[Biopython-dev] [Bug 2815] Bio.Application command line interfaces

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2815





------- Comment #36 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-13 11:23 EST -------
(In reply to comment #35)
> 
> Note that the _Mafft.py command line interface is currently broken due the
> restriction only having a single instance of a parameter on the command line.
> Mafft uses the following option: 
> 
> --seed alignment1 [--seed alignment2 --seed alignment3 ...]
> 
> We could remove support this option in Mafft.

Removing the --seed argument might be a pragmatic short term solution.

I'd considered this type of thing as a possible corner case - but hadn't
mentioned it as I didn't have a concrete example.  I would suggest setting the
parameter value to a list could work:

i.e. Support any of:

cline = MafftCommandline(seed=["alignment1", "alignment2", "alignment3"])
cline.set_paramter("seed", ["alignment1", "alignment2", "alignment3"])
cline.seed = ["alignment1", "alignment2", "alignment3"]

giving:

mafft --seed alignment1 --seed alignment2 --seed alignment3

We'd need to introduce a new _Option subclass for this.  A similar situation
applies to optional argument lists, like the Unix zip command:

zip zipfile file1 file2 file3 ...

where there is a single output filename (here zipfile), and then one or more
input files or filespecifiers (here three entries).

Peter


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