Eliminate two Biopython deprecation warnings #458
Conversation
- Bio.pairwise2 has been deprecated -> Use Bio.Align.PairwiseAligner instead - SeqRecord constructor: Using a string as the sequence is deprecated -> Convert to Seq The changes are based on https://github.com/speleo3/pymol-psico/blob/ae2b92c262bc/psico/seqalign.py
|
🚀 |
| aligner = PairwiseAligner(internal_open_gap_score=-10, | ||
| extend_gap_score=-.5, | ||
| substitution_matrix=blosum62) | ||
| assert aligner.mode == "global" |
There was a problem hiding this comment.
Is the intent here that we should always use global even if Biopython changes this as its default? If so, would a
aligner.mode = "global"be more future-proof?
There was a problem hiding this comment.
Yes, the intent is to always use global. The documentation of PairwiseAligner is a bit vague for my taste, it says that it "automatically chooses the appropriate alignment algorithm [...] based on the values of the gap scores". And it says "Specify the aligner mode as local to generate local alignments". So my understanding is that we get Needleman-Wunsch or an equivalent algorithm with the given gap scores, and that global is the default for that. I actually coded this 2 years ago, and I'm not 100% sure anymore if there was a strong reason for the assert. I think I just added it out of habit to verify my assumption.
I'd be fine to remove the assert, I think it's rather unlikely that they'll change that.
- Bio.pairwise2 has been deprecated -> Use Bio.Align.PairwiseAligner instead - SeqRecord constructor: Using a string as the sequence is deprecated -> Convert to Seq The changes are based on https://github.com/speleo3/pymol-psico/blob/ae2b92c262bc/psico/seqalign.py
3 participants
Bio.pairwise2has been deprecated -> UseBio.Align.PairwiseAlignerinsteadSeqRecordconstructor: Using a string as the sequence is deprecated -> Convert toSeqThe changes are based on
https://github.com/speleo3/pymol-psico/blob/ae2b92c262bc/psico/seqalign.py
Unit testing:
Covered by
tests/api/seqalign.py::TestSeqalign