[Biopython-dev] Bio.EMBOSS wrappers

[Peter]

On Mon, Apr 13, 2009 at 1:32 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
>> Brad, seeing as Bio.EMBOSS is "your baby" how do you feel about adding
>> these features?  The needle wrapper would make an excellent basis for
>> a new water wrapper.  For adding -auto and -filter support, there is
>> probably a clever approach with a common EMBOSS specific subclass of
>> Bio.Application.AbstractCommandline, but I haven't tried.
>
> Definitely go for it. My approach on this has mostly been to add
> command lines as they are requested, or if I need them for something
> I am doing. Not ideal.
>
> Having a subclass with -auto and -filter is a really good idea;
> unfortunately nothing clever is designed into the command line builders
> right now. Feel free to add away.

I need to work on my delegation skills - that seems to have back fired ;)

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?

Peter