[Bioperl-l] GMAP IO?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Jul 22 20:40:08 UTC 2009

Hi George,
I'll have to admit, I've never used the "-f 9" table format but if you have a parser you're willing to share, I'll give it a go.
Fortunately, GMAP is fairly quick once you have the indices built so I can do a bit of experimenting to find a good compromise.

Thanx for your help,


> -----Original Message-----
> From: George Hartzell [mailto:hartzell at alerce.com]
> Sent: Thursday, 23 July 2009 3:51 a.m.
> To: Smithies, Russell
> Cc: 'bioperl-l at lists.open-bio.org'
> Subject: Re: [Bioperl-l] GMAP IO?
> 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.
> g.
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