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

John M.C. Ma manchunjohn-ma at uiowa.edu
Mon Jul 28 16:45:57 EDT 2008


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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