[Biopython-dev] [Bug 2961] Adding undocumented file format switches to MUSCLE wrapper

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http://bugzilla.open-bio.org/show_bug.cgi?id=2961





------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2009-12-04 08:36 EST -------
(In reply to comment #3)
> (In reply to comment #2)
> > (From update of attachment 1408 [details] [details])
> > Patch applied.
> > 
> > Should we also add -phyiout, -physout, -htmlout, -msfout, -clwout etc (which
> > all take a filename)?
> 
> ! Is there anything else undocumented?

Robert did imply there could be other things as his documentation
was out of sync with the code :(

These after of limited value given you can use "-phyi -out filename.phy"
as an alternative to "-phyiout filename.phy" however one bonus feature
is these options allow you to get multiple output files in one run (e.g.
both HTML output to inspect visually and ClustalW output to parse).

> OK, I'll do that asap. I'll also add tests - change test suite to use
> subprocess module etc.

I'd forgotten about that (using subprocess rather than generic_run
in our unit tests). Could you do that as a separate patch please?

Thanks,

Peter


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