[Bioperl-l] GMAP IO?
hartzell at alerce.com
Wed Jul 22 15:51:26 UTC 2009
Smithies, Russell writes:
> 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.
What output format are you using.
I have a parser for the '-f 9' style of output, with tests, etc...,
but I built it at my Day Job and while I know that I can get it pushed
back to the repository I haven't dealt with it yet. If it'd be useful
I'll figure out what I need to do.
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