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelsFileLow, just_print_commands = OPTIONS.dry, waitID = mergeid)
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snpsFile = outputFileTech(snp_output, tech, "calls")
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cmd = SnpCaller(bamToCallFrom, snpsFile)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, snpsFile, just_print_commands = OPTIONS.dry, waitID = jobid) # wait on the low indel calls
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varFiltFile = os.path.join(filter_output, "%s.%s" % ( sample, tech ))
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if ( tech != "454" ):
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cmd = VarFiltration(bamToCallFrom, varFiltFile, snpsFile, badsnpsFile, indelsFileLow, str(DoC), str(mappingQuality))
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else:
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cmd = VarFiltration454(bamToCallFrom, varFiltFile, snpsFile, str(DoC), str(mappingQuality))
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, varFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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def SnpCaller(bams, outputFile):
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return config.gatkCmd('SingleSampleGenotyper') + " -o " + outputFile + " ".join(map( lambda x: " -I " + x, bams ))
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def VarFiltration(bams, outputHead, snpcalls, badsnps, indelcalls, depth, mq):
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return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -B variant,Variants," + snpcalls + ",cleaned,CleanedOutSnp," + badsnps + ",indels,SimpleIndel," + indelcalls + " -X DepthOfCoverage:max=" + depth + " -X MappingQualityZero:max=" + mq + " ".join(map( lambda x: " -I " + x, bams ))
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#
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# HOW DO I MAKE THESE JOBS DEPEND ON THE MERGE IDS OF THE INDIVIDUAL SAMPLES???
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# (Or until everything else is done?)
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#
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solid454SnpsFile = outputFileTech(snp_output, "454-SOLID", "calls")
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cmd = SnpCaller([finalBam("SOLID"),finalBam("454")], solid454SnpsFile)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, solid454SnpsFile, just_print_commands = OPTIONS.dry, waitID = allMergeIds)
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solid454VarFiltFile = os.path.join(filter_output, "%s.454-SOLID" % ( sample ))
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cmd = VarFiltration([finalBam("SOLID"),finalBam("454")], solid454VarFiltFile, solid454SnpsFile, badSnps("SOLID"), indelsForFiltering("SOLID"), str(DoC), str(mappingQuality))
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, allVarFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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allSnpsFile = outputFileTech(snp_output, "allTechs", "calls")
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cmd = SnpCaller([finalBam("SLX"),finalBam("SOLID"),finalBam("454")], solid454SnpsFile)
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, allSnpsFile, just_print_commands = OPTIONS.dry, waitID = allMergeIds)
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allVarFiltFile = os.path.join(filter_output, "%s.allTechs" % ( sample ))
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cmd = VarFiltration([finalBam("SLX"),finalBam("SOLID"),finalBam("454")], varFiltFile, allSnpsFile, badSnps("SLX"), indelsForFiltering("SLX"), str(DoC), str(mappingQuality))
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, allVarFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid)
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#
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# HOW DO I COMBINE ALL OF THE MQs AND DOCs?
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#
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