[Bioperl-l] Overlapping sets of coordinates?

[Fields, Christopher J]

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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>> 
> 
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