[Bioperl-l] bl2seq parsing

[Emilie Lalonde]

wonderful, thank you!



On Thursday, August 1, 2013 12:47:03 PM UTC-4, Jason Stajich wrote:
>
> Try giving your sequences names -- a simple 'q' and 'h' is fine.
> If I edit your output file and add a name after Query= and the > it works.
>
>
> On Aug 1, 2013, at 6:21 AM, Emilie Lalonde <emilie.... at gmail.com<javascript:>> 
> wrote:
>
> 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
> <CPCG0003F_PIK3CA_chr3_exon13_1_bl2seq.out>
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>
> Jason Stajich
> jason.... at gmail.com <javascript:>
> ja... at bioperl.org <javascript:>
>  
>