[Biopython-dev] Bio.Application interface

[Peter]

On Fri, Apr 24, 2009 at 12:43 PM, Cymon Cox <cy at cymon.org> wrote:
> 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"

I had misunderstood the quotes to be literally typed on the command line ;)

Peter