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

Caroline caroline.johnston at iop.kcl.ac.uk
Wed Oct 22 14:07:23 EDT 2008


Hi Paola,

Your script seems to work for me. Do you want to chuck me a copy of your
test sequence and I'll try it with that? Maybe the default primer3
settings in Bioperl are different to those used by the web interface?

Cheers,
Cass xx

On Wed, 2008-10-22 at 15:02 +0100, Paola Bignone wrote:
> 
> 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";
> 


More information about the Bioperl-l mailing list