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

[Jason Stajich]

To answer your question "there might be a bug"

But there won't be any hsps or hits so why do you care if the counter is wrong? 


On Jun 28, 2011, at 2:32 PM, Das, Abhiram wrote:

> 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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> 
> <all_reads.fasta>