[Biopython] retrieve gene name and exon

[Ogan ABAAN]

Thanks Peter,

Now that you mention it I remember reading that thread. I don't have an 
exact number but for chr1 I have about 350 of these. I parsed them out a 
separate chr files.

Thank you



Peter wrote:
> 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?
>