[Bioperl-l] Issues on Bio::Tools::Primer3->next_primer

Chris Fields cjfields at uiuc.edu
Mon Jul 28 19:13:32 EDT 2008


You should send this in as a bug report, attaching an example script.   
I'll be using Primer3 soon so I'll try taking a look at it once it's  
filed.

chris

On Jul 28, 2008, at 3:45 PM, John M.C. Ma wrote:

> Hi,
>
> I am trying a generic script to parse outputs for Primer3 results from
> Bio::Tools::Run::Primer3:
>
> use Bio::Tools::Run::Primer3;
> use Bio::Tools::Primer3;
> use Bio::Seq::PrimedSeq;
> [...]
> my $primer3_handle=Bio::Tools::Run::Primer3->new(-path=>'foobar');
> [...]
> my $primer3_results=$primer3_handle->run();
> my $primer_test=$primer3_results->next_primer;
> [...]
>
> Which is similar to what was on the docs, but when Perl gives the  
> following
> error at running next_primer:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: No target sequence
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /usr/lib/perl5/site_perl/5.10.0/Bio/Root/Root.pm:359
> STACK: Bio::Tools::Primer3::next_primer
> /usr/lib/perl5/site_perl/5.10.0/Bio/Tools/Primer3.pm:306
> STACK: /home/johnma/workspace/NCBI-test/NCBI-test.pl:208
> -----------------------------------------------------------
>
> Whereas line 208 is the line that contained the next_primer.
>
> I tried to access the results manually by primer_results() and hard- 
> calling
> fields, but the output of primer_results() is a hash and not very  
> convenient
> for further processing. Is there a way that I can go back to  
> next_primer...?
>
> Cheers,
>
> John
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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