[Biopython-dev] Bio.EMBOSS wrappers

[Brad Chapman]

Hi Peter;
The tests from EMBOSS look great; thanks for putting this together.

> For now I build the command line strings for seqret and needle "by
> hand", as Bio.EMBOSS doesn't have wrappers for them yet.  I also note
> that the existing wrappers in Bio.EMBOSS don't support the very handy
> -auto and -filter command line arguments supported by all (or at least
> most) of the EMBOSS command line tools.  Using -auto turns off any
> user prompting for missing arguments (very important for calling from
> a script).  Using -filter is useful for running the tools with pipes
> (i.e. no output file is required as stdout can be used instead, and
> potentially no input file if we write to stdin correctly).
> 
> 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.

Brad