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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 19:13:00 UTC (over 3 years ago)
All great ideas. Thanks much!

-b

On Jun 5, 2013, at 1:56 PM, "Fields, Christopher J" 
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 
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
> 

-----------------------------------------------------
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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