def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument("--pattern", dest="pattern", default=r'{{CHROM}}.phastCons46way.bw')
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')
# find bigwig files
chrom_bigwig_dict = find_bigwig_files(args.bigwig_file_dir, args.pattern)
i = 0
for f in BEDFeature.parse(open(args.bed_file)):
# read conservation
bigwig_file = chrom_bigwig_dict[f.chrom]
arr = extract_bigwig_data(f, bigwig_file)
fields = [f.chrom, str(f.tx_start), str(f.tx_end), str(np.mean(arr))]
print '\t'.join(fields)
i += 1
if (i % 1000) == 0:
logging.debug("finished %d" % (i))
return 0
def main():
logging.basicConfig(level=logging.DEBUG,
format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
parser = argparse.ArgumentParser()
parser.add_argument("--bin-path", dest="bin_path", default='')
parser.add_argument('--window-size', type=int, dest='window_size', default=300)
parser.add_argument('--threshold', type=float, dest='mapability_threshold', default=0.99)
parser.add_argument('-n', type=int, dest='num_samples', default=1000)
parser.add_argument('bigwig_file')
parser.add_argument('genome_bed_file')
parser.add_argument('transcript_bed_file')
# parse arguments
args = parser.parse_args()
bigwig_file = args.bigwig_file
genome_bed_file = args.genome_bed_file
transcript_bed_file = args.transcript_bed_file
window_size = max(1, args.window_size)
mapability_threshold = args.mapability_threshold
num_samples = max(1, args.num_samples)
# check arguments
if which(BIGWIG_TO_BEDGRAPH_BIN) is None:
parser.error('bigWigToBedGraph binary not found in PATH')
if not os.path.exists(bigwig_file):
parser.error('bigwig file %s not found' % (bigwig_file))
if not os.path.exists(genome_bed_file):
parser.error('genome bed file %s not found' % (genome_bed_file))
if not os.path.exists(transcript_bed_file):
parser.error('transcript bed file %s not found' % (transcript_bed_file))
# parameters
logging.info("Window size: %d" % (window_size))
logging.info("Mapability file: %s" % (bigwig_file))
logging.info("Mapability threshold: %f" % (mapability_threshold))
# get transcript lengths from transcript bed file
transcript_lengths = []
for f in BEDFeature.parse(open(transcript_bed_file)):
length = sum((e[1]-e[0]) for e in f.exons)
transcript_lengths.append(length)
# first pass to index windows
features = []
window_cumsums = []
num_windows = 0
for f in BEDFeature.parse(open(genome_bed_file)):
length = sum((e[1]-e[0]) for e in f.exons)
if length == 0:
continue
if window_size > length:
continue
window_cumsums.append(num_windows)
features.append(f)
num_windows += length - window_size + 1
logging.debug('Found %d total windows' % (num_windows))
# get windows
for i in xrange(num_samples):
# now sample windows
if num_windows < num_samples:
logging.warning('Only sampling %d windows' % (num_windows))
num_samples = min(num_samples, num_windows)
windows = []
trials = 0
while len(windows) < num_samples:
# choose random window
windex = random.randrange(num_windows)
feature_index = bisect.bisect_right(window_cumsums, windex) - 1
woffset = windex - window_cumsums[feature_index]
f = features[feature_index]
# fetch data in window
arr = extract_bigwig_data(f, bigwig_file)
score = np.mean(arr[woffset:woffset+window_size])
if score >= mapability_threshold:
windows.append((f.chrom, f.tx_start + woffset, f.tx_start + woffset + window_size))
logging.debug('Sampled %d windows (%d trials)' % (len(windows), trials))
trials += 1
for window in sorted(windows):
print '\t'.join(map(str, window))
return 0
if __name__ == '__main__':
sys.exit(main())