[Biopython-dev] [Bug 2969] Addition of SeqmatchallCommandline to Emboss/Applications.py

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2969





------- Comment #2 from lpritc at scri.sari.ac.uk  2009-12-10 06:12 EST -------
(In reply to comment #1)
> A nice easy one to wrap at first glance. I would like to also include the
> "aformat" output to set the output alignment format (useful to set to pair or
> simple for AlignIO to parse it as the "emboss" alignment format - see the
> needle and water wrappers). You could then also add a run time test to
> test_Emboss.py piping this to AlignIO... ;)

That shouldn't take too long to do (though probably won't get done by me this
week).  Do we want to set any particular policy for the sequence-associated and
outfile-associated arguments?  Their inclusion in the command-line wrappers is
pretty inconsistent, which is why I left them out in the first place.


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