[Biopython-dev] Bio.EMBOSS wrappers

[Brad Chapman]

Hi Peter;

> >> 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 ;)

Oops. I honestly read that as "do I have your permission?" I can of
course tackle this, but am a bit underwater now.

> 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.

Brad