[Bioperl-l] GMAP IO?
Russell.Smithies at agresearch.co.nz
Tue Jul 21 23:14:30 UTC 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
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
More information about the Bioperl-l