[Bioperl-l] Overlapping sets of coordinates?

[Evgeny Gordienko]

I did overlapping test of intervals with "Set::IntervalTree" package - it 
is ultra-fast.
Best wishes.

On Wednesday, June 5, 2013 11:13:00 PM UTC+4, Bob Freeman wrote:
>
> All great ideas. Thanks much! 
>
> -b 
>
> On Jun 5, 2013, at 1:56 PM, "Fields, Christopher J" <cjfi... at illinois.edu<javascript:>> 
> wrote: 
>
> > If this is in an almost GFF3-like format, it might be easy enough to do 
> a transform on the data and use BEDTools, or possibly (if going the BioPerl 
> route) use Lincoln's Bio::DB::SeqFeature::Store. 
> > 
> > chris 
> > 
> > On Jun 5, 2013, at 12:06 PM, Bob Freeman <bobfre... at speakeasy.net<javascript:>> 
> wrote: 
> > 
> >> No alignment -- I used PASA to generate (properly) align transcripts 
> against a genome. Among the PASA outputs is a tab-delimited file that lists 
> the alignments of all my input transcripts in an almost GFF3 file like 
> format. So I need to iterate through the alignments that are valid (one of 
> the columns) and see if any of these match (overlap, include, etc) the 
> coordinates of certain gene models. 
> >> 
> >> 
> >> On Jun 5, 2013, at 12:03 PM, Brian Osborne <bosbo... at verizon.net<javascript:>> 
> wrote: 
> >> 
> >>> Bob, 
> >>> 
> >>> Flattery will get you everywhere. 
> >>> 
> >>> Are you saying that you have this mapping in the form of an alignment 
> file of some kind? 
> >>> 
> >>> BIO 
> >>> 
> >>> On Jun 5, 2013, at 10:53 AM, Bob Freeman <bobfre... at speakeasy.net<javascript:>> 
> 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 
> >>>> 
> >>>> 
> >>>> _______________________________________________ 
> >>>> Bioperl-l mailing list 
> >>>> Biop... at lists.open-bio.org <javascript:> 
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> >>> 
> >> 
> >> ----------------------------------------------------- 
> >> 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 
> >> 
> >> 
> >> 
> >> 
> >> _______________________________________________ 
> >> Bioperl-l mailing list 
> >> Biop... at lists.open-bio.org <javascript:> 
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
> > 
>
> ----------------------------------------------------- 
> 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 
>
>
>
>
> _______________________________________________ 
> Bioperl-l mailing list 
> Biop... at lists.open-bio.org <javascript:> 
> http://lists.open-bio.org/mailman/listinfo/bioperl-l 
>