[Bioperl-l] Reg. Objects created by default on Bioperl

[Jason Stajich]

The documentation here http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/Tools/Run/StandAloneBlast.pm says:
"For blastall and non-psiblast blastpgp runs, report object is a Bio::SearchIO object"
 
On Jun 24, 2011, at 5:13 AM, ravikumar jayachandran wrote:

> Hi,
> 
> I have a doubt regarding the object name created automatically on the perl
> script. What basis are the objects assigned to a specific module on? Please
> find the link below which I found on the link,
> http://www.bioperl.org/wiki/HOWTO:Beginners.
> 
> ---------------------------------
> use Bio::Seq;
> use Bio::Tools::Run::StandAloneBlast;
> 
> $blast_obj = Bio::Tools::Run::StandAloneBlast->new(-program  =>
> 'blastn', -database => 'db.fa'));
> 
> $seq_obj = Bio::Seq->new(-id  =>"test query", -seq
> =>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
> 
> $report_obj = $blast_obj->blastall($seq_obj);
> 
> $result_obj = $report_obj->next_result;
> 
> print <http://perldoc.perl.org/functions/print.html> $result_obj->num_hits;
> 
> -------------------------------------------------
> 
> For example, "next_result" method is present in Bio::SearchIO module.
> $report_obj has been used to access this "next_result" method. I don't
> understand on what basis $report_obj has been defined to Bio::SearchIO by
> default. Please help me understand the concept.
> 
> Thanks & Regards,
> Ravi.
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