def _bigwig_extractor(datafile, intervals, **kwargs):
width = intervals[0].stop - intervals[0].start
data = np.zeros((len(intervals), 1, 1, width))
wWigIO.open(datafile)
for index, interval in enumerate(intervals):
wWigIO.getData(datafile, interval.chrom, interval.start, interval.stop,
data[index, 0, 0, :])
wWigIO.close(datafile)
return data
def main():
try:
infile = sys.argv[1]
COUNT_U = int(sys.argv[2])
COUNT_M = int(sys.argv[3])
CUTOFF = int(sys.argv[4])
except IndexError:
show_help()
sys.exit(1)
# l_line= f_cntfile.readlines()
CHROM = infile.split("/")[-1].split(".")[0]
DEPTH = 3
tb_file = tabix.open(infile)
m_NDR = NDR(CHROM,
COUNT_U,
COUNT_M,
tb_file,
CUTOFF,
DEPTH,
bin_len=40,
step_len=20,
dist_len=140)
f_infile = gzip.open(infile, "rb")
for line in f_infile:
line = line.strip("\n")
f = line.split()
pos_beg = int(f[1])
cnt_umt = int(f[3])
cnt_met = int(f[4])
cnt_tot = cnt_umt + cnt_met
if cnt_tot < DEPTH:
continue
m_NDR.parse_line(pos_beg, cnt_umt, cnt_met)
f_infile.close()
wWigIO.close()
def extract_bigwig_to_npy(bigwig, output_dir, dtype=np.float32):
wWigIO.open(bigwig)
chrom_sizes = wWigIO.getChromSize(bigwig)
file_shapes = {}
for chrom, size in zip(*chrom_sizes):
data = np.empty(size)
wWigIO.getData(bigwig, chrom, 0, size, data)
np.save('{}.npy'.format(os.path.join(output_dir, chrom)),
data.astype(dtype))
file_shapes[chrom] = data.shape
wWigIO.close(bigwig)
with open(os.path.join(output_dir, 'metadata.json'), 'w') as fp:
json.dump(
{
'file_shapes': file_shapes,
'type': 'array',
'source': bigwig
}, fp)
def getChromSizesWigIO(self):
wWigIO.open(self.path)
out = wWigIO.getChromSize(self.path)
out = dict(zip(out[0], out[1]))
wWigIO.close(self.path)
return out
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
# get information from bigwig file
wWigIO.open('test.bw')
chroms = wWigIO.getChromSize('test.bw')
wigs = wWigIO.getIntervals('test.bw', 'chr1', 10, 200)
wWigIO.close('test.bw')
print wigs
# bigwig -> wig
wWigIO.bigWigToWig('test.bw','test.wig')
# write the chrom sizes into test.sizes
with open('test.sizes','w') as fh:
for chrom in chroms:
print >>fh, chrom+"\t"+str(chroms[chrom])
# wig -> bigwig
wWigIO.wigToBigWig('test.wig','test.sizes','test2.bw')
def __del__(self):
''' Close BigWig file. Avoid memory leaks.'''
wWigIO.close(self.fname)
def close(self):
''' Close BigWig file. '''
wWigIO.close(self.fname)
def __del__(self):
''' Close BigWig file. Avoid memory leaks.'''
wWigIO.close(self.fname)
def close(self):
''' Close BigWig file. '''
wWigIO.close(self.fname)
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
# get information from bigwig file
wWigIO.open('test.bw')
chroms = wWigIO.getChromSize('test.bw')
wigs = wWigIO.getIntervals('test.bw', 'chr1', 10, 200)
wWigIO.close('test.bw')
print wigs
# bigwig -> wig
wWigIO.bigWigToWig('test.bw', 'test.wig')
# write the chrom sizes into test.sizes
with open('test.sizes', 'w') as fh:
for chrom in chroms:
print >> fh, chrom + "\t" + str(chroms[chrom])
# wig -> bigwig
wWigIO.wigToBigWig('test.wig', 'test.sizes', 'test2.bw')
