[Biopython-dev] Bio.Application interface

[Peter]

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.

Peter