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

Brian Osborne osborne1 at optonline.net
Fri Mar 17 08:58:55 EST 2006


Andy,

Change "btblastall" to "blastall", let's see what happens.

A question: does your search work from the commandline?

>blastall -p blastx -d Tetraodon_nigroviridis.TETRAODON7.mar.pep.fa -i
blast_input.fasta

Something like that...

Brian O.


On 3/16/06 6:53 PM, "Andrew Norman" <anorman at stanford.edu> wrote:

> Hi Everyone
> 
> 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"
> 
> Here's the script:
> 
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::Tools::Run::StandAloneBlast;
> 
> 
> 
> open OUTPUT, ">>blast_output.txt";
> 
> 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){
>     
>  my $report_obj = $blast_obj->btblastall($seq_obj);
>  
>  my $result_obj = $report_obj->next_result;
>   print OUTPUT $result_obj->num_hits,"\t",$result_obj->hits, "\n";
> 
> 
> 
> }
> 
> close OUTPUT;
> 
> 
> I'd appreciate any help anyone has to offer.  Thanks!
> 
> andy
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