[Biopython-dev] Where to put command line wrappers

[Peter]

Hi all,

We were recently discussing alignment tools like MUSCLE and ClustalW
and putting together a set of command line wrappers under Bio.Align
for them.  I think Bio.Align.Applications was suggested to match
Bio.EMBOSS.Applications.

For EMBOSS we have a single file, Bio/Emboss/Applications.py, which
has about 15 wrappers (all very similar as the EMBOSS applications are
very consistent).  This is nice in that all the wrappers are in the
Bio.Emboss.Application namespace.

Bartek and I have been having a similar discussion for Motif tools,
and if the AliceAce wrappers should go in Bio.Motif.Applications to
match.  For now Bio.Motif has just one wrapper for AlignACE and sister
tool CompareACE.  Now giving each tool-set its own file is possible
(Bio/Motif/Applications/AlignAce.py) but would one (large) file be
simpler? (i.e. Bio/Motif/Applications.py).

I'm not sure how many wrappers we might eventually expect for multiple
sequence alignments, maybe ten or twenty, mostly from different tool
sets.  Maybe Bio/Align/Applications/Muscle.py etc is the way to go,
but we can then import all the command line objects under the
Bio.Align.Applications namespace.

Any comments?

Peter