[Bioperl-l] Overlapping sets of coordinates?

[Bob Freeman]

All great ideas. Thanks much!

-b

On Jun 5, 2013, at 1:56 PM, "Fields, Christopher J" <cjfields at illinois.edu> 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 <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
>>>> 
>>>> 
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>>> 
>> 
>> -----------------------------------------------------
>> 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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> 

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