[Bioperl-l] Extract features from GFF
cjfields at uiuc.edu
Mon Oct 22 20:43:31 EDT 2007
On Oct 22, 2007, at 5:30 PM, Hang wrote:
> 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.
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