[Biopython] Working with genomic intervals

[Sean Davis]

On Sun, Aug 14, 2011 at 7:11 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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.

I would second the bx-python vote.  Not only are the "normal" interval
classes covered, but there are also some variants (clustering is one
that comes to mind).

Sean