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Published 20 hours ago • verified publisher icon MDAnalysis

Biopython applications cli wrapper interfaces deprecated for removal: clustalw

Open IAlibay opened this issue 1 year ago • 4 comments

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 avatar Dec 24 '23 13:12 IAlibay

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

IAlibay avatar Dec 24 '23 13:12 IAlibay

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.

orbeckst avatar Jan 03 '24 07:01 orbeckst

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

hmacdope avatar Feb 11 '24 22:02 hmacdope

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.

orbeckst avatar Mar 29 '24 23:03 orbeckst