[Bioperl-l] "strand" line in bl2seq output

[Remo Sanges]

Hi Dominique,

I'm not using this module...
however you can access this information in such way

use Bio::Tools::BPbl2seq;
   my $report = Bio::Tools::BPbl2seq->new(-file => 'bl2seq.out', 
-report_type => 'blastn');

   while(my $hsp = $report->next_feature) {
	print
       $hsp->query->strand."\n".
       $hsp->sbjct->strand."\n";
  }

keep in mind that you must use report_type in order to have right 
parsing of strand

Remo

On Mar 29, 2004, at 2:20 PM, Dominique Vlieghe wrote:

> Hello all,
>
> I have a question regarding the parsing of bl2seq output (using 
> Bio::Tools::BPbl2seq). In the bl2seq output there is a line for strand 
> orientation (e.g. "Strand = Plus / Plus"). I looked at the modules 
> that parse this file, but I don't see where those lines are processed. 
> Is this correct? If it is, what's the alternative for getting this 
> valuable information?
>
> Regards
>
> Dominique
>
> -- 
> -----------------------------
> Save the Hubble petition: http://www.savethehubble.org
> ------------------------------
> Dominique Vlieghe, Ph.D.,
> Bioinformatics Core,
> Department for Molecular Biomedical Research (DMBR)
> VIB - Ghent University
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> B-9052 Ghent (Zwijnaarde), Belgium
>
> Tel : +32-(0)9-33-13.693
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> email:dominique.vlieghe at dmbr.ugent.be
> www:http://www.dmbr.ugent.be/
> ------------------------------
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