Comments (9)
I just open the issues page on pyvcf3 ! It was disabled, sorry...
dridk#1
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I suggest to start from the last critical fix
https://github.com/ousamg/[email protected]
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I did one here named "PyVCF3" . Those one works on python3 only :
https://pypi.org/project/PyVCF3/1.0.0/
I m going to merge some pull request right now.
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I'll start using that and have some fixes I can prob add. This has been abandoned a long time, but still one of the better VCF parsers. Thanks for rescuing it.
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No problem ! I already merge some pull request and did some improvement
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@dridk Thank you. I don't work with vcf files that often and just found the bug in the original version. Unfortunately, maintaining repos is a drudge.
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Thank you very much @dridk
Could you open the issues on your repository? I encounter #337 even with PyVCF3 (edit: the problem was the VCF file and not pyvcf)
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you can rate the project to make it known by other
from pyvcf.
Could you open the issues on your repository?
Agreed, this would be very handy.
I've also created a recipe on bioconda for pyvcf3 bioconda/bioconda-recipes#34505
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Related Issues (20)
- VCF Filtration doesn't work with uncompressed, or UTF-8 HOT 1
- ValueError: could not convert string to float: 'NA' HOT 5
- Filtering REF column of VCF file
- Is the project dead ? HOT 1
- Single threaded but uses pysam, so not single threaded
- Getting an OSError when trying vcf.fetch()
- Pandas dataframe integration
- Custom section delimited by ";" and not ":" HOT 2
- vcf_filter.py python3 error with --output
- Resource warning while using the library due to file not being closed in parser.py HOT 3
- parsing converts QUAL == zero to period, inconsistent numeric type breaks downstream filtering HOT 1
- VCF reader.fetch
- install fails if setuptools >= 58 HOT 1
- Write --output HOT 1
- error in PyVCF setup command: use_2to3 is invalid HOT 11
- Cannot use import vfc HOT 1
- FILTER line is malformed HOT 2
- import error
- AttributeError: 'MyReader' object has no attribute 'info' for vcf file
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