Fields, Christopher J | 5 Jun 19:56 2013

Re: Overlapping sets of coordinates?

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 <bobfreemanma <at> speakeasy.net> 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 <bosborne11 <at> verizon.net> 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 <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
>>> 
>>> 
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l <at> lists.open-bio.org
>>> 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
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Gmane