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hic_qc's Issues

Errow when installing hic_qc

Hi,

I followed the instructions to install hic_qc on HPC with my own account. The error message is as following. I know nothing about Python. Could anyone help me solve this?

Thanks!

(hic_qc)
/home/lson1234/tools/hic_qc $ python setup.py install --user
usage: git rev-list [OPTION] ... [ -- paths... ]
limiting output:
--max-count=nr
--max-age=epoch
--min-age=epoch
--sparse
--no-merges
--remove-empty
--all
--branches
--tags
--remotes
--stdin
--quiet
ordering output:
--topo-order
--date-order
--reverse
formatting output:
--parents
--children
--objects | --objects-edge
--unpacked
--header | --pretty
--abbrev=nr | --no-abbrev
--abbrev-commit
--left-right
special purpose:
--bisect
--bisect-vars
--bisect-all
Traceback (most recent call last):
File "setup.py", line 6, in
version=versioneer.get_version(),
File "/home/lson1234/tools/hic_qc/versioneer.py", li ne 1480, in get_version
return get_versions()["version"]
File "/home/lson1234/tools/hic_qc/versioneer.py", li ne 1453, in get_versions
pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
File "/home/lson1234/tools/hic_qc/versioneer.py", li ne 1110, in git_pieces_from_vcs
pieces["distance"] = int(count_out) # total number of commits
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

ERROR provided too many kwargs,

Hi

I want to measure the quality of my HiC data reads, I tried to run ALIGNING AND QCING PHASE GENOMICS HI-C DATA tutorial, hic_qc script install and bwa step runs well, so when I tried to execute hic_qc.py script from installation path I obtain ValueError provided too many kwargs, can only pass {'basex', 'subsx', nonposx'} or {'basey', 'subsy', nonposy'}. You passed {'nonpositive': 'clip'}

And extract of terminal output as follows:

(hic_qc) ddelgadillo@COMOSPLNXU09:~/Software/hic_qc$ python hic_qc.py -b tests/collateral/input/abc_test.bam -r
[hic_qc - 2021-03-26 15:31:59,685] parsing the first 1000000 read pairs in bam file tests/collateral/input/abc_test.bam to Q                  C Hi-C library quality
Traceback (most recent call last):
  File "hic_qc.py", line 1147, in <module>
    QC.plot_histograms()
  File "hic_qc.py", line 596, in plot_histograms
    plt.yscale('log', nonpositive='clip')
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/pyplot.py", line 3084, in yscale
    return gca().set_yscale(value, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 3704, in set_ys                  cale
    ax.yaxis._set_scale(value, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/axis.py", line 767, in _set_scale
    self._scale = mscale.scale_factory(value, self, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/scale.py", line 569, in scale_factor                  y
    return _scale_mapping[scale](axis, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/scale.py", line 249, in __init__
    "{!r}".format(kwargs))
ValueError: provided too many kwargs, can only pass {'basex', 'subsx', nonposx'} or {'basey', 'subsy', nonposy'}.  You passe                  d {'nonpositive': 'clip'}
(hic_qc) ddelgadillo@COMOSPLNXU09:~/Software/hic_qc$ python hic_qc.py -b /home/bioinfo/HiFiPotato/Hi-C/alCnV1PEHQC.bam -r -o qc
[hic_qc - 2021-03-26 15:36:19,863] parsing the first 1000000 read pairs in bam file /home/bioinfo/HiFiPotato/Hi-C/alCnV1PEHQC.bam to QC Hi-C library quality
Traceback (most recent call last):
  File "hic_qc.py", line 1147, in <module>
    QC.plot_histograms()
  File "hic_qc.py", line 596, in plot_histograms
    plt.yscale('log', nonpositive='clip')
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/pyplot.py", line 3084, in yscale
    return gca().set_yscale(value, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/axes/_base.py", line 3704, in set_yscale
    ax.yaxis._set_scale(value, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/axis.py", line 767, in _set_scale
    self._scale = mscale.scale_factory(value, self, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/scale.py", line 569, in scale_factory
    return _scale_mapping[scale](axis, **kwargs)
  File "/home/ddelgadillo/miniconda3/envs/hic_qc/lib/python3.6/site-packages/matplotlib/scale.py", line 249, in __init__
    "{!r}".format(kwargs))
ValueError: provided too many kwargs, can only pass {'basex', 'subsx', nonposx'} or {'basey', 'subsy', nonposy'}.  You passed {'nonpositive': 'clip'}

