[Biopython-dev] Bio.Application interface

[Brad Chapman]

Peter and Cymon;

> >> 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?

My comment is: I think it is awesome MAFFT made up their own way
of doing the command line.

Seriously, y'all are doing the right thing. Add a new class to
Bio.Application: _OptionAlt or whatever you'd like to call MAFFT's
inventive new way to specify command line arguments. Adapt the 
__str__ from _Option to do it the "--param val" way in this class.
Then use this for your MAFFT commandline.

I believe I just summarized your discussion, so you can replace this
whole message with +1.

Brad