[Bioperl-l] GMAP IO?

George Hartzell 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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