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Human mitochondrial variants annotation using HmtVar.

Home Page: https://hmtnote.readthedocs.io

License: MIT License

Makefile 2.12% Python 97.88%

bioinformatics python variant-annotation vcf

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hmtnote's Issues

Redirecting hmtnote dump

Hi,
We are using hmtnote in our research and want to use it within an nf-core pipeline. We have tried running hmtnote dump while using docker and singularity containers but it fails because hmtnote tries to place the database within the container. Would it be possible to add an optional --out_dir parameter to hmtnote dump to redirect the output? I would be willing to do it myself if you like the idea but don't have the time to do so yourself.

HmtNote annotation failed

HmtNote version: 0.7.2
Python version: 3.7
Operating System: macOS

Description

HmtNote failed the annotation of the "bcftools.vcf" file available in the data folder from the repository.

What I Did

pip install hmtnote

hmtnote annotation bcftools.vcf bcftools_annot.vcf

This is the error I obtain when executing hmtnote annotation:

File "init.pxd", line 242, in init allel.opt.model
ValueError: numpy.ndarray size changed, may indicate binary incompatibility. Expected 88 from C header, got 80 from PyObject

hmtnote dump failed

HmtNote version: 0.7.2
Python version: 3.6.15
Operating System: linux

Description

I would greatly appreciate it if you could look into this matter and help me to resolve the issue as soon as possible. If there is any further information that you require from me, please do not hesitate to let me know.

Thank you very much for your attention to this matter.

What I Did

hmtnote dump 


requests.exceptions.ConnectionError: HTTPSConnectionPool(host='www.hmtvar.uniba.it', port=443): Max retries exceeded with url: /api/main/mutation/73G (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2b0de6a9e208>: Failed to establish a new connection: [Errno 110] Connection timed out',))

Initial Update

The bot created this issue to inform you that pyup.io has been set up on this repo.
Once you have closed it, the bot will open pull requests for updates as soon as they are available.

hmtnote installation

HmtNote version:2019
Python version: 3.7.7
Operating System: linux ubuntu

Description

Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.

What I Did

I installed hmtnote in the following way:
git clone https://github.com/robertopreste/HmtNote

and then
python setup.py install

Paste the command(s) you ran and the output
If there was a crash, please include the traceback here.
########################################################

zip_safe flag not set; analyzing archive contents...
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 243, in run_setup
    DirectorySandbox(setup_dir).run(runner)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 273, in run
    return func()
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 242, in runner
    _execfile(setup_script, ns)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-6b8mdx33/pytest-runner-5.2/setup.py", line 21, in <module>
    author="Roberto Preste",
  File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 209, in run
    os.path.join(archive_root, 'EGG-INFO'), self.zip_safe()
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 245, in zip_safe
    return analyze_egg(self.bdist_dir, self.stubs)
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 355, in analyze_egg
    safe = scan_module(egg_dir, base, name, stubs) and safe
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 395, in scan_module
    symbols = dict.fromkeys(iter_symbols(code))
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 414, in iter_symbols
    for name in code.co_names:
AttributeError: type object 'StopIteration' has no attribute 'co_names'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "setup.py", line 51, in <module>
    zip_safe=False,
  File "/usr/lib/python3.7/distutils/core.py", line 108, in setup
    _setup_distribution = dist = klass(attrs)
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 269, in __init__
    self.fetch_build_eggs(attrs['setup_requires'])
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 313, in fetch_build_eggs
    replace_conflicting=True,
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 826, in resolve
    dist = best[req.key] = env.best_match(req, ws, installer)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1092, in best_match
    return self.obtain(req, installer)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1104, in obtain
    return installer(requirement)
  File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 380, in fetch_build_egg
    return cmd.easy_install(req)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 663, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 693, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 873, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1101, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1087, in run_setup
    run_setup(setup_script, args)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 246, in run_setup
    raise
  File "/usr/lib/python3.7/contextlib.py", line 130, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python3.7/contextlib.py", line 130, in __exit__
    self.gen.throw(type, value, traceback)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/six.py", line 685, in reraise
    raise value.with_traceback(tb)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 243, in run_setup
    DirectorySandbox(setup_dir).run(runner)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 273, in run
    return func()
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 242, in runner
    _execfile(setup_script, ns)
  File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 46, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-6b8mdx33/pytest-runner-5.2/setup.py", line 21, in <module>
    author="Roberto Preste",
  File "/usr/lib/python3.7/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 209, in run
    os.path.join(archive_root, 'EGG-INFO'), self.zip_safe()
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 245, in zip_safe
    return analyze_egg(self.bdist_dir, self.stubs)
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 355, in analyze_egg
    safe = scan_module(egg_dir, base, name, stubs) and safe
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 395, in scan_module
    symbols = dict.fromkeys(iter_symbols(code))
  File "/usr/lib/python3/dist-packages/setuptools/command/bdist_egg.py", line 414, in iter_symbols
    for name in code.co_names:
AttributeError: type object 'StopIteration' has no attribute 'co_names'


