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vcf_gff.py change #1

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26 changes: 2 additions & 24 deletions vcf_gff.py
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Expand Up @@ -75,31 +75,9 @@ def get_gen(formatcols, ref):
reads = sample_dict.get("DP")
else:
reads = "NA"
if sample_dict.has_key("NF"):
if sample_dict.has_key("GT"):
"""
polysnp tool output
"""
freq = sample_dict.get("NF")
variants = freq.split("|")
if int(variants[0]) >= 1:
var += "A"
if int(variants[1]) >= 1:
var += "C"
if int(variants[2]) >= 1:
var += "G"
if int(variants[3]) >= 1:
var += "T"
if var == "":
gen = "NA"
elif var == ref:
gen = "HOM_ref"
elif len(var) >= 2:
gen = "HET"
else:
gen = "HOM_mut"
elif sample_dict.has_key("GT"):
"""
mpileup output, recommend ALWAYS have GT, note this only good scoring for diploids too!
mpileup output, recommend ALWAYS have GT, note this only good for scoring diploids too!
"""
genotypes = sample_dict.get("GT")
if genotypes == "1/1":
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