[Bioperl-l] GMAP IO?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Jul 21 19:14:30 EDT 2009

Is there an IO module for GMAP output?
I looked in the obvious places (Bio::AlignIO, Google etc..)
I know GMAP will do gff or psl output and there are parsers for those (they're SeqIO, not AlignIO?), but I was hoping there might be a better way as I've found GMAP's gff needs a bit of post-processing to make it usable.

It's a fairly large job (mammalian refseqs vs. a mammalian genome) so I want to do it as efficiently as possible.


Russell Smithies 

Bioinformatics Applications Developer 
T +64 3 489 9085 
E  russell.smithies at agresearch.co.nz 

Invermay  Research Centre 
Puddle Alley, 
New Zealand 
T  +64 3 489 3809   
F  +64 3 489 9174  

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