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():
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():
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("-t", dest="sig_threshold", type=float, default=2.0)
parser.add_argument('--window-sizes', dest='window_sizes', default='')
parser.add_argument("--pattern",
dest="pattern",
default=r'{{CHROM}}.phyloP46way.bw')
parser.add_argument('--bed', dest='bed_file')
parser.add_argument("bigwig_file_dir")
args = parser.parse_args()
num_processes = max(1, args.num_processes)
sig_threshold = args.sig_threshold
if args.window_sizes:
window_sizes = map(int, args.window_sizes.split(','))
else:
window_sizes = []
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')
# find bigwig files
logging.info("Indexing bigWig files at path %s" % (args.bigwig_file_dir))
chrom_bigwig_dict = find_bigwig_files(args.bigwig_file_dir, args.pattern)
header_fields = ['name', 'mean', 'frac', 'length']
header_fields.extend(map(str, [('window%d' % x) for x in window_sizes]))
print '\t'.join(header_fields)
if num_processes > 1:
conservation_parallel(args.bed_file, chrom_bigwig_dict, sig_threshold,
window_sizes, num_processes)
else:
conservation_serial(args.bed_file, chrom_bigwig_dict, sig_threshold,
window_sizes, num_processes)
return 0
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("-t", dest="sig_threshold", type=float, default=2.0)
parser.add_argument('--window-sizes', dest='window_sizes', default='')
parser.add_argument("--pattern", dest="pattern", default=r'{{CHROM}}.phyloP46way.bw')
parser.add_argument('--bed', dest='bed_file')
parser.add_argument("bigwig_file_dir")
args = parser.parse_args()
num_processes = max(1, args.num_processes)
sig_threshold = args.sig_threshold
if args.window_sizes:
window_sizes = map(int, args.window_sizes.split(','))
else:
window_sizes = []
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')
# find bigwig files
logging.info("Indexing bigWig files at path %s" % (args.bigwig_file_dir))
chrom_bigwig_dict = find_bigwig_files(args.bigwig_file_dir, args.pattern)
header_fields = ['name', 'mean', 'frac', 'length']
header_fields.extend(map(str, [('window%d' % x) for x in window_sizes]))
print '\t'.join(header_fields)
if num_processes > 1:
conservation_parallel(args.bed_file, chrom_bigwig_dict, sig_threshold,
window_sizes, num_processes)
else:
conservation_serial(args.bed_file, chrom_bigwig_dict, sig_threshold,
window_sizes, num_processes)
return 0