lldelisle
commented
1 year ago Waiting for a better solution, this python script is working, using hicstraw (available on pip: https://pypi.org/project/hic-straw/) and cooler (https://cooler.readthedocs.io/en/latest/):
import numpy as np
import hicstraw
import os
import pandas as pd
hic_file = 'ENCFF080DPJ.hic'
cool_file = 'ENCFF080DPJ_250kb.cool'
data_type = 'observed' # (previous default / "main" data) or 'oe' (observed/expected)
normalization = "NONE" # , VC, VC_SQRT, KR, SCALE, etc.
resolution = 250000
hic = hicstraw.HiCFile(hic_file)
assert resolution in hic.getResolutions(), \
f"{resolution} is not part of the possible resolutions {','.join(hic.getResolutions())}"
chrom_sizes = pd.Series({chrom.name: chrom.length for chrom in hic.getChromosomes() if chrom.name != "All"})
# First write the chromosome sizes:
with open(hic.getGenomeID() + '.size', 'w') as fsize:
for chrom in hic.getChromosomes():
if chrom.name != "All":
fsize.write(f"{chrom.name}\t{chrom.length}\n")
# Then write the counts in text file:
with open(cool_file.replace('.cool', ".txt"), 'w') as fo:
for i in range(len(chrom_sizes)):
for j in range(i, len(chrom_sizes)):
chrom1 = chrom_sizes.index[i]
chrom2 = chrom_sizes.index[j]
result = hicstraw.straw(data_type, normalization, hic_file, chrom1, chrom2, 'BP', resolution)
for k in range(len(result)):
start1 = result[k].binX
start2 = result[k].binY
value = result[k].counts
fo.write(f"{chrom1}\t{start1}\t{start1}\t{chrom2}\t{start2}\t{start2}\t{value}\n")
os.system(f"cooler load -f bg2 {hic.getGenomeID()}.size:{resolution} {cool_file.replace('.cool', '.txt')} {cool_file}")
ENCODE is using a new .hic format. How does hic2cool handle/read .hic files? Easiest option would be to use the latest version of straw. Alternatively, details about the new format are in this repo.
Related thread https://github.com/deeptools/HiCExplorer/issues/798#issuecomment-1142319166