[Bioperl-l] can't locate object method "next_result" (probablya simple problem)

Chris Fields cjfields at uiuc.edu
Fri Mar 17 12:27:39 EST 2006


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Shawn Hoon
> Sent: Friday, March 17, 2006 11:02 AM
> To: Torsten Seemann
> Cc: Andrew Norman; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] can't locate object method "next_result"
> (probablya simple problem)
> 
> 
> On Mar 17, 2006, at 3:37 AM, Torsten Seemann wrote:
> 
> > Andrew,
> >
> >> I'm brand new to bioperl and object oriented programming in
> >> general.  I've been trying some of the example scripts in the
> >> HOWTO and I ran into the following error (I'm using bioperl v.
> >> 1.2.3, windows XP) while trying to get some blast results to print:
> >> "can't locate object method "next_result" via package "Bio::Seq"
> >> at blast_tetra.pl"
> >
> > StandAloneBlast has never supported "btblastall".
> >
> >> my $file_obj = Bio::SeqIO->new(-file => "blast_input.fasta", -
> >> format => "fasta" );
> >> my @params = (program  => 'blastx', database =>
> >> 'Tetraodon_nigroviridis.TETRAODON7.mar.pep.fa', _READMETHOD =>
> >> 'SearchIO' );
> >> my $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
> >> while (my $seq_obj = $file_obj->next_seq){
> >
> > I'm not even sure why you even got past this line without a Perl
> > error?
> > (perhaps try "use strict;" at the top of your script)
> >
> 
> i think StandAloneBlast was interpreting btblastall as a -b parameter
> to feed into to blastall.
> 
...

Yep.  AUTOLOADed it.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign



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