[Bioperl-l] Overlapping sets of coordinates?

[Roy Chaudhuri]

Hi Bob,

There are methods for this in Bio::RangeI (overlaps, contains), which are
inherited by SeqFeatures, so you could do something like:

#$transcript_feat and $gene_feat are Bio::SeqFeatureI objects

if ($gene_feat->contains($transcript_feat)) { $overlap=1 }
elsif ($gene_feat->overlaps($transcript_feat)) {$partial_overlap=1}
else {$no_overlap=1}

However, depending on the form of your data, you may be better off using
off-the-shelf software such as bedtools or htseq-count.

Cheers,
Roy.

On 5 June 2013 15:53, Bob Freeman <bobfreemanma at speakeasy.net> wrote:

> Dear knowledgeable & experienced community,
>
> I've been racking my brains on this one and I'm sure it's been solved
> before, but can't seem to find where/how to do this without major amounts
> of custom coding: I have a set of transcripts mapped against a genome. I'd
> like to know which transcripts overlap a given set of coordinates (e.g.
> coordinates for a certain gene model). Is there an easy way to ascertain
> overlap, non-overlap, partial overlap, etc. in BioPerl??
>
> Thanks,
> Bob
>
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> Acorn Worm Informatics, Kirschner lab
> Dept of Systems Biology, Alpert 524
> Harvard Medical School
> 200 Longwood Avenue
> Boston, MA  02115
> 617/432.2294, vox
>
> "Sorry I'm late. Oh, God, that sounded insincere. I'm late."
>         -- Karen Walker, from Will and Grace
>
>
>
>
>
> -----------------------------------------------------
> Bob Freeman, Ph.D.
> 51 Downer Avenue, #2
> Dorchester, MA  02125
> 617/699.7057, vox
>
> "Well, I'm thankful that I found a pharmacologist who is as dumb as a box
> of hair."
>         -- Karen Walker, from Will and Grace
>
>
>
>
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