|
|
|
|
|
|
|
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(',') |
|
|
|
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'] |
|
|
|
|
|
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) |
|
|
|
|
|
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 |
|
|
|
|
|
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() |
