def filter_vcf(pileup, outfile=None, chr_col=0, ref_col=3, alt_col=4, sep='\t'):
""" Removes lines where ALT==REF and chromosomes other than 1 - 22, X, Y and MT"""
fh = open(pileup, "r")
if outfile is None:
outfile=pileup+'.filt'
fu.delete(outfile)
fh_out = open(outfile, "w")
for line in fh:
line = line.strip()
if line.startswith('#'):
fh_out.write(str(line)+'\n')
else:
fields=line.split(sep)
if(len(fields)>=8):
chr=str(fields[chr_col])
ref=str(fields[ref_col])
alt=str(fields[alt_col])
if (alt != ref) and (fu.find_first_index(ACCEPTED_CHR, chr.strip()) > -1):
fh_out.write(str(line)+'\n')
def filter_pileup(pileup,
outfile=None,
chr_col=0,
ref_col=2,
alt_col=3,
sep='\t'):
fh = open(pileup, "r")
if outfile is None:
outfile = pileup + '.vcf'
fu.delete(outfile)
fh_out = open(outfile, "w")
fh_out.write(vcfheader(pileup) + '\n')
for line in fh:
line = line.strip()
fields = line.split(sep)
chr = str(fields[chr_col])
ref = str(fields[ref_col])
alt = str(fields[alt_col])
if (alt != ref) and (fu.find_first_index(ACCEPTED_CHR, chr.strip()) >
-1):
fh_out.write(varpileup_line2vcf_line(fields[0:9]) + '\n')
def filter_vcf(pileup,
outfile=None,
chr_col=0,
ref_col=3,
alt_col=4,
sep='\t'):
""" Removes lines where ALT==REF and chromosomes other than 1 - 22, X, Y and MT"""
fh = open(pileup, "r")
if outfile is None:
outfile = pileup + '.filt'
fu.delete(outfile)
fh_out = open(outfile, "w")
for line in fh:
line = line.strip()
if line.startswith('#'):
fh_out.write(str(line) + '\n')
else:
fields = line.split(sep)
if (len(fields) >= 8):
chr = str(fields[chr_col])
ref = str(fields[ref_col])
alt = str(fields[alt_col])
if (alt != ref) and (fu.find_first_index(
ACCEPTED_CHR, chr.strip()) > -1):
fh_out.write(str(line) + '\n')
def filter_vcf(pileup,
outfile=None,
chr_col=0,
ref_col=3,
alt_col=4,
sep='\t'):
fh = open(pileup, "r")
if (outfile is None):
outfile = pileup + '.filt'
fu.delete(outfile)
fh_out = open(outfile, "w")
for line in fh:
line = line.strip()
if line.startswith('#'):
fh_out.write(str(line) + '\n')
else:
fields = line.split(sep)
if (len(fields) >= 8):
chr = str(fields[chr_col])
ref = str(fields[ref_col])
alt = str(fields[alt_col])
if ((alt != ref) and \
(fu.find_first_index(ACCEPTED_CHR, chr.strip()) > -1)):
fh_out.write(str(line) + '\n')
### EOF
def filter_pileup(pileup, outfile=None, chr_col=0, ref_col=2, alt_col=3, sep='\t'):
fh = open(pileup, "r")
if outfile is None:
outfile=pileup+'.vcf'
fu.delete(outfile)
fh_out = open(outfile, "w")
fh_out.write(vcfheader(pileup)+'\n')
for line in fh:
line = line.strip()
fields=line.split(sep)
chr=str(fields[chr_col])
ref=str(fields[ref_col])
alt=str(fields[alt_col])
if (alt != ref) and (fu.find_first_index(ACCEPTED_CHR, chr.strip()) > -1):
fh_out.write(varpileup_line2vcf_line(fields[0:9]) +'\n' )
