[Biopython] Working with genomic intervals

[Peter Cock]

On Friday, August 12, 2011, Aaron Quinlan <aaronquinlan at gmail.com> wrote:
> All,
>
> I apologize in advance if this is a naive question.
> I am wondering if BioPython provides libraries for
> working with genomic intervals in BED, GFF, or
> any other like format?  I am looking for libraries
> that handle the parsing of files in these formats
> into Python objects, as well as libraries for
> manipulating (intersection, merging, counting,
> etc.) intervals.  I know this exists in Galaxy's
> bx-python, but am wondering if there are similar
> libraries in BioPython?
>
> Gratefully,
> Aaron

Hi Aaron,

Have a look at http://biopython.org/wiki/GFF_Parsing
wher Brad is working on this. He's also spoken
highly of bx-python as I recall.

Peter