[BioPython] contig mapping in BioPython

[Brad Chapman]

Hi Alan;

> I'm thinking about writing some BioPython modules for contig/genome mapping 
> - something akin to BioPerl's Bio::Assembler::contig - for use in genome 
> mapping (and whatever else it ends up lending itself to).

Cool. This is definitely something we can use. A reasonable set of
Python objects to hold contig information, and annotations on the
assemblies of contigs, would be excellent. BioPerl does seem a
reasonable place to start to look at these objects, especially since
they've dealt with some of the messy problems of sequence
coordinates along contigs.

> Can't find any references to any such projects that are ongoing but would 
> like to check if anyone else is working on this before I put in too much 
> time in reinventing more wheels than we need.
> Anyone think this would/would not be useful?

Definitely useful. As Andy pointed out, the helpful code along these
lines that we currently have is in CVS in Bio/Sequencing. These are
parsers for Phred and Ace contig files, the latter of which I
imagine might be most useful/relevant.

But yes, I do offer definite encouragement :-). Please do keep us up
to date with ideas/code.

Thanks for the mail.
Brad