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 chromSizes(self):
''' Get chromosome sizes.'''
chroms = wWigIO.getChromSize(self.fname)
return chroms
def chromSizes(self):
''' Get chromosome sizes.'''
chroms=wWigIO.getChromSize(self.fname)
return chroms
# ------------------------------------
# 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')
