def sort_vcf( input, reference, output ):
contig_list = get_contig_list( reference )
print "read {} contigs".format(len(contig_list))
v = VCF( input, True ) # request index of VCF upon open
with open( output, 'w') as fd_out:
fd_out.writelines( [ line+"\n" for line in v.metadata ] )
for contig in contig_list:
print "writing entries for contig {}".format(contig)
# filter lines from vcf by contig
count = 0
if v.seek(contig) < 0:
print "skipped {} because it's not in the VCF".format( contig )
else:
for line in v.lines( True, \
lambda raw_line: VCFLine(raw_line).chr == contig ):
fd_out.write( line.line+"\n" )
count += 1
print "wrote {} entries for {}".format( count, contig )
