[Bioperl-l] Runnig bl2seq throws error + Failure to parse BlastResult

[Smithies, Russell]

Did you try printing the result with Data::Dumper to see what's in it?

use Data::Dumper;

if($result = $fac->next_result){
  print Dumper $result;
  .
  .
  .
  .

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Das, Abhiram
> Sent: Wednesday, 29 June 2011 8:27 a.m.
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] Runnig bl2seq throws error + Failure to parse
> BlastResult
> 
> Hi,
> 
> Running the following code throws the message:
> 
> "Use of uninitialized value in numeric le (<=) at
> /Library/Perl/5.8.8/Bio/SearchIO/IteratedSearchResultEventBuilder.pm
> line 315, <GEN6> line 26."
> 
> Even though the output file shows no hit's, the BlastResult->num_hits
> returns 1.
> 
> 
> 
> CODE:
> 
> use strict;
> use Bio::Seq;
> use Bio::SeqIO;
> use Bio::DB::GenBank;
> use Bio::Tools::Run::StandAloneBlastPlus;
> use Bio::Search::Result::BlastResult;
> use Bio::Search::Hit::HitI;
> 
> my $fac = Bio::Tools::Run::StandAloneBlastPlus->new();
> 
> my $seq_obj = Bio::SeqIO->new(-file => "all_reads.fasta", -format =>
> "fasta", -alphabet => "dna");
> 
> #loop through each seq in the seq-obj and blast it with the next
> sequence
> my @seq_list;
> while(my $seq = $seq_obj->next_seq()){
> push(@seq_list, $seq);
> }
> 
> my $eval = 0.000001;
> my $word = 16;
> my $match = 0;
> no strict;
> for(my $i = 0; $i < @seq_list; $i++){
> for(my $j = $i+1; $j < @seq_list; $j++){
> $fac->bl2seq(-method=>'blastn', -query => $seq_list[$j], -subject =>
> $seq_list[$i], -outfile=>'test.out');
> $fac->rewind_results;
> if($result = $fac->next_result){
> print "# hits found:: ", $result->num_hits,"\n";
> if(my $hit = $result->next_hit){
> $match++;
> }
> }
> }
> }
> $fac->cleanup();
> 
> 
> Appreciate any help.
> 
> 
> 
> 
> 
> 
> 
> Thanks
> -Abhi
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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