def main():
"""Run a few length or intersection calculations on human BED files.
"""
parser = argparse.ArgumentParser(
description='Compute coverage and other stats of BED files.')
parser.add_argument('bed_files', nargs='+', metavar='BEDFILE',
help='One or more BED files.')
parser.add_argument('-o', '--output', metavar='FN_OUT',
help='Save the intersection file.')
args = parser.parse_args()
get_coverage_chrom = ft.partial(get_coverage, pred=in_mapped_contig)
beds = map(get_coverage_chrom, args.bed_files)
if len(beds) > 1:
intersect = reduce(overlap_coverages, beds)
beds.append(intersect)
if args.output is not None:
intersect.saveas(args.output)
args.bed_files.append(args.output)
else:
args.bed_files.append('intersect')
bases = map(number_of_bases_covered, beds)
percents = map(lambda x: 100 * float(x) / genome_length, bases)
print "filename, number of bases, percent of genome"
for fn, base, perc in zip(args.bed_files, bases, percents):
print fn, to_si(base), '%.2f' % perc
def main():
"""Run a few length or intersection calculations on human BED files.
"""
parser = argparse.ArgumentParser(
description='Compute coverage and other stats of BED files.')
parser.add_argument('bed_files', nargs='+', metavar='BEDFILE',
help='One or more BED files.')
parser.add_argument('-v', '--verbose', action='store_true',
help='Print runtime information')
args = parser.parse_args()
get_coverage_v = ft.partial(get_coverage, verbose=args.verbose)
beds = map(get_coverage_v, args.bed_files)
if len(beds) > 1:
intersect = reduce(overlap_coverages, beds)
beds.append(intersect)
args.bed_files.append('intersect')
bases = map(number_of_bases_covered, beds)
percents = map(lambda x: 100 * float(x) / genome_length, bases)
print "filename, number of bases, percent of genome"
for fn, base, perc in zip(args.bed_files, bases, percents):
print fn, to_si(base), '%.2f' % perc
