[Biopython-dev] Bio.Application interface

[Cymon Cox]

2009/4/22 Peter <biopython at maubp.freeserve.co.uk>

> On Wed, Apr 22, 2009 at 6:00 PM, Cymon Cox <cy at cymon.org> wrote:
> >>
> >> This might be a silly question, but do you actually these exact option
> >> layouts for MUSCLE and MAFFT?  Many Unix tools use something like
> >> libopt and will actually take slight variations, and may also offer
> short
> >> and long names for the same option.  Perhaps the existing option code
> >> in Bio.Application will suffice?
> >
> > MAFFT uses "--param value" style options, and won't accept
> "--param=value"
> > or "-param value" as alternatives.
>
> OK.  Then yes, we should support that.  Brad, as Bio.Application is your
> module, would you like to comment?
>
> >
> > Neither use "-param=value", but if more applications it may turn up.
> >
>
> I don't think I have ever see a command line application that used that.


PRANK - Probabilistic Alignment Kit
http://www.ebi.ac.uk/goldman-srv/prank/prank/

Advanced usage: 'prank [optional parameters] -d=sequence_file [optional
parameters]'

Doesn't accept "-d sequence_file" or "- -d=sequence_file"

C.
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