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miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
18 stars 21 forks source link

`BiopythonDeprecationWarning`: `Bio.pairwise2` has been deprecated, please consider using `Bio.Align.PairwiseAligner` #79

Open bounlu opened 10 months ago

bounlu commented 10 months ago

mirtop --help gives the below warning:

/opt/anaconda3/lib/python3.9/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.
  warnings.warn(

Can you please update the package?

lpantano commented 10 months ago

Happy to accept a PR with the changes to make this faster.