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