[Biopython-dev] Bio.Application interface

[Cymon Cox]

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

> On Wed, Apr 22, 2009 at 2:23 PM, Cymon Cox <cy at cymon.org> wrote:
> > 2009/4/22 Peter <biopython at maubp.freeserve.co.uk>
> >>
> >> On Wed, Apr 22, 2009 at 10:48 AM, Cymon Cox <cy at cymon.org> wrote:
> >>
> >> > Ive written Application.AbstractCommandline for both MUSCLE and MAFFT.
> >> > However, each of these programmes uses a variation on the parameter
> >> > styles
> >> > not easily covered by the current _AbstractParameter classes _Option
> and
> >> > _Argument. The _Option class deals with parameters of the type "-
> >> > -append=yes" and "-a yes", ...
> >> > A muscle command might be:
> >> > "muscle -in Fasta/f002 -out Fasta/temp_align_out2.fa -objscore sp
> >> > -noanchors"
> >> > ie with a "-noanchors" command
> >>
> >> Those kind of options which don't take a value are really common on
> >> Unix,  I suspect we already have things like this in the other wrappers.
> >> I'd guess they just use the _Option class and omit the value.
> >
> > Yes, I see now... they need to be _Options with a "lambda x: 0" value
> > checker function - for some reason was trying to force them into
> _Argument
> >
> > This is the current _Option class:
> > ...
> > So _Option covers: "- -param=value", "-param value", "-param", "- -param"
> >
> > What it doesnt cover is "- -param value" and "-param=value"
> > ...
>
> 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. Neither use "-param=value", but if more
applications it may turn up.

C.



>
>
> Peter
>



-- 
____________________________________________________________________

Cymon J. Cox

Centro de Ciencias do Mar
Faculdade de Ciencias do Mar e Ambiente (FCMA)
Universidade do Algarve
Campus de Gambelas
8005-139 Faro
Portugal

Phone: +0351 289800909 ext 7909
Fax: +0351 289800051
Email: cy at cymon.org, cymon at ualg.pt, cymon.cox at gmail.com
HomePage : http://biology.duke.edu/bryology/cymon.html
-8.63/-6.77