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vcf_intersect.py
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vcf_intersect.py
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#!/usr/bin/python
import sys
import os
import string
import re
from optparse import OptionParser
from VcfFile import *
from bx.bitset import *
from bx.bitset_builders import *
def binned_bitsets_from_vcffile( vcfilename, chrom_col=0, start_col=1, upstream_pad=0, downstream_pad=0, lens={} ):
"""
Read a vcffile into a dictionary of bitsets. The defaults arguments
- 'vcfilename' should be a filename for vcf file
- 'chrom_col', 'start_col', and 'end_col' must exist in each line.
- if 'lens' is provided bitset sizes will be looked up from it, otherwise
chromosomes will be assumed to be the maximum size
- the bitset interval made into a zero-based, half-open interval!!!!!!!
"""
last_chrom = None
last_bitset = None
bitsets = dict()
MAX=2147483647
vcfobj=VcfFile(vcfilename)
fh=open(vcfilename,'r')
for vrec in vcfobj.yieldVcfRecord(fh):
filtercode = vrec.getFilter()
chrom = vrec.getChrom()
pos=int( vrec.getPos() )
#if filtercode != filtercodeoption and filtercodeoption != None:
# continue
if filtercode != 'PASS':
if filtercode == '.':
pass
else:
continue
chrom="chr"+chrom
if chrom != last_chrom:
if chrom not in bitsets:
if chrom in lens:
size = lens[chrom]
else:
size = MAX
bitsets[chrom] = BinnedBitSet( size )
last_chrom = chrom
last_bitset = bitsets[chrom]
start, end = (pos-1, pos)
if upstream_pad: start = max( 0, start - upstream_pad )
if downstream_pad: end = min( size, end + downstream_pad )
if start > end: warn( "Interval start after end!" )
last_bitset.set_range( start, end-start )
fh.close()
return bitsets
def main():
usage = "usage: %prog [options] vcf_file_one vcf|bed_file_two\n\nFind regions in the first vcf file that overlap regions of the second vcf or bed file\n"
parser = OptionParser(usage)
parser.add_option("--minCols", type="int", dest="mincols", default=1, help="mininum basepair overlap (default is one)")
parser.add_option("--v", action="store_true", dest="reverse", help="Print regions in first vcf that DO NOT overlap second vcf|bed file")
parser.add_option("--filter", type="string", dest="filter", default=None, help="intersect records only set with filter (default is None")
parser.add_option("--info", type="string", dest="infotag", help="INFO tag id that annotates what type of variant the VCF record is", default="TYPE")
parser.add_option("--type", type="string", dest="variantype", help="type of variant (SNP INS DEL)", default=None)
parser.add_option("--noheader", action="store_true", dest="noheader", help="VCF file one has no header line", default=False)
parser.add_option("--nochrprefix", action="store_false", dest="chrprefix", help="use if the bed doesn't have chr prefix in chrom column", default=True)
(options, args)=parser.parse_args()
sys.stderr.write("intersecting two files ...\n")
vcf_file_one=args[0]
in2_fname=args[1]
in2_fname_ext= os.path.splitext(in2_fname)[1][1:]
if "bed" == in2_fname_ext:
bitsets = binned_bitsets_from_file( open( in2_fname ) )
if "vcf" == in2_fname_ext:
bitsets = binned_bitsets_from_vcffile( in2_fname , options.filter)
vcfobj=VcfFile(vcf_file_one)
vcfh=open(vcf_file_one,'r')
if options.noheader == False:
vcfobj.parseMetaAndHeaderLines(vcfh)
header=vcfobj.returnHeader()
#print header
#vcfobj.parseMetaAndHeaderLines(vcfh)
#descriptors = vcfobj.getMetaInfoDescription()
#infoids=[]
#for (tag, description) in descriptors:
# infoids.append(tag)
#if options.infotag not in infoids and options.infotag != 'QUAL' and options.infotag != "" and options.noheader == False:
# sys.stderr.write(options.infotag + " tag not in ##INFO headers!\n")
# exit(1)
print header
for dataline in vcfobj.yieldVcfDataLine(vcfh):
fields=dataline.strip().split('\t')
(chrom,pos,id,ref,alt,qual,filtercode,info)=fields[0:8]
(start,end) = (int(pos)-1, int(pos))
#pass the filter code
if filtercode != options.filter and options.filter != None:
continue
#check to see if record is the correct variant TYPE
if options.variantype != None:
pattern=options.infotag+'=('+options.variantype+')'
if re.search(pattern, info ) == None:
continue
if options.chrprefix == True:
chrom="chr"+chrom
if chrom in bitsets and bitsets[chrom].count_range( start, end-start ) >= options.mincols:
if not options.reverse:
print dataline
else:
if options.reverse == True:
print dataline
if __name__ == "__main__":
main()