def main(options):
hdr = []
hdrlen = 0
count = 0
try:
fh = open(options.chrommap)
chrom_map = load_chrom_map(fh)
except:
print "Unable to open", options.chrommap
exit()
dbsnpfile = Dbsnpfile()
dbsnpfile.set_tabix_file(options.dbsnpfile)
for line in sys.stdin:
count += 1
line = line.strip()
if (line.startswith('#')):
print line
else:
vcfr = VCFrecord(line)
posn = vcfr.get_posn_as_int()
try:
dbsnprecs = dbsnpfile.get_dbsnp_file_record(
options.dbsnpfile, chrom_map[options.chrom], posn)
except:
print "Chromosome not found in map", options.chrom
exit()
if len(dbsnprecs) > 0:
vcfr.set_varid(dbsnpfile.get_rsid(dbsnprecs[0]))
else:
logging.info("NOT FOUND for %s at %d" % (options.chrom, posn))
print vcfr.get_record()
return count
def main(options):
hdr = []
hdrlen = 0
count = 0
try:
fh = open(options.chrommap)
chrom_map = load_chrom_map(fh)
except:
print "Unable to open", options.chrommap
exit()
for line in sys.stdin:
count += 1
line = line.strip()
if (line.startswith('#')):
print line
else:
vcfr = VCFrecord(line)
strchrom = vcfr.get_chr()
try:
vcfr.set_chr(chrom_map[strchrom])
except:
logging.info("Chromosome not found in map %s, %s" % (options.chrommap, strchrom))
exit()
print vcfr.get_record()
return count