Closed tekpinar closed 4 years ago
Hi Mustafa,
Thanks for the message.
I also noticed this deprecation warning too so I looked into it and we do not actually use the substitution matrices from Biopython so I removed this import in https://github.com/prody/ProDy/pull/1138. The next release should, therefore, not give the deprecation warning.
If you can find a way to incorporate the substitution matrices, that would of course be much better.
Best wishes James
Hi, I am using prody in a project to parse MSA files (and some other stuff). When trying to package it, it gives the following warning:
/prody/sequence/msa.py:11:from Bio.SubsMat import MatrixInfo as matlist 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.
It would be nice to consider it in a future release. Best, Mustafa