def main():
usage = "usage: %prog [options] file.vcf\n print records belonging to a certain type of variant class (e.g. SNP) in a VCF file\n\n"
parser = OptionParser(usage)
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(
"--filter", type="string", dest="filter", help="extract records matching filter (default is None)", default=None
)
parser.add_option("--noheader", action="store_true", dest="noheader", help="VCF file has no header file")
(options, args) = parser.parse_args()
if options.infotag == "":
sys.stderr.write("provide a value for --info parameter!\n")
exit(1)
if options.variantype == "":
sys.stderr.write("provide a value of --type parameter!\n")
exit(1)
variant_dict = {}
vcfilename = args[0]
vcfh = open(vcfilename, "r")
# instantiate a VcfFile object
vcfobj = VcfFile(vcfilename)
# parse its metainfo lines (ones that begin with ##)
vcfobj.parseMetaAndHeaderLines(vcfh)
vcfobj.printMetaAndHeaderLines()
descriptors = vcfobj.getMetaInfoDescription()
infoids = []
for (tag, description) in descriptors:
infoids.append(tag)
if options.infotag not in infoids and options.infotag != "QUAL":
sys.stderr.write(options.infotag + " tag not in ##INFO headers!\n")
exit(1)
if options.variantype != None:
pattern = options.infotag + "=(" + options.variantype + ")"
for dataline in vcfobj.yieldVcfDataLine(vcfh):
fields = dataline.strip().split("\t")
(chrom, pos, id, ref, alt, qual, filtercode, info) = fields[0:8]
if filtercode != options.filter and options.filter != None:
continue
if options.variantype != None:
if re.search(pattern, info) == None:
continue
else:
value = re.search(pattern, info).groups()[0]
print dataline
else:
print dataline
