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Gmane
From: Fields, Christopher J <cjfields <at> illinois.edu>
Subject: Re: Overlapping sets of coordinates?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 5th June 2013 17:56:37 UTC (over 3 years ago)
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 
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 
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 
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
>>> [email protected]
>>> 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
> [email protected]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
 
CD: 3ms