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

[Roy Chaudhuri]

Hi John,

I'm not sure if you want to run Primer3 using BioPerl, or just use 
BioPerl to parse an existing Primer3 output file.

For the former you need to specify a target using the -seq argument when 
you create your Bio::Tools::Run::Primer3 object (the argument value 
should be a Bio::Seq object). It's also possible to add the sequence 
between the new() and run() methods using add_targets(), but you snipped 
out that section so I can't tell if you did that and there is some other 
problem. The run() method does not seem to check if a target sequence is 
present, hence you only get an error when you call next_primer() on the 
returned Bio::Tools::Primer3 object.

If you just want to parse an existing Primer3 output file then you need 
to use Bio::Tools::Primer3, specifying the path to the ouput file using 
the -file argument to new(). The documentation to Bio::Tools::Run::Primer3:
http://search.cpan.org/~sendu/bioperl-run/Bio/Tools/Run/Primer3.pm#new()
suggests that you can also provide a -file argument in that module, but 
there doesn't seem to be any evidence of that in the code.


Hope this helps.
Roy.
--
Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

> 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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