[Biopython-dev] Bio.EMBOSS wrappers

[Peter]

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.

>> Regarding adding -auto support, I have a question about the needle
>> wrapper and the gap parameters.  Using the needle tool at the command
>> line will prompt for the gap parameters UNLESS the -auto argument has
>> been used.  i.e. Without -auto, it makes sense to insist on the gap
>> parameters being included, which is what the current wrapper does.
>> However, if we add support for -auto, then these parameters can be
>> optional.  We could handle this in the wrapper, but it would be messy
>> (and there may be similar questions with other EMBOSS tools).  What do
>> you think - stick with the simple option of insisting the Biopython
>> user set the gap parameters, even if they are using -auto?
>
> I think we should stick with the simple option. These were meant to
> be pretty dumb specifiers that help users write more modular code than
> simply pasting in a raw string for the command line. Trying to get
> too fancy is probably overkill.

Agreed.

Peter