48 lines
1.3 KiB
Python
48 lines
1.3 KiB
Python
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print("opening...")
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ea_vcf = open("/humgen/gsa-hpprojects/analysis/privateMutations/eomi+autism/resources/callsets/eomi+autism/eomi+autism_batch.merged.vcf")
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print("reading past header...")
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ln = ea_vcf.readline()
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import random
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while (ln.startswith("#")):
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ln = ea_vcf.readline()
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numcalc = 0
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nread = -1
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def getAC(e):
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if ( e.startswith("0/0") ):
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return 0
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elif ( e.startswith("0/1") or e.startswith("1/0") ):
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return 1
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elif ( e.startswith("1/1") ):
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return 2
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else:
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print("Warning: "+e)
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return 0
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def calcTrans(line):
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spline = line.strip().split("\t")
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gtypes = filter(lambda y: y.find("./.") == -1, spline[9:len(spline)])
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if ( len(gtypes) < 1800 ):
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return (-1,-1)
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random.shuffle(gtypes)
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firstAC = reduce(lambda x,y: x + y , map(lambda u: getAC(u),gtypes[0:900]))
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if ( firstAC > 5 ):
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return (-1,-1)
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secondAC = reduce(lambda x,y: x + y, map(lambda u: getAC(u),gtypes[900:1800]))
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return (firstAC,secondAC)
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print("Calculating...")
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counts = filter(lambda u: u[0] > -1, map(lambda z: calcTrans(z) ,ea_vcf.readlines()))
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print("Lines actually processed: %d" % len(counts))
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cdict = dict()
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for c in counts:
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if ( not c in cdict ):
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cdict[c] = 0
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cdict[c] += 1
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out = open("posterior_counts.txt",'w')
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for c in cdict:
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out.write("%d\t%d\t%d\n" % (c[0],c[1],cdict[c]))
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