def main():
""" prints the description of ##FILTER metalines in a VCF """
usage = "usage: %prog [options] file.vcf"
parser = OptionParser(usage)
parser.add_option("--filtertag", type="string", dest="filtertag", help="prints the description for the FILTER id filtertag")
parser.add_option("--all", action="store_true", dest="all", help="prints the description for *every* FILTER tag in VCF")
parser.add_option
(options, args)=parser.parse_args()
vcfilename=args[0]
vcfh=open(vcfilename, 'r')
#instantiate a VcfFile object
vcfobj=VcfFile(vcfilename)
#parse its metainfo lines (ones that begin with ##)
vcfobj.parseMetaLines(vcfh)
descriptors = vcfobj.getMetaFilterDescription()
if len(descriptors) == 0:
sys.stderr.write("No ##FILTER lines in vcf!\n")
return
found_tag=0
for (id, description) in descriptors:
if options.all==True:
print id, description
found_tag=1
continue
if id == options.filtertag:
print id, "\t", description
found_tag=1
if found_tag ==0 : sys.stderr.write(options.filtertag + " not in ##FILTER headers\n")
