[Bioperl-l] GMAP IO?
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.
Bioinformatics Applications Developer
T +64 3 489 9085
E russell.smithies at agresearch.co.nz
Invermay Research Centre
T +64 3 489 3809
F +64 3 489 9174
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