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Gmane
From: Emilie Lalonde <emilie.lalonde <at> gmail.com>
Subject: bl2seq parsing
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 1st August 2013 13:21:58 UTC (over 3 years ago)
Hi all,

I'm trying to parse bl2seq output but am not getting any data in the 
returned object. My bl2seq output file contains an alignment, but it isn't 
being loaded into an object, which is undefined.

I've tried by simply parsing the bl2seq report:

# make Seq objects for forward and reverse reads
my $rev_hsp = Bio::Seq->new(-seq =>$proper_pairs{$ampl}{R}->query_string, 
-alphabet => 'dna');
my $fwd_hsp = Bio::Seq->new(-seq =>$proper_pairs{$ampl}{F}->query_string, 
-alphabet => 'dna');

# make Blast factory and run bl2seq
my $paired_blast_obj = Bio::Tools::Run::StandAloneBlast->new(-program => 
'blastn', -outfile => 'blast/paired_alignment/bl2seq.out');
my $bl2seq_report = $paired_blast_obj->bl2seq($rev_hsp, $fwd_hsp);

# parse bl2seq report
if(my $r = $bl2seq_report->next_result){
   while( my $hit = $r->next_hit ) {
     while( my $hsp = $hit->next_hsp ) {
         print $hsp->get_aln->consensus_iupac()."\n";
       }
     }
 }


And I've also tried with AlignIO:
# read and parse bl2seq output file
my $str = Bio::AlignIO->new(-file => 'blast/paired_alignment/bl2seq.out', 
'-format' => 'bl2seq'); 
while(my $aln = $str->next_aln() ){
     print $aln->length . "\n";
}

I've attached my bl2seq report (output file).



Any help would be greatly appreciated! 


Emilie
 
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