def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument("-p", dest="num_processes", type=int, default=1)
parser.add_argument("--pattern", dest="pattern", default=r'{{CHROM}}.phastCons46way.bw')
parser.add_argument('--window-sizes', dest='window_sizes', default='30,60,90,150,300,600,900,1500,3000')
parser.add_argument('--bed', dest='bed_file', default=None)
parser.add_argument("bigwig_file_dir")
args = parser.parse_args()
if which(BIGWIG_TO_BEDGRAPH_BIN) is None:
parser.error('bigWigToBedGraph binary not found in PATH')
if args.bed_file is not None:
if not os.path.exists(args.bed_file):
parser.error('bed file %s not found' % (args.bed_file))
else:
parser.error('specify a bed file using --bed')
window_sizes = map(int, args.window_sizes.split(','))
num_processes = max(1, args.num_processes)
# find bigwig files
chrom_bigwig_dict = find_bigwig_files(args.bigwig_file_dir, args.pattern)
if num_processes > 1:
conservation_parallel(args.bed_file, window_sizes, chrom_bigwig_dict, num_processes)
else:
conservation_serial(args.bed_file, window_sizes, chrom_bigwig_dict)
return 0
def main():
# parse command line
parser = argparse.ArgumentParser()
parser.add_argument("-v",
"--verbose",
action="store_true",
dest="verbose",
default=False)
parser.add_argument('-p',
'--num-processes',
type=int,
dest='num_processes',
default=1)
parser.add_argument("--pattern",
dest="pattern",
default=r'{{CHROM}}.phyloP46way.bw')
parser.add_argument("bigwig_file_dir")
parser.add_argument("bed_file")
args = parser.parse_args()
# set logging level
if args.verbose:
level = logging.DEBUG
else:
level = logging.INFO
logging.basicConfig(
level=level,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
# check command line parameters
if which(BIGWIG_TO_BEDGRAPH_BIN) is None:
parser.error('bigWigToBedGraph binary not found in PATH')
if not os.path.exists(args.bed_file):
parser.error("BED file %s not found" % (args.bed_file))
prefix = os.path.splitext(args.bed_file)[0]
results_file = prefix + '.results.txt'
hists_file = prefix + '.hists.npz'
# find bigwig files
logging.info("Indexing bigWig files")
chrom_bigwig_dict = find_bigwig_files(args.bigwig_file_dir, args.pattern)
# process bed file
logging.info("Measuring conservation")
if args.num_processes > 1:
conservation_parallel(args.bed_file, chrom_bigwig_dict,
args.num_processes, results_file, hists_file)
else:
hists = collections.defaultdict(
lambda: np.zeros(NUM_BINS - 1, dtype=np.float))
with open(results_file, 'w') as outfile:
for f in BEDFeature.parse(open(args.bed_file)):
fields = bed_feature_conservation(f, chrom_bigwig_dict, hists)
print >> outfile, '\t'.join(fields)
np.savez(hists_file, **hists)
return 0
def main():
# parse command line
parser = argparse.ArgumentParser()
parser.add_argument("-v", "--verbose", action="store_true",
dest="verbose", default=False)
parser.add_argument('-p', '--num-processes', type=int,
dest='num_processes', default=1)
parser.add_argument("--pattern", dest="pattern",
default=r'{{CHROM}}.phyloP46way.bw')
parser.add_argument("bigwig_file_dir")
parser.add_argument("bed_file")
args = parser.parse_args()
# set logging level
if args.verbose:
level = logging.DEBUG
else:
level = logging.INFO
logging.basicConfig(level=level,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
# check command line parameters
if which(BIGWIG_TO_BEDGRAPH_BIN) is None:
parser.error('bigWigToBedGraph binary not found in PATH')
if not os.path.exists(args.bed_file):
parser.error("BED file %s not found" % (args.bed_file))
prefix = os.path.splitext(args.bed_file)[0]
results_file = prefix + '.results.txt'
hists_file = prefix + '.hists.npz'
# find bigwig files
logging.info("Indexing bigWig files")
chrom_bigwig_dict = find_bigwig_files(args.bigwig_file_dir, args.pattern)
# process bed file
logging.info("Measuring conservation")
if args.num_processes > 1:
conservation_parallel(args.bed_file, chrom_bigwig_dict, args.num_processes,
results_file, hists_file)
else:
hists = collections.defaultdict(lambda: np.zeros(NUM_BINS-1, dtype=np.float))
with open(results_file, 'w') as outfile:
for f in BEDFeature.parse(open(args.bed_file)):
fields = bed_feature_conservation(f, chrom_bigwig_dict, hists)
print >>outfile, '\t'.join(fields)
np.savez(hists_file, **hists)
return 0