87 lines
4.0 KiB
Python
87 lines
4.0 KiB
Python
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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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import string
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import re
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import glob
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import picard_utils
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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 main():
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global OPTIONS, ROOT
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usage = "usage: %prog lanes.list nIndividuals [options]"
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parser = OptionParser(usage=usage)
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parser.add_option("-q", "--farmQueue", dest="farmQueue",
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type="string", default=None,
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help="Farm queue to submit jobs to. Leave blank for local processing")
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parser.add_option("-l", "--lod", dest="lod",
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type="float", default=5,
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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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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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(OPTIONS, args) = parser.parse_args()
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if len(args) != 2:
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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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print gelis
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print variantsOut
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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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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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nNovelSnps += int(NOVEL_SNPS)
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print 'DATA: ', flowcellDotlane, TOTAL_SNPS, NOVEL_SNPS, PCT_DBSNP, NUM_IN_DB_SNP, dbsnp_matches
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print 'DATA: TOTAL SNP CALLS SUMMED ACROSS LANES, NOT ACCOUNT FOR IDENTITY', nTotalSnps
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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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jobid = None
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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, variantsOut) )
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#jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, just_print_commands=False)
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cmd = ("cat %s | awk '$1 !~ \"@\" && $1 !~ \"#Sequence\" && $0 !~ \"GeliToText\"' | sort -k 1 -k 2 -n > tmp.calls" % ( ' '.join(variantsOut) ) )
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, just_print_commands=False, waitID = jobid)
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sortedCallFile = 'all.sorted.calls'
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cmd = ("~/dev/GenomeAnalysisTK/trunk/perl/sortByRef.pl -k 1 tmp.calls ~/work/humanref/Homo_sapiens_assembly18.fasta.fai > %s" % ( sortedCallFile ) )
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jobid = farm_commands.cmd(cmd, OPTIONS.farmQueue, just_print_commands=False, waitID = jobid)
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sortedCalls = [line.split() for line in open(sortedCallFile)]
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aggregratedCalls = picard_utils.aggregateGeliCalls(sortedCalls)
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outputFile = open(OPTIONS.output, 'w')
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print >> outputFile, 'loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom'
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for snp in map( lambda x: picard_utils.aggregatedGeliCalls2SNP(x, nIndividuals), aggregratedCalls ):
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if snp == None: continue # ignore bad calls
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#print snp
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#sharedCalls = list(sharedCallsGroup)
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#genotype = list(sharedCalls[0][5])
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print >> outputFile, '%s %s %s %.6f -420.0 -420.0 0.000000 100.0 %d %d %d %d' % (snp.loc, snp.ref, snp.alt(), snp.q(), nIndividuals, snp.nRefGenotypes(), snp.nHetGenotypes(), snp.nHomVarGenotypes())
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outputFile.close()
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if __name__ == "__main__":
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main()
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