[Bioperl-l] Run::Primer3 and no primer return

Paola Bignone pabignone at gmail.com
Wed Oct 22 10:02:18 EDT 2008


Dear all,

I trying to use Primer3 through Bioperl.
I copied the basic script from the Run::Primer3 documentation module, and
although it is reading the sequence from the file, no primer is designed.
If I use that sequence in the web-base interface of Primer3, several primers
were obtained; so there is no problem with the sequence.

It is a very basic problem, but I cannot get this to work.
I will appreciate any help as I'm stuck even before I started to change the
code to suit my needs.
TIA,
Paola

----
use Bio::Tools::Run::Primer3;
use Bio::SeqIO;

   my $seqio=Bio::SeqIO->new(-file=>'data/test.fasta');
   my $seq=$seqio->next_seq;

   my $primer3 = Bio::Tools::Run::Primer3 -> new(
   -seq => $seq,
   -outfile => 'data/temp.out',
   -path => '/usr/local/pkgbin/primer3_core',
   );

    unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
   }

$results=$primer3->run();
print "There were ", $results->number_of_results, " primers\n";

----
the data/temp.out file is created but it is empty.


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