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#! /usr/bin/env python
from __future__ import print_function
import argparse
import sys
import cyvcf2
import collections
def argument_parsing():
"""
Parse command-line options.
"""
parser = argparse.ArgumentParser(description='Split BND calls')
parser.add_argument('-v', '--vcf', metavar='input.vcf.gz', required=True, dest='vcf', help='input VCF/BCF file (required)')
parser.add_argument('-r', '--ref', metavar='ref.fa', required=True, dest='ref', help='input reference (required)')
parser.add_argument('-o', '--out', metavar='out.vcf', required=True, dest='out', help='output VCF file (required)')
return parser.parse_args()
"""Heng Li's FASTA/FASTQ parser
"""
def readfq(fp): # this is a generator function
last = None # this is a buffer keeping the last unprocessed line
while True: # mimic closure; is it a bad idea?
if not last: # the first record or a record following a fastq
for l in fp: # search for the start of the next record
if l[0] in '>@': # fasta/q header line
last = l[:-1] # save this line
break
if not last: break
name, seqs, last = last[1:].partition(" ")[0], [], None
for l in fp: # read the sequence
if l[0] in '@+>':
last = l[:-1]
break
seqs.append(l[:-1])
if not last or last[0] != '+': # this is a fasta record
yield name, ''.join(seqs), None # yield a fasta record
if not last: break
else: # this is a fastq record
seq, leng, seqs = ''.join(seqs), 0, []
for l in fp: # read the quality
seqs.append(l[:-1])
leng += len(l) - 1
if leng >= len(seq): # have read enough quality
last = None
yield name, seq, ''.join(seqs); # yield a fastq record
break
if last: # reach EOF before reading enough quality
yield name, seq, None # yield a fasta record instead
break
def delly2bnd(args):
# Fetch breakpoint positions
bndPos = collections.defaultdict(dict)
oldChr = None
if not len(bndPos):
vcf = cyvcf2.VCF(args.vcf)
for record in vcf:
if record.CHROM != oldChr:
oldChr = record.CHROM
print("Fetching BND calls...", oldChr, file=sys.stderr)
# Ignore multi-allelics
if len(record.ALT) > 1:
continue
# Only delly BND and TRA calls
if record.INFO.get("SVTYPE") == "BND":
ct = record.INFO.get("CT")
chrom2 = record.INFO.get("CHR2")
pos2 = record.INFO.get("POS2")
elif record.INFO.get("SVTYPE") == "TRA":
ct = record.INFO.get("CT")
chrom2 = record.INFO.get("CHR2")
pos2 = record.INFO.get("END")
else:
continue
chrom = record.CHROM
pos = record.POS
bndPos[chrom][pos] = 'N'
bndPos[chrom2][pos2] = 'N'
# Fetch nucleotides
if True:
f_in = gzip.open(args.ref) if args.ref.endswith('.gz') else open(args.ref)
for seqName, seqNuc, seqQuals in readfq(f_in):
if seqName in bndPos.keys():
print("Fetching breakpoint nucleotides...", seqName, file=sys.stderr)
for pos in bndPos[seqName].keys():
bndPos[seqName][pos] = seqNuc[(pos-1):pos]
# Parse VCF/BCF
vcf = cyvcf2.VCF(args.vcf)
vcf.add_info_to_header({'ID': 'MATEID', 'Description': 'ID of mate breakends', 'Type':'String', 'Number': '.'})
w = cyvcf2.Writer(args.out, vcf)
oldChr = None
for record in vcf:
if record.CHROM != oldChr:
oldChr = record.CHROM
print("Processing...", oldChr, file=sys.stderr)
# Ignore multi-allelics
if len(record.ALT) > 1:
continue
# Only delly BND and TRA calls
if record.INFO.get("SVTYPE") == "BND":
ct = record.INFO.get("CT")
chrom2 = record.INFO.get("CHR2")
pos2 = record.INFO.get("POS2")
elif record.INFO.get("SVTYPE") == "TRA":
ct = record.INFO.get("CT")
chrom2 = record.INFO.get("CHR2")
pos2 = record.INFO.get("END")
else:
continue
chrom = record.CHROM
pos = record.POS
id1 = record.ID + "_2nd"
id2 = record.ID + "_1st"
if ct == '3to5':
template = bndPos[chrom][pos] + "[" + chrom2 + ":" + str(pos2) + "["
template2 = "]" + chrom + ":" + str(pos) + "]" + bndPos[chrom2][pos2]
elif ct == '5to3':
template = "]" + chrom2 + ":" + str(pos2) + "]" + bndPos[chrom][pos]
template2 = bndPos[chrom2][pos2] + "[" + chrom + ":" + str(pos) + "["
elif ct == '3to3':
template = bndPos[chrom][pos] + "]" + chrom2 + ":" + str(pos2) + "]"
template2 = bndPos[chrom2][pos2] + "]" + chrom + ":" + str(pos) + "]"
else:
template = "[" + chrom2 + ":" + str(pos2) + "[" + bndPos[chrom][pos]
template2 = "[" + chrom + ":" + str(pos) + "[" + bndPos[chrom2][pos2]
# 2nd breakend
record.ID = id1
record.INFO['MATEID'] = id2
record.ALT = [template]
w.write_record(record)
# 1st breakend
record.CHROM = chrom2
record.set_pos(pos2 - 1)
record.ID = id2
record.INFO['MATEID'] = id1
record.REF = bndPos[chrom2][pos2]
record.ALT = [template2]
record.INFO['CHR2'] = chrom
record.INFO['POS2'] = pos
record.INFO['END'] = pos2 + 1
if ct == '5to3':
record.INFO['CT'] = '3to5'
elif ct == '3to5':
record.INFO['CT'] = '5to3'
w.write_record(record)
# Close file
w.close()
def main():
arguments = argument_parsing()
delly2bnd(arguments)
if __name__ == '__main__':
main()
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