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MDAnalysis is a Python library to analyze molecular dynamics simulations.
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Biopython applications cli wrapper interfaces deprecated for removal: clustalw #4386

Open IAlibay opened 7 months ago

IAlibay commented 7 months ago

The alignment commandline wrappers via Biopython are deprecated and will be removed in a future version.

This means that the use of the clustalw wrapper in align.py will no longer work once this has been acheived.

Options are:

  1. We build our own CLI interface to clustalw
  2. We remove the option from MDAnalysis
IAlibay commented 7 months ago

This is a reasonably large change - pinging @MDAnalysis/coredevs

orbeckst commented 6 months ago

fasta2select() https://github.com/MDAnalysis/mdanalysis/blob/b9f321c1d27efe5562421edf33d78ea4fdf82734/package/MDAnalysis/analysis/align.py#L1102 is a reasonably interesting function. We could probably just replace the clustalw call with Bio.Align.PairwiseAligner.

hmacdope commented 5 months ago

I would say remove the clustalW wrapper, unsure how that intersects with @orbeckst's suggestions

orbeckst commented 3 months ago

I think we can remove clustalw functionality and just use Bio.Align.PairwiseAligner internally. If we don't get regressions then I'd be ok just noting that we internally changed the alignment algorithm from clustalw to Biopython with no changes in our tests.