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Fix PyVCF3 requirement#23

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ckopanos merged 1 commit intomasterfrom
SP-4502_Fix_PyVCF3_requirement
Oct 26, 2023
Merged

Fix PyVCF3 requirement#23
ckopanos merged 1 commit intomasterfrom
SP-4502_Fix_PyVCF3_requirement

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@gpanouts
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If a user has a python virtual environment with PyVCF3==1.0.0 and then install the varsome api client, the PyVCF3 will not be updated since it meets the project’s requirement which is PyVCF3>=1.0.0. However this leads to an error:

$ varsome_api_annotate_vcf.py -g hg19 -k ${API_KEY} -i plain_variants.vcf -o out.vcf -p add-all-data=1
Traceback (most recent call last):
  File "/tmp_varsome_api/test_varsome_102423/bin/varsome_api_annotate_vcf.py", line 19, in <module>
    from varsome_api.vcf import VCFAnnotator
  File "/tmp_varsome_api/test_varsome_102423/lib/python3.7/site-packages/varsome_api/vcf.py", line 20, in <module>
    from vcf.parser import _Info, _encode_type
ImportError: cannot import name '_encode_type' from 'vcf.parser' (/tmp_varsome_api/test_varsome_102423/lib/python3.7/site-packages/vcf/parser.py)

We need to update the requirement to PyVCF3>=1.0.1 to resolve this.

@ckopanos ckopanos merged commit 96b54d2 into master Oct 26, 2023
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4 participants