[Bioperl-l] BLAST in Bioperl - Can't call method "next_result"

Casandra crrcri at ibmb.csic.es
Fri Feb 24 10:40:48 EST 2012


Hi, I am installing BLAST to use it into BioPerl but I'm having some  
problems and I can't find how to fix them:

  I follow the steps in here: http://www.ncbi.nlm.nih.gov/books/NBK52640/ 
  (at least I think I did it right) for mac.

and I downloaded swissprot.gz db to try with the following script:

#!/bin/perl -w

use Bio::Seq;
use Bio::SearchIO;
use Bio::Tools::Run::StandAloneBlast;

$blast_obj = Bio::Tools::Run::StandAloneBlast->new(-program  =>  
'blastp', -database => '~/scripts/ncbi-blast-2.2.25+/db/swissprot.fa');
$seq_obj = Bio::Seq->new(-id  =>"test query", -seq =>"MMSMLGGL");
$report_obj = $blast_obj->blastall($seq_obj);
$result_obj = $report_obj->next_result;
print $result_obj->num_hits;

That I wrote based on http://www.bioperl.org/wiki/HOWTO:Beginners   
BLAST section.

But I'm not sure if this step that they say " The example code assumes  
that you used the formatdb program to index the database sequence file  
"db.fa"" I did it properly. I just downloaded the swissprot db, keep  
it into /db directory and adapt the script to this. I haven't used  
this "formatdb" so I don't know if this script is not updated or if it  
should run anyway.

This is what I get:

Mercuri:BioPerl Casandra$ perl bp_blast.pl

--------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [test query]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: No whitespace allowed in FASTA ID [test query]
---------------------------------------------------
Use of uninitialized value in join or string at /Library/Perl/Updates/ 
5.8.8/darwin-thread-multi-2level/File/Spec/Unix.pm line 86.

--------------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------
Can't call method "next_result" on an undefined value at bp_blast.pl  
line 13.


Just for curiosity, when I change
$report_obj = $blast_obj->blastall($seq_obj);

to
$report_obj = $blast_obj->blast($seq_obj);

I get this message instead:

Mercuri:BioPerl Casandra$ perl bp_blast.pl
Can't locate object method "next_result" via package "Bio::Seq" at  
bp_blast.pl line 13.

Thanks a lot





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