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) 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") samples = ["NA12878","NA12891","NA12892","NA19238","NA19239","NA19240"] DoCs = [76,88,66,56,68,86] chrs = range(1, 22) + ["X"] for sample, DoC in zip(samples, DoCs): # # Actually do some work here # myChrs = chrs if sample in ["NA12891", "NA19239"]: myChrs = chrs + ["Y"] for chr in myChrs: def filepath(tech): return "/broad/1KG/DCC/ftp/pilot_data/%s/alignment/%s.chrom%s.%s.SRP000032.2009_07.bam" % ( sample, sample, chr, tech ) techs = ["SLX", "SOLID", "454"] MQs = [100,5,5] solexaBamFile = None solidBamFile = None for tech,mappingQuality in zip(techs,MQs): bam = filepath(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('MergeIntervals') + " -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 def IndelCaller(bam, outputFile, intervals, fraction): return config.gatkCmd('IndelGenotyper') + " -O " + outputFile + " -L " + intervals + " -I " + bam + " -minFraction " + fraction def SnpCaller(bam, outputFile, intervals): return config.gatkCmd('SingleSampleGenotyper') + " -o " + outputFile + " -L " + intervals + " -I " + bam def VarFiltration(bam, outputHead, intervals, snpcalls, badsnps, indelcalls, depth, mq): return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -L " + intervals + " -I " + bam + " -B variant,Variants," + snpcalls + ",cleaned,CleanedOutSnp," + badsnps + ",indels,SimpleIndel," + indelcalls + " -X DepthOfCoverage:" + depth + " -X MappingQualityZero:" + mq def VarFiltration454(bam, outputHead, intervals, snpcalls, depth, mq): return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -L " + intervals + " -I " + bam + " -B variant,Variants," + snpcalls + " -X DepthOfCoverage:" + depth + " -X MappingQualityZero:" + mq jobid = None indelsFileLow = None if ( tech != "454" ): 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 = jobid) 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 = jobid) 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 = jobid) cleanedFile = outputFile(cleaner_output, "bam") badsnpsFile = outputFile(cleaner_output, "realigner.badsnps") 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) if ( tech == "SLX" ): solexaBamFile = injectedFile if ( tech == "SOLID" ): solidBamFile = injectedFile cmd = "samtools index " + injectedFile jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, injectedFile + ".bai", just_print_commands = OPTIONS.dry, waitID = jobid) indelsFileLow = outputFile(indel_output, "low.calls") cmd = IndelCaller(injectedFile, indelsFileLow, str(chr), "0.1") jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelsFileLow, just_print_commands = OPTIONS.dry, waitID = jobid) indelsFileHigh = outputFile(indel_output, "high.calls") cmd = IndelCaller(injectedFile, indelsFileHigh, str(chr), "0.3") jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, indelsFileHigh, just_print_commands = OPTIONS.dry, waitID = jobid) snpsFile = outputFile(snp_output, "calls") cmd = SnpCaller(injectedFile, snpsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, snpsFile, just_print_commands = OPTIONS.dry, waitID = jobid) varFiltFile = os.path.join(filter_output, "%s.chr%s.%s" % ( sample, chr, tech )) cmd = VarFiltration(injectedFile, varFiltFile, str(chr), snpsFile, badsnpsFile, indelsFileLow, str(DoC), str(mappingQuality)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, varFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid) else: snpsFile = outputFile(snp_output, "calls") cmd = SnpCaller(bam, snpsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, snpsFile, just_print_commands = OPTIONS.dry, waitID = jobid) varFiltFile = os.path.join(filter_output, "%s.chr%s.%s" % ( sample, chr, tech )) cmd = VarFiltration454(bam, varFiltFile, str(chr), snpsFile, str(DoC), str(mappingQuality)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, varFiltFile, just_print_commands = OPTIONS.dry, waitID = jobid) def outputFile(root, techs, name): return os.path.join(root, "%s.chr%s.%s.%s" % ( sample, chr, techs, name )) def SnpCaller(bams, outputFile, intervals): return config.gatkCmd('SingleSampleGenotyper') + " -o " + outputFile + " -L " + intervals + " ".join(map( lambda x: " -I " + x, bams )) def VarFiltration(bams, outputHead, intervals, snpcalls, badsnps, indelcalls, depth, mq): return config.gatkCmd('VariantFiltration') + " -VOH " + outputHead + " -L " + intervals + " -B variant,Variants," + snpcalls + ",cleaned,CleanedOutSnp," + badsnps + ",indels,SimpleIndel," + indelcalls + " -X DepthOfCoverage:" + depth + " -X MappingQualityZero:" + mq + " ".join(map( lambda x: " -I " + x, bams )) solid454SnpsFile = outputFile(snp_output, "454-SOLID", "calls") cmd = SnpCaller([solidBamFile,filepath("454")], solid454SnpsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, solid454SnpsFile, just_print_commands = OPTIONS.dry, waitID = jobid) allSnpsFile = outputFile(snp_output, "allTechs", "calls") cmd = SnpCaller([solexaBamFile,solidBamFile,filepath("454")], allSnpsFile, str(chr)) jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, allSnpsFile, just_print_commands = OPTIONS.dry, waitID = jobid)