[Bioperl-l] GMAP IO?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Wed Jul 22 16:40:08 EDT 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.
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
sender immediately.

More information about the Bioperl-l mailing list