I have pip3 installed. However pip3 install hmtnote does not work for me. Please advise

vcfpy2

Hi @robertopreste,

Is the requirement for hmtnote still vcfpy2 or the issue is fixed with vcfpy. I am bundling hmtnote into bioconda. Is it fine to change requirement to vcfpy

Fix CSV output format

When multiple alternative alleles are present for a variant, the whole resulting CSV file will have separate columns for each allele and for each feature, as follows:

CHROM	POS	ID	REF	ALT_1	ALT_2	Locus_1	Locus_2
chrMT	73	.	A	G	.	MT-DLOOP
chrMT	97	.	GC	G	GCT	MT-DLOOP	.

This is not convenient, and in this case it would be better to split different values in the same column with semicolons.

Initial Update

The bot created this issue to inform you that pyup.io has been set up on this repo.
Once you have closed it, the bot will open pull requests for updates as soon as they are available.

VCF file parsing

HmtNote version:
Python version:3.6
Operating System: Linux

Description

I am using a vcf file to annotate. However, when I see the output csv file , it is not parsed propoerly.

What I Did

hmtnote annotate R4006.vcf 1.vcf --csv

Paste the command(s) you ran and the output.
If there was a crash, please include the traceback here.

Annotating... [------------------------------------] 1% 00:14:37/home/smukherjee/.local/lib/python3.6/site-packages/vcfpy2/parser.py:256: CannotConvertValue: 1,1,1 cannot be converted to Integer, keeping as string.
CannotConvertValue,
Annotating... [------------------------------------] 1% 00:14:34/home/smukherjee/.local/lib/python3.6/site-packages/vcfpy2/parser.py:256: CannotConvertValue: 1,1 cannot be converted to Integer, keeping as string.
CannotConvertValue,
Annotating... [##----------------------------------] 8% 00:12:53/home/smukherjee/.local/lib/python3.6/site-packages/vcfpy2/parser.py:256: CannotConvertValue: 1,1,1,1 cannot be converted to Integer, keeping as string.
CannotConvertValue,
Annotating... [###---------------------------------] 8% 00:13:02/home/smukherjee/.local/lib/python3.6/site-packages/vcfpy2/parser.py:256: CannotConvertValue: 1,1,1,1,1 cannot be converted to Integer, keeping as string.
CannotConvertValue,
Annotating... [####################################] 100%
Converting annotated VCF file to CSV format... /home/smukherjee/.local/lib/python3.6/site-packages/allel/io/vcf_read.py:1870: UserWarning: not all characters parsed for integer value; field: INFO; variant: 12 (chrMT:302)
chunks = [d[0] for d in it]
/home/smukherjee/.local/lib/python3.6/site-packages/allel/io/vcf_read.py:1870: UserWarning: not all characters parsed for integer value; field: INFO; variant: 14 (chrMT:309)
chunks = [d[0] for d in it]
/home/smukherjee/.local/lib/python3.6/site-packages/allel/io/vcf_read.py:1870: UserWarning: not all characters parsed for integer value; field: INFO; variant: 15 (chrMT:310)
chunks = [d[0] for d in it]
/home/smukherjee/.local/lib/python3.6/site-packages/allel/io/vcf_read.py:1870: UserWarning: not all characters parsed for integer value; field: INFO; variant: 37 (chrMT:929)
chunks = [d[0] for d in it]

And the csv looks like this :(Just partial shown)

CHROM	POS	ID	REF	ALT	QUAL	AC	AN	NtVarH	NtVarP
chrMT	73	.	A	G;.;.;.;.	.	1;-1;-1;-1;-1	2	0.693878;.;.;.;.	0.48675;.;.;.;.
chrMT	152	.	T	C;.;.;.;.	.	1;-1;-1;-1;-1	2	0.710753;.;.;.;.	0.392746;.;.;.;.
chrMT	182	.	C	T;.;.;.;.	.	1;-1;-1;-1;-1	2	0.067017;.;.;.;.	0.017046;.;.;.;.
chrMT	185	.	G	T;.;.;.;.	.	1;-1;-1;-1;-1	2	0.162199;.;.;.;.	0.098877;.;.;.;.
chrMT	195	.	T	C;.;.;.;.	.	1;-1;-1;-1;-1	2	0.580496;.;.;.;.	0.300672;.;.;.;.

Any help ?

Fix echoed string when converting to CSV

When using the --csv option, the following string is printed on screen:

Converting annotated VCF file to CSV format...Done.

It would be better to add a whitespace before Done.

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