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phbradley / TCRdock

python tools for TCR:peptide-MHC modeling and analysis
MIT License
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`BiopythonDeprecationWarning` in `tcrdock/sequtil.py` #15

Open kamurani opened 5 months ago

kamurani commented 5 months ago

When running the python setup_for_alphafold.py script, the alignment performed by tcrdock.sequtil.blosum_align involves the deprecated Bio.SubsMat module, triggering the following warning at the start of each run:

/home/cam/anaconda3/envs/tcrdock_test/lib/python3.8/site-packages/Bio/SubsMat/__init__.py:126: BiopythonDeprecationWarning: Bio.SubsMat has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.substitution_matrices as a replacement, and contact the Biopython developers if you still need the Bio.SubsMat module.
mdehoon commented 5 months ago

tcrdock.sequtil.blosum_align uses Bio.pairwise2, which in itself is deprecated. The solution would be to ask the tcrdock.sequtil.blosum_align maintainers to switch to the newer PairwiseAligner in Bio.Align.

kamurani commented 4 months ago

Thanks for the heads up @mdehoon , I will update the PR accordingly. I'm guessing I don't see the deprecation warning for pairwise2 because this repo's environment has an older version of Bio?