[Biopython] retrieve gene name and exon

[Peter]

On Mon, Jul 6, 2009 at 4:19 PM, Ogan ABAAN<oda.gumail at gmail.com> wrote:
> Hi all,
>
> I have a number of genomic position from the human genome and I want to know
> which genes these positions belong to. I also would like to know which exon
> (if they are from a gene, or even intron if possible) the location is on.
> For example, I want to put in chr1:10,000,000 and would like to see an
> output as such geneX-exon5 or something like that. I know ensemble stores
> that information but I couldn't find the proper tool in Biopython, so I
> would apritiate if anyone could direct me to one. Thank you very much
>
> Ogan

This thread was on a similar topic:
http://lists.open-bio.org/pipermail/biopython/2009-June/005193.html
Given the GenBank file (or in theory an EMBL file or something else
like a GFF file) for a chromosome, and a position within it, how could
you determine which feature(s) a given position was within.

Note that there are already three different human genomes available
in GenBank, so as mentioned in the earlier thread, you need to know
which human genome your location refers to - and work from the
appropriate GenBank/EMBL/GFF/other data file.

Peter

P.S. How many of these locations do you have?