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

[Das, Abhiram]

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