Open kamurani opened 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
.
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
?
When running the
python setup_for_alphafold.py
script, the alignment performed bytcrdock.sequtil.blosum_align
involves the deprecatedBio.SubsMat
module, triggering the following warning at the start of each run: