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# Modified from RefHiC: https://github.com/BlanchetteLab/RefHiC（Analysis code）
# --------------------------------------------------------------
import click
import cooler
import h5py
from cooler.create._create import write_pixels,write_indexes,index_bins,index_pixels,prepare_pixels,PIXEL_DTYPES,_set_h5opts,write_info
from cooler.util import get_meta
import posixpath
@click.command()
@click.option('-u', type=int, default=3000000, help='distance upperbund [bp] [default=3000000]')
@click.option('--resol',default=None,help='comma separated resols for output')
@click.argument('mcool', type=str,required=True)
@click.argument('bcool', type=str,required=True)
def cool2bcool(mcool, bcool,u,resol):
'''covert a .mcool file to a .bcool file'''
h5opts = _set_h5opts(None)
copy = ['bins', 'chroms']
Ofile = h5py.File(bcool, 'w')
Ifile = h5py.File(mcool, 'r')
if resol is None:
resols = [r.split('/')[-1] for r in cooler.fileops.list_coolers(mcool)]
else:
resols = resol.split(',')
# copy bins and chroms
for grp in Ifile:
Ofile.create_group(grp)
for subgrp in Ifile[grp]:
if subgrp in resols:
Ofile[grp].create_group(subgrp)
for ssubgrp in Ifile[grp][subgrp]:
if ssubgrp in copy:
Ofile.copy(Ifile[grp + '/' + subgrp + '/' + ssubgrp], grp + '/' + subgrp + '/' + ssubgrp)
Ofile.flush()
Ifile.close()
for group_path in ['/resolutions/'+str(r) for r in resols]:
c = cooler.Cooler(mcool + '::' + group_path)
nnz_src = c.info['nnz']
n_bins = c.info['nbins']
n_chroms = c.info['nchroms']
bins = c.bins()[:]
pixels = []
info = c.info
info['subformat'] = 'bcool'
info['max_distance'] = u
info['full_nnz'] = info['nnz']
info['full_sum'] = info['sum']
# collect pixels
for lo, hi in cooler.util.partition(0, nnz_src, nnz_src // 100):
pixel = c.pixels(join=False)[lo:hi].reset_index(drop=True)
bins1 = bins.iloc[pixel['bin1_id']][['chrom', 'start']].reset_index(drop=True)
bins2 = bins.iloc[pixel['bin2_id']][['chrom', 'start']].reset_index(drop=True)
pixel = pixel[
(bins1['chrom'] == bins2['chrom']) & ((bins1['start'] - bins2['start']).abs() < u)].reset_index(
drop=True)
pixels.append(pixel)
columns = list(pixels[0].columns.values)
meta = get_meta(columns, dict(PIXEL_DTYPES), default_dtype=float)
# write pixels
with h5py.File(bcool, "r+") as f:
h5 = f[group_path]
grp = h5.create_group("pixels")
max_size = n_bins * (n_bins - 1) // 2 + n_bins
prepare_pixels(grp, n_bins, max_size, meta.columns, dict(meta.dtypes), h5opts)
target = posixpath.join(group_path, 'pixels')
nnz, ncontacts = write_pixels(bcool, target, columns, pixels, h5opts, lock=None)
info['nnz'] = nnz
info['sum'] = ncontacts
# write indexes
with h5py.File(bcool, "r+") as f:
h5 = f[group_path]
grp = h5.create_group("indexes")
chrom_offset = index_bins(h5["bins"], n_chroms, n_bins)
bin1_offset = index_pixels(h5["pixels"], n_bins, nnz)
write_indexes(grp, chrom_offset, bin1_offset, h5opts)
write_info(h5, info)
if __name__ == '__main__':
cool2bcool() |