[Biopython-dev] Bio.EMBOSS wrappers

[Peter]

On Mon, Apr 13, 2009 at 2:49 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Mon, Apr 13, 2009 at 2:44 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>>> > ... Feel free to add away.
>>>
>>> I need to work on my delegation skills - that seems to have back fired ;)
>>
>> Oops. I honestly read that as "do I have your permission?" I can of
>> course tackle this, but am a bit underwater now.
>
> Looking back, I was a bit ambiguous.  I don't mind who does it - let's
> see who has time free first.

OK, I've added a minimal needle wrapper based on the water wrapper.
As part of this I remove the -nosimilarity option which doesn't work on
the current versions of EMBOSS needle and water (5.0 or 6.0).

For -auto and -filter, I think we probably should extend the parameter
classes to explicitly cover these switch arguments which take no value
(they are either part of the command line, or omitted).  We've touched
on this already on Cymon's thread...

Peter