[Bioperl-l] Parse BLAST to find mismatches

[Ken Graham]

Thanks Jason,
I thought I was going out of my mind!
Ryan, I'm not THAT much of a Perl newbie! :)
I tired every permutation of Bio::Search object I could find before I posted.
Thanks again for the quick response.

At 03:25 PM 5/30/02 -0400, you wrote:
>There is no seq_inds method (yet) for genericHSP objects - this is a
>stevec specific method for blastHSP objects.  I am porting it over to the
>generic ones and adding it to the interface (grr).  I'm going to break
>protocol and add it to the branch so this will be part of the forthcoming
>1.01 release next week.
>
>-jason
>On Thu, 30 May 2002, Ryan Brinkman wrote:
>
> > >I get the following error:
> > >Can't locate object method "seq_inds" via package
> > >"Bio::Search::HSP::GenericHSP"
> > >(perhaps you forgot to load "Bio::Search::HSP::GenericHSP"?) at
> > >blast_parser_sm line 16,
> > ><GEN1> line 2661.
> > >I tried this code on another computer and got the same results.
> > >Am I forgetting something?
> > >Thanks in advance,
> >
> > >#!/usr/bin/perl -w
> > >use Bio::SearchIO;
> >
> > >$blastfile ='/home/ken/blastFile';
> >
> > The error says it all, add the following:
> >
> > use Bio::Search::HSP::GenericHSP;
> >
> >
> >
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>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu

Ken Graham
UC Davis School of Medicine
Biological Chemistry
4405 Tupper Hall
(530) 752-2928 (Lab)
(530) 752-3516 (Fax)