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.
On Jun 5, 2013, at 12:06 PM, Bob Freeman
> 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
>> Flattery will get you everywhere.
>> Are you saying that you have this mapping in the form of an alignment
file of some kind?
>> On Jun 5, 2013, at 10:53 AM, Bob Freeman
>>> 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??
>>> Bioperl-l mailing list
>>> [email protected]
> Bob Freeman, Ph.D.
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> -- Karen Walker, from Will and Grace
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