Thank some much for your attention

HiCQC' object has no attribute 'ref_assembly

Hello

I aligned my HiC data on reference using Bowties. Then I used hic-qc but I get the following error:

(base) user@fl017:.../project/qaafi-cnafs/bowtie2-master> hic_qc.py -b align.bam -n 1750306
[hic_qc - 2022-02-14 16:55:44,615] parsing the first 1750306 read pairs in bam file align.bam to QC Hi-C library quality
Traceback (most recent call last):
File "/sw/QFAB/miniconda3/envs/hic_qc_20211115/bin/hic_qc.py", line 1151, in
QC.stringify_stats()
File "/sw/QFAB/miniconda3/envs/hic_qc_20211115/bin/hic_qc.py", line 870, in stringify_stats
'ref_assembly': (self.ref_assembly, '{}'),
AttributeError: 'HiCQC' object has no attribute 'ref_assembly'

Python setup.py install ERROR!!!

Hi,
I have the same question about the install step, but the questioner didn't update on last issue, maybe he solved the question? So I create a new issue.
We used conda to create env to installation just following README.

git clone https://github.com/phasegenomics/hic_qc.git
cd hic_qc/
conda env create -n hic_qc --file env.yml
conda activate hic_qc
python setup.py install --user

But it failed at the last step setup.pyinstall, below is the wrong message

And we checked the files were all exsit in the hic_qc file without anything missing.


(hic_qc) [crlee@h71 hic_qc]$ python setup.py
usage: git rev-list [OPTION] <commit-id>... [ -- paths... ]
  limiting output:
    --max-count=nr
    --max-age=epoch
    --min-age=epoch
    --sparse
    --no-merges
    --remove-empty
    --all
    --branches
    --tags
    --remotes
    --stdin
    --quiet
  ordering output:
    --topo-order
    --date-order
    --reverse
  formatting output:
    --parents
    --children
    --objects | --objects-edge
    --unpacked
    --header | --pretty
    --abbrev=nr | --no-abbrev
    --abbrev-commit
    --left-right
  special purpose:
    --bisect
    --bisect-vars
    --bisect-all
Traceback (most recent call last):
  File "setup.py", line 6, in <module>
    version=versioneer.get_version(),
  File "/home/hpc/crlee/softwares/hic_qc/versioneer.py", line 1480, in get_version
    return get_versions()["version"]
  File "/home/hpc/crlee/softwares/hic_qc/versioneer.py", line 1453, in get_versions
    pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
  File "/home/hpc/crlee/softwares/hic_qc/versioneer.py", line 1110, in git_pieces_from_vcs
    pieces["distance"] = int(count_out)  # total number of commits
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

Could anyone help me about this? Thank you so much.

qc_repo_path not defined in write_pdf_report()

Hi,

Installed the package, along with its requirements with conda. When running the following command line:
$ hic_qc.py -b KO61_aligned.bam -r -o K061_output

At the end we get an error about qc_repo_path not defined, and no html nor pdf file is generated.

    QC.write_pdf_report()
  File "/usr/local/hic_qc/hic_qc.py", line 1105, in write_pdf_report
    qc_repo_path)
NameError: global name 'qc_repo_path' is not defined

Thanks in advance for your help.

The --make_report flag doesn't get used

hic_qc/hic_qc.py

Line 1101 in 219b0aa

parser.add_argument('--make_report', '-r', default=False, action='store_true',

I noticed that the PDF report is generated by default, and the flag never gets used even though it has a default value of false according to its help description.

hic_qc/hic_qc.py

Line 1153 in 219b0aa

QC.write_pdf_report()

I personally think the report is great, and should probably be made by default, so I guess the flag could do the opposite if you guys wanted.

AttributeError: 'dict' object has no attribute 'references'

I encountered the following error:

Traceback (most recent call last):
  File "/path/hic_qc/hic_qc.py", line 1182, in <module>
    QC.parse_bam(args.bam_file, max_read_pairs=args.num_reads)
  File "/path/hic_qc/hic_qc.py", line 235, in parse_bam
    self.extract_header_info(bam_fh.header)
  File "/path/hic_qc/hic_qc.py", line 285, in extract_header_info
    self.refs = header.references
AttributeError: 'dict' object has no attribute 'references'

Which traces back to:

hic_qc/hic_qc.py

Line 285 in 1e132fb

self.refs = header.references

Changing line 285 to:

self.refs = header['SQ']

appears to remedy the issue.

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