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Gmane
From: Bob Freeman <bobfreemanma <at> speakeasy.net>
Subject: Re: Overlapping sets of coordinates?
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Wednesday 5th June 2013 17:06:20 UTC (over 3 years ago)
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
 
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