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CG_caller update #2

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merged 2 commits into from
Aug 11, 2014
Merged

CG_caller update #2

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345a503
Update cgCaller.py
songsy Aug 8, 2014
66f674d
Update cgCaller.py
songsy Aug 8, 2014
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43 changes: 43 additions & 0 deletions tools/cgCaller.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,3 +105,46 @@
allele_indices.append(2)
print("{chrom}\t{pos}\t.\t{ref_a}\t{alt_a}\t.\tPASS\t.\tGT\t{gen1}/{gen2}".format(chrom=args.chr,
pos=begin+1, ref_a=allele_ref, alt_a=",".join(alt_alleles), gen1=allele_indices[0], gen2=allele_indices[1]))

if var_type == "sub":
if zygosity in ["hom", "het-ref", "het-alt"]:
allele_ref = fields[7]
allele_1 = fields[8]
allele_2 = fields[9]
allele1_qual = fields[14]
allele2_qual = fields[15]
if allele1_qual == "VQHIGH" and allele2_qual == "VQHIGH" and len(allele_ref)==len(allele_1) and len(allele_ref)==len(allele_2):
for i in range(0,len(allele_1)):
mask_generator.addCalledPosition(begin + 1)
allele_indices = []
alt_alleles = []
if allele_1[i] != allele_ref[i]:
alt_alleles.append(allele_1[i])
allele_indices.append(1)
elif allele_1[i] == allele_ref[i]:
allele_indices.append(0)
if allele_2[i] == allele_ref[i]:
allele_indices.append(0)
elif allele_2[i] == allele_1[i]:
allele_indices.append(1)
else:
if len(alt_alleles)==0:
alt_alleles.append(allele_2[i])
allele_indices.append(1)
else:
alt_alleles.append(allele_2[i])
allele_indices.append(2)
if allele_indices[0]==0 and allele_indices[1]==0:
if sites_parser is not None:
while not sites_parser.end and sites_parser.pos < begin+i+1:
sites_parser.tick()
if sites_parser.pos == begin+i+1:
assert allele_ref[i] == sites_parser.ref_a
print("{chrom}\t{pos}\t.\t{ref_a}\t{alt_a}\t.\tPASS\t.\tGT\t0/0".format(chrom=args.chr, pos=begin+i+1,ref_a=sites_parser.ref_a,alt_a=sites_parser.alt_a))
else:
if sites_parser is not None:
while not sites_parser.end and sites_parser.pos < begin+i+1:
sites_parser.tick()
if sites_parser.pos == begin+i+1:
assert allele_ref[i] == sites_parser.ref_a
print("{chrom}\t{pos}\t.\t{ref_a}\t{alt_a}\t.\tPASS\t.\tGT\t{gen1}/{gen2}".format(chrom=args.chr, pos=begin+i+1, ref_a=allele_ref[i], alt_a=",".join(alt_alleles), gen1=allele_indices[0], gen2=allele_indices[1]))