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prody / ProDy

A Python Package for Protein Dynamics Analysis
http://prody.csb.pitt.edu
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Bio.SubsMat has been deprecated #1150

Closed tekpinar closed 4 years ago

tekpinar commented 4 years ago

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

jamesmkrieger commented 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