def main():
usage = "usage: %prog [options] interval.bed"
parser = argparse.ArgumentParser(description='make reference vcf records based on non-variant interval bed file and pedfile')
parser.add_argument('bed', metavar='bed', type=str, help='interval.bed')
parser.add_argument("-ped", metavar='pedfile', type=str, help="file.ped")
parser.add_argument("-twobitfile", metavar='tbf', type=str, help="file.2bit")
args=parser.parse_args()
samples=[]
pedfh=open(args.ped)
bedfh=open(args.bed)
tbf=bx.seq.twobit.TwoBitFile( open( args.twobitfile ) )
for line in pedfh:
samples.append( line.split('\t')[1] )
print "##fileformat=VCFv4.1"
print "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">"
print "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">"
print "\t".join(["#CHROM", "POS" ,"ID", "REF", "ALT", "QUAL", "FILTER", "INFO","FORMAT"]+samples)
for (chrom,start,end) in yield_bedcoordinate(bedfh):
for pos in range(start+1,end+1):
sequence=tbf[chrom][pos-1:pos]
vrec=VcfRecord(chrom,str(pos), '.', sequence,info="NS=8")
genotypelist=[ VcfGenotype("GT","0/0") for z in range(len(samples)) ]
vrec.addGenotypeList(genotypelist)
print vrec.toStringwithGenotypes()
def main():
""" This program adds non-reference positions to a VCF file with variant positions.
It does this by the following. Given a bed file of non-variant intervals and a 2bit file of the reference genome,
it retrieves the refernce alllele, and prints out the VCF data line with the ref/ref genotypes. Then
it prints a single line from the segregating VCF file, and then start the loop again.
It assumes that the input vcf is position sorted.
To generate the non-segrgating bed interval file, run the following program from bx-python:
bed_subtract_basewise.py reference_genome.bed segregating.sites.bed
bed_subtract_basewise.py ~/software/Pgmsnp/PythonNotebook/simref.1.bed Simulation1.segregating.bed """
usage = "usage: %prog [options] file.vcf"
parser = OptionParser(usage)
parser.add_option("--bed", type="string", dest="bed", help="bed file with non-variant intervals")
parser.add_option("--tbf", type="string", dest="tbf", help="2bit file of reference genome", default='/Users/amit/data/MySimulations/Simulation1/Reference/simref.1.2bit')
(options, args)=parser.parse_args()
try:
sys.stderr.write("opening twobitfile...\n")
twobit=bx.seq.twobit.TwoBitFile( open( options.tbf ) )
except:
sys.stderr.write("unable to open twobit file!\n")
segregatingVcf=args[0]
bedfh=open(options.bed,'r')
vcfh=open(segregatingVcf,'r')
vcfobj=VcfFile(segregatingVcf)
vcfobj.parseMetaAndHeaderLines(vcfh)
header=vcfobj.returnHeader()
formatstring="GT"
print header
for (chrom,start,end) in yield_bedcoordinate(bedfh):
start=int(start)
end=int(end)
for i in range(start,end):
begin=i
end=i+1
refseq=twobit[chrom][begin:end]
vrec=VcfRecord(chrom,str(end),'.',refseq,'.','.','.','NS=3')
vrec.addGenotype( VcfGenotype(formatstring,'0/0') )
vrec.addGenotype( VcfGenotype(formatstring,'0/0') )
vrec.addGenotype( VcfGenotype(formatstring,'0/0') )
print vrec.toStringwithGenotypes()
vcf_gen=vcfobj.yieldVcfRecordwithGenotypes(vcfh)
print vcf_gen.next().toStringwithGenotypes()