[Bioperl-l] Alignment Blast parser

[Jason Stajich]

The code to do it is in Bio::SearchIO::Writer::TextResultWriter
but that recapitulates a whole report from a SearchIO object not just the
HSP alignment part, you'll have to dig out the code which does
the HSP printing or post process the returned string to clip out just the
part you want.

-jason


On Thu, 22 Jan 2004, Agrin, Nathan wrote:

> Yes exactly
>
> -Nate
>
> -----Original Message-----
> From: Brian Osborne [mailto:brian_osborne at cognia.com]
> Sent: Thursday, January 22, 2004 2:24 PM
> To: Jason Stajich; Agrin, Nathan
> Cc: bioperl-l at bioperl.org
> Subject: RE: [Bioperl-l] Alignment Blast parser
>
> Jason,
>
> I think he wants to print out the exact same alignment as you see in the
> BLAST report, which you can't do using AlignIO.
>
> Nathan, do you mean "exactly", with that "Query: 2" and "Subject: 2"
> business as well?
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Jason Stajich
> Sent: Thursday, January 22, 2004 2:14 PM
> To: Agrin, Nathan
> Cc: bioperl-l at portal.open-bio.org
> Subject: Re: [Bioperl-l] Alignment Blast parser
>
> You want to retain it meaning what?
>  Bio::SearchIO(-format => 'blast')
> parses blast for you.
>
> -jason
> On Thu, 22 Jan 2004, Agrin, Nathan wrote:
>
> > I need a way to retain the EXACT alignment found in a blast file.
> > Ex-
> >
> >
> > Query: 1
> MAGRGK-GKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLT
> > 59
> >            M+GRGK G  +  KA SRS++AGLQFPVGR+ R L+KG
> YAER+GAGAPVYLAAVLEYLT
> > Sbjct: 1
> MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
> > 60
> >
> >
> > Query: 60  AEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASGGVLPNIHAVLLP
> > 117
> >            AE+LELAGNAARDNKK RI+PRH+QLAIRNDEEL KLLG VTIA GGVLPNI AVLLP
> > Sbjct: 61  AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLP
> > 118
> >
> > I have tried everything to no avail.  AlignIO almost works out, but
> > instead of doing a typical blast alignment, the best it can do is a
> > clustalw like alignment.
> >
> > Any help is much appreciated.
> >
> > -Nate
> >
> > Nathan Agrin
> > Research Associate
> > UMass Medical Center
> > 55 Lake Ave. N.
> > Worcester MA, 01655
> > (508)-856-6018
> > nathan.agrin at umassmed.edu
> >
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu