UnicodeDecodeError When running hicConvertFormat to convert HiC to Cool format

[ashishjain1988]

Welcome to the HiCExplorer GitHub repository! Before opening the issue please check that the following requirements are met :

• [ ] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below.

• [ ] Paste your HiCExplorer version (hicInfo --version) and your python version (python --version) below. HiC Version: 3.7.2 and Python version 3.9

• [ ] Have you checked our documentation on hicexplorer.readthedocs.io? Yes

• [ ] Do you use conda to install HiCExplorer? Yes

• [ ] Do you use the latest HiCExplorer release? If not, please install it via a conda environment: conda create --name hicexplorer hicexplorer=3.6 python=3.8 -c bioconda -c conda-forge and activate the environment: conda activate hicexplorer. Retry your command. You can exit a conda environment via conda deactivate. To learn more about conda and environments, please consider the following documentation.

Retry your command, is it solved now? If not please continue with the following:

• [ ] Paste the full HiCExplorer command that produces the issue below (ignore if you simply spotted the issue in the code/documentation). hicConvertFormat -m K0_S2_mapped_contact_map.hic --inputFormat hic --outputFormat cool -o K0_S2_mapped_contact_map.cool
• [ ] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation). INFO:hicexplorer.hicConvertFormat:Converting with hic2cool. Traceback (most recent call last): File "/programs/x86_64-linux/hicexplorer/3.7.2/bin/hicConvertFormat", line 7, in main() File "/programs/x86_64-linux/hicexplorer/3.7.2/lib/python3.9/site-packages/hicexplorer/hicConvertFormat.py", line 131, in main hic2cool_convert(matrix, args.outFileName[i], 0) File "/programs/x86_64-linux/hicexplorer/3.7.2/lib/python3.9/site-packages/hic2cool/hic2cool_utils.py", line 860, in hic2cool_convert pair_footer_info, expected, factors, norm_info = read_footer(req, mmap_buf, masteridx) File "/programs/x86_64-linux/hicexplorer/3.7.2/lib/python3.9/site-packages/hic2cool/hic2cool_utils.py", line 131, in read_footer unit = readcstr(f) File "/programs/x86_64-linux/hicexplorer/3.7.2/lib/python3.9/site-packages/hic2cool/hic2cool_utils.py", line 59, in readcstr return buf.decode("utf-8") UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa5 in position 1: invalid start byte

[lldelisle]

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

[xiaohuli-45]

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!

[lldelisle]

Would you mind to give the URL? Thanks

[xiaohuli-45]

The URL is https://www.encodeproject.org/files/ENCFF080DPJ/@@download/ENCFF080DPJ.hic. Thanks

[lldelisle]

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).

[lldelisle]

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.

[xiaohuli-45]

Hi, I successfully converted the file format with your code. Thank you very much !

[lldelisle]

Glad it has been useful for someone. :wink:

[LinearParadox]

Hi,

I tried your code, however I'm getting chrom_sizes is not defined, as the variable does not seem to be declared anywhere.

[lldelisle]

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}")

[caragraduate]

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!