def parse_alleles(toks, options):
""" return the alleles (first sample /last column) todo: more general?"""
if toks[-2].split(":")[0] == "GT":
gtcol = len(toks) - 1
if options.g:
gttok = "0|1"
else:
gttok = toks[gtcol].split(":")[0]
gts = "|".join(gttok.replace(".", "0").split("/")).split("|")
vals = [parse_ref(toks)] + parse_alts(toks)
alleles = [vals[int(x)] for x in gts]
return alleles
return []
def parse_alleles(toks, options):
""" return the alleles (first sample /last column) todo: more general?"""
if toks[-2].split(":")[0] == "GT":
gtcol = len(toks) - 1
if options.g:
gttok = "0|1"
else:
gttok = toks[gtcol].split(":")[0]
gts = "|".join(gttok.replace(".", "0").split("/")).split("|")
vals = [parse_ref(toks)] + parse_alts(toks)
alleles = [vals[int(x)] for x in gts]
return alleles
return []
def make_allele_dict(vcf_path, options):
""" load up all variants by their coordinates
map (chrom, pos) -> [allele1, allele2]
"""
vcf_dict = dict()
ref_dict = dict()
with open(vcf_path) as f:
for line in f:
skip = line[0] == "#"
for ignore_keyword in options.i:
if ignore_keyword in line:
skip = True
if not skip:
toks = line.split()
chrom = toks[0] if options.c is False else None
pos = int(toks[1])
alleles = parse_alleles(toks, options)
vcf_dict[(chrom, pos)] = alleles
ref_dict[(chrom, pos)] = [parse_ref(toks)]
return vcf_dict, ref_dict
def make_allele_dict(vcf_path, options):
""" load up all variants by their coordinates
map (chrom, pos) -> [allele1, allele2]
"""
vcf_dict = dict()
ref_dict = dict()
with open(vcf_path) as f:
for line in f:
skip = line[0] == "#"
for ignore_keyword in options.i:
if ignore_keyword in line:
skip = True
if not skip:
toks = line.split()
chrom = toks[0] if options.c is False else None
pos = int(toks[1])
alleles = parse_alleles(toks, options)
vcf_dict[(chrom, pos)] = alleles
ref_dict[(chrom, pos)] = [parse_ref(toks)]
return vcf_dict, ref_dict
