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use Bio::Tools::Run::StandAloneBlast

P: 7
Hi..
I am trying to run a bioperl program but it is giving some strange errors.My program code is as follows:

Expand|Select|Wrap|Line Numbers
  1. use Bio::SeqIO;
  2. use Bio::Tools::Run::StandAloneBlast;
  3. use Bio::DB::SwissProt;
  4. my $database = new Bio::DB::SwissProt;
  5. my $query = $database->get_Seq_by_id('TAUD_ECOLI');
  6.  
  7. my $factory = Bio::Tools::Run::StandAloneBlast->new(
  8.                 'program'  => 'blastp',
  9.                 'database' => 'swissprot',
  10.                  _READMETHOD => "Blast"
  11.              );
  12. my $blast_report = $factory->blastall($query);
  13. my $result = $blast_report->next_result;
  14. while( my $hit = $result->next_hit()) {
  15.     print "\thit name: ", $hit->name(), 
  16.     " significance: ", $hit->significance(), "\n";
  17. }
The Error is :
-------------- WARNING ---------------------
MSG: cannot find path to blastall
---------------------------------------------------
Can't call method "next_result" on an undefined value at
C:\Perl\bin\biotool.pl line 13.


Any help will be appreciated !!
Nov 15 '08 #1
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1 Reply


KevinADC
Expert 2.5K+
P: 4,059
I don't know anything about the module but the problem appears to be here:

Expand|Select|Wrap|Line Numbers
  1. my $factory = Bio::Tools::Run::StandAloneBlast->new(
  2.                 'program'  => 'blastp',
  3.                 'database' => 'swissprot',
  4.                  _READMETHOD => "Blast"
  5.              );
  6.  
my guess is that the value of 'program' is wrong. Hence the warning/error: cannot find path to blastall. You will have to figure out what that should be, I have no idea. Or ask on a Bioperl forum, I think there is one if you go to the bioperl website. Or maybe a mailing list.
Nov 15 '08 #2

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