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

Shawn Hoon shawnh at stanford.edu
Fri Mar 17 12:02:10 EST 2006


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.



>>  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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> Bioperl-l at lists.open-bio.org
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