import farm_commands import os.path import sys from optparse import OptionParser from gatkConfigParser import * import glob import itertools if __name__ == "__main__": usage = """usage: %prog [-c config.cfg]*""" parser = OptionParser(usage=usage) parser.add_option("-q", "--farm", dest="farmQueue", type="string", default=None, help="Farm queue to send processing jobs to") parser.add_option("-c", "--config", dest="configs", action="append", type="string", default=[], help="Configuration file") parser.add_option("-w", "--wait", dest="initialWaitID", type="string", default=None, help="If providedm the first job dispatched to LSF will use this id as it ended() prerequisite") parser.add_option("", "--dry", dest="dry", action='store_true', default=False, help="If provided, nothing actually gets run, just a dry run") parser.add_option("-i", "--ignoreExistingFiles", dest="ignoreExistingFiles", action='store_true', default=False, help="Ignores already written files, if present") parser.add_option("-d", "--dir", dest="outputdir", type="string", default="./", help="Output directory") (OPTIONS, args) = parser.parse_args() if len(args) != 0: parser.error("incorrect number of arguments") config = gatkConfigParser(OPTIONS.configs) if not os.path.exists(OPTIONS.outputdir): os.mkdir(OPTIONS.outputdir) def outputDir(suffix): return os.path.join(OPTIONS.outputdir, suffix) # Official genome-wide Depth of Coverage tables for pilot 2, freeze 5: # NA12878 NA12891 NA12892 NA19238 NA19239 NA19240 # 454: 36 18 # SLX: 82 91 70 56 68 86 # SOLID: 37 64 # 454+SLD: 64 77 # ALL: 138 150 DoC_454 = {"NA12878":36,"NA19240":18} DoC_slx = {"NA12878":82,"NA12891":91,"NA12892":70,"NA19238":56,"NA19239":68,"NA19240":86} DoC_solid = {"NA12878":37,"NA19240":64} DoC_454solid = {"NA12878":64,"NA19240":77} DoC_all = {"NA12878":138,"NA19240":150} DoC_hash = {"454":DoC_454,"SLX":DoC_slx,"SOLID":DoC_solid,"454SOLID":DoC_454solid,"ALL":DoC_all} MQ_hash = {"SLX":100,"SOLID":5,"454":5,"454SOLID":10,"ALL":110} intervals_dir = outputDir("intervals") cleaner_output = outputDir("cleaner") injector_output = outputDir("bams") snp_output = outputDir("calls/unfiltered_snps") filter_output = outputDir("calls/filtered_snps") indel_output = outputDir("calls/indels") final_bam_dir = outputDir("useTheseBamsForAnalyses") #final_bam_dir = "/humgen/gsa-hphome1/projects/1kg_pilot2/useTheseBamsForAnalyses" samples = ["NA12878","NA12891","NA12892","NA19238","NA19239","NA19240"] techs = ["SLX"] chrs = range(1, 23) + ["X"] for sample in samples: # # Actually do some work here # def finalBam(tech): return os.path.join(final_bam_dir, "%s.%s.bam" % ( sample, tech )) def outputFileTech(root, tech, name): return os.path.join(root, "%s.%s.%s" % ( sample, tech, name )) def badSnps( tech ): return os.path.join(cleaner_output, "%s.%s.realigner.badsnps" % ( sample, tech )) def indelsForFiltering( tech ): return outputFileTech(indel_output, tech, "low.calls") myTechs = techs if sample in ["NA12878", "NA19240"]: myTechs = techs + ["SOLID","454"] for tech in myTechs: if ( tech != "454" ): myChrs = chrs if sample in ["NA12891", "NA19239"]: myChrs = chrs + ["Y"] def badSnpsChr( tech, chr ): return os.path.join(cleaner_output, "%s.chr%s.%s.realigner.badsnps" % ( sample, chr, tech )) def makeJobName(suffix): return sample + "." + tech + "." + suffix def makeJobClass(suffix): return sample + ".*." + suffix for chr in myChrs: bam = "/broad/1KG/DCC/ftp/pilot_data/%s/alignment/%s.chrom%s.%s.SRP000032.2009_07.bam" % ( sample, sample, chr, tech ) def outputFile(root, name): return os.path.join(root, "%s.chr%s.%s.%s" % ( sample, chr, tech, name )) def MismatchIntervals(bam, outputFile, intervals): return config.gatkCmd('MismatchIntervals') + " -o " + outputFile + " -L " + intervals + " -I " + bam def IndelIntervals(bam, outputFile, intervals): return config.gatkCmd('IndelIntervals') + " -o " + outputFile + " -L " + intervals + " -I " + bam def MergeIntervals(bam, files, outputFile, intervals): return config.gatkCmd('IntervalMerger') + " -o " + outputFile + " ".join(map( lambda x: " -intervals " + x, files )) + " -L " + intervals + " -I " + bam def CleanIntervals(bam, outputFile, intervals, snpfile): return config.gatkCmd('IntervalCleaner') + " -O " + outputFile + " -L " + intervals + " -I " + bam def Injector(bam, outputFile, intervals, inputfile): return config.gatkCmd('CleanedReadInjector') + " --output_bam " + outputFile + " -L " + intervals + " -I " + bam + " --cleaned_reads " + inputfile jobid = None mismatchIntervalsFile = outputFile(intervals_dir, "mismatches.intervals") cmd = MismatchIntervals(bam, mismatchIntervalsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, mismatchIntervalsFile, just_print_commands = OPTIONS.dry, waitID = None, jobName = makeJobName("phase1." + str(chr))) indelIntervalsFile = outputFile(intervals_dir, "indels.intervals") cmd = IndelIntervals(bam, indelIntervalsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelIntervalsFile, just_print_commands = OPTIONS.dry, waitID = None, jobName = makeJobName("phase1." + str(chr))) mergedIntervalsFile = outputFile(intervals_dir, "merged.intervals") cmd = MergeIntervals(bam, [mismatchIntervalsFile, indelIntervalsFile], mergedIntervalsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, mergedIntervalsFile, just_print_commands = OPTIONS.dry, waitID = makeJobName("phase1." + str(chr))) cleanedFile = outputFile(cleaner_output, "bam") badsnpsFile = badSnpsChr(tech, str(chr)) cmd = CleanIntervals(bam, cleanedFile, mergedIntervalsFile, badsnpsFile) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, cleanedFile, just_print_commands = OPTIONS.dry, waitID = jobid) injectedFile = outputFile(injector_output, "bam") cmd = Injector(bam, injectedFile, str(chr), cleanedFile) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, injectedFile, just_print_commands = OPTIONS.dry, waitID = jobid) cmd = "samtools index " + injectedFile jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, injectedFile + ".bai", just_print_commands = OPTIONS.dry, waitID = jobid, jobName = makeJobName("phase2")) def MergeBams(outputFile): return "MergeBAMBatch.py -d " + cleaner_output + " -q " + OPTIONS.farmQueue + " -s '" + outputFile + "\t" + os.path.join(cleaner_output, "%s.chr*.%s.bam" % ( sample, tech )) + "'" cmd = MergeBams(finalBam(tech)) mergeJobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, finalBam(tech), just_print_commands = OPTIONS.dry, waitID = makeJobName("phase2"), jobName = makeJobName("phase3")) cmd = "cat " for chr in myChrs: cmd = cmd + " " + badSnpsChr(tech, chr) cmd = cmd + " > " + badSnps(tech) badsnpsJobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, badSnps(tech), just_print_commands = OPTIONS.dry, waitID = makeJobName("phase2"), jobName = makeJobName("phase4")) def IndelCaller(bam, outputFile, fraction): return config.gatkCmd('IndelGenotyper') + " -O " + outputFile + " -I " + bam + " -minFraction " + fraction def SnpCaller(bam, outputFile): return config.gatkCmd('SingleSampleGenotyper') + " -varout " + outputFile + " -I " + bam def VarFiltration(bam, outputHead, snpcalls, badsnps, indelcalls, depth, mq): 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 def VarFiltration454(bam, outputHead, snpcalls, depth, mq): return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -I " + bam + " -B variant,Variants," + snpcalls + " -X DepthOfCoverage:max=" + depth + " -X MappingQualityZero:max=" + mq waitid = makeJobName("phase3") if ( tech == "454" ): waitid = None bamToCallFrom = finalBam(tech) indelsFileHigh = outputFileTech(indel_output, tech, "high.calls") cmd = IndelCaller(bamToCallFrom, indelsFileHigh, "0.3") jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelsFileHigh, just_print_commands = OPTIONS.dry, waitID = waitid) indelsFileLow = indelsForFiltering(tech) cmd = IndelCaller(bamToCallFrom, indelsFileLow, "0.1") jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelsFileLow, just_print_commands = OPTIONS.dry, waitID = waitid, jobName = makeJobName("phase4")) snpsFile = outputFileTech(snp_output, tech, "calls") cmd = SnpCaller(bamToCallFrom, snpsFile) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, snpsFile, just_print_commands = OPTIONS.dry, waitID = waitid, jobName = makeJobName("phase4")) varFiltFile = os.path.join(filter_output, "%s.%s" % ( sample, tech )) if ( tech != "454" ): cmd = VarFiltration(bamToCallFrom, varFiltFile, snpsFile, badSnps(tech), indelsFileLow, str(DoC_hash[tech][sample]), str(MQ_hash[tech])) else: cmd = VarFiltration454(bamToCallFrom, varFiltFile, snpsFile, str(DoC_hash[tech][sample]), str(MQ_hash[tech])) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, varFiltFile, just_print_commands = OPTIONS.dry, waitID = makeJobName("phase4")) def SnpCaller(bams, outputFile): return config.gatkCmd('SingleSampleGenotyper') + " -varout " + outputFile + " ".join(map( lambda x: " -I " + x, bams )) def VarFiltration(bams, outputHead, snpcalls, badsnps, indelcalls, depth, mq): 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 )) if sample in ["NA12878", "NA19240"]: solid454SnpsFile = outputFileTech(snp_output, "454-SOLID", "calls") cmd = SnpCaller([finalBam("SOLID"),finalBam("454")], solid454SnpsFile) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, solid454SnpsFile, just_print_commands = OPTIONS.dry, waitID = makeJobClass("phase3")) solid454VarFiltFile = os.path.join(filter_output, "%s.454-SOLID" % ( sample )) cmd = VarFiltration([finalBam("SOLID"),finalBam("454")], solid454VarFiltFile, solid454SnpsFile, badSnps("SOLID"), indelsForFiltering("SOLID"), str(DoC_hash["454SOLID"][sample]), str(MQ_hash["454SOLID"])) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, solid454VarFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid) allSnpsFile = outputFileTech(snp_output, "allTechs", "calls") cmd = SnpCaller([finalBam("SLX"),finalBam("SOLID"),finalBam("454")], allSnpsFile) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, allSnpsFile, just_print_commands = OPTIONS.dry, waitID = makeJobClass("phase3")) allVarFiltFile = os.path.join(filter_output, "%s.allTechs" % ( sample )) cmd = VarFiltration([finalBam("SLX"),finalBam("SOLID"),finalBam("454")], allVarFiltFile, allSnpsFile, badSnps("SLX"), indelsForFiltering("SLX"), str(DoC_hash["ALL"][sample]), str(MQ_hash["ALL"])) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, allVarFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid)