[Bioperl-l] Extract features from GFF

[Chris Fields]

On Oct 22, 2007, at 5:30 PM, Hang wrote:

> Hello,
>
> I have a list of about 100,000 short genomic regions with paired  
> start and end
> coordinations on reference fly genome (R5.3). I also have GFF files  
> from the
> same genome release. I wonder how I can extract all overlapping  
> features from
> these regions.
>
> For example:
>
> region A is on chromosome 2L between 123,456 bp to 123,489 bp. What  
> code should
> I use to extract feature, like gene, CDS etc., that overlaps with  
> this region?
>
> Thank you in advance!
>
> -- Hang

Look into using Bio::DB::GFF or Bio::DB::SeqFeature::Store; this will  
depend on the GFF version of the data you have.

chris