def main():
usage = "usage: %prog [options] file.vcf"
parser = OptionParser(usage)
parser.add_option("--filter", type="string", dest="filter", help="analyze only those records matching filter (default is None)", default=None)
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)
(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)
vcfobj.addMetaInfoHeader("CR", "D", 1, "site call rate")
vcfobj.printMetaLines()
vcfh.seek(0)
vcfobj.parseHeaderLine(vcfh)
vcfobj.printHeaderLine()
samplelist = vcfobj.getSampleList()
sampleCalls={} #key sample name value #called genotypes
for s in samplelist: sampleCalls[s]=0
totalrecords=0
for vrec in vcfobj.yieldVcfRecordwithGenotypes(vcfh ):
if vrec.getFilter() != options.filter and options.filter != None : continue
totalrecords+=1
sitecallrate=vrec.siteCallrate()
vrec.appendInfoString("CR="+str(sitecallrate))
vrec.sampleCallrate(samplelist,sampleCalls)
#print vrec.toStringwithGenotypes()
for s in samplelist:
callrate=float(sampleCalls[s])/float(totalrecords)
print s, sampleCalls[s], totalrecords, callrate
