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

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Fri Mar 17 06:37:39 EST 2006


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)

>  my $report_obj = $blast_obj->btblastall($seq_obj);

If it has the same command line parameters as standard "blastall" you could 
hack it to work by renaming your btblastall.exe to blastall.exe ...

It may also work if you can hack into the module internals, but this is not 
recommended.

Either way, could you please email me a URL out "btblastall /?" output so I/we 
can consider it for inclusion in the future rewrite of the StandAloneBlast 
modules? Thanks.

-- 
Torsten Seemann
Victorian Bioinformatics Consortium, Monash University, Australia
http://www.vicbioinformatics.com/


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