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

[Das, Abhiram]

Jason, thanks for your reply.

I have two issues:

1. While running the program it shows up the following message:

"Use of uninitialized value in numeric le (<=) at /Library/Perl/5.8.8/Bio/SearchIO/IteratedSearchResultEventBuilder.pm line 367, <GEN4> line 26."

2. Even though there is no hit; $results->num_hits get's me 1 hit.


What I am trying to do:

"Find number of pairwise similar sequences from a set of sequences."

Please find attached the sequence file.

Thanks again
-Abhi

----- Original Message -----
From: "Jason Stajich" <jason.stajich at gmail.com>
To: "Abhiram Das" <abhiram.das at gatech.edu>
Cc: bioperl-l at bioperl.org
Sent: Tuesday, June 28, 2011 5:02:39 PM
Subject: Re: [Bioperl-l] Runnig bl2seq throws error + Failure to parse BlastResult

I'm sorry but I don't understand your question, are you worried that the num_hits is 1 simply? I think this is a function of a forced result from bl2seq -- can you better explain what you are trying to do or provide your sequence file so the issue you are concerned with can be replicated.

Are you trying to construct an all-vs-all pairwise distances based on bl2seq?

On Jun 28, 2011, at 1:26 PM, Das, Abhiram wrote:

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