Open ashishjain1988 opened 1 year ago
Hi, Would you mind to download the file we use in tests here and check if the following command works:
hicConvertFormat -m SRR1791297_30.hic --inputFormat hic --outputFormat cool -o test.cool
Hello, I have encountered the same problem. But SRR1791297_ 30. hic succeeded in hic2cool. My hic file is downloaded from ENCODE, could you help me? Thank you very much!
Would you mind to give the URL? Thanks
The URL is https://www.encodeproject.org/files/ENCFF080DPJ/@@download/ENCFF080DPJ.hic. Thanks
Hi, In fact this issue is the same as #798 : the format behind .hic changed and it seems that hic2tool is not updated (see https://github.com/4dn-dcic/hic2cool/issues/60).
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
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())}"
# 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}")
The code above has a mistake, please use the one below.
Hi, I successfully converted the file format with your code. Thank you very much !
Glad it has been useful for someone. :wink:
Hi,
I tried your code, however I'm getting chrom_sizes is not defined, as the variable does not seem to be declared anywhere.
Oups indeed... I tried to simplify but I did a mistake, here is the correct one:
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}")
Hi there, thank you for providing the code above which can be successfully run in my case. But when I check the information inside the converted .cool file using 'hicInfo' command, it only has 'chrom', 'start', 'end' columns available. I did not see any 'weight' column or in my case, it should be 'SCALE' column.
Is it normal to see or do you have any advice to deal with this problem?
Many thanks!
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