def main(args):
annot = tabio.read_auto(args.annotate)
cnarr = read_cna(args.cnv_file)
cnarr['gene'] = annot.into_ranges(cnarr, 'gene', '-')
tabio.write(cnarr, args.output or sys.stdout)
def main(args):
annot = tabio.read_auto(args.annotate)
cnarr = read_cna(args.cnv_file)
cnarr['gene'] = annot.into_ranges(cnarr, 'gene', '-')
tabio.write(cnarr, args.output or sys.stdout)
def main(args):
print("Sample", "CNA_Fraction", "CNA_Count", sep='\t', file=args.output)
for fname in args.cnv_files:
cnarr = read_cna(fname)
frac, count = cna_stats(cnarr)
print(fname, frac, count, sep='\t', file=args.output)