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

Roy Chaudhuri roy.chaudhuri at gmail.com
Wed Oct 22 10:56:05 EDT 2008

Hi Paola,

I tried your code using a sequence I had lying around, and it seemed to
work fine, designing 5 primers. I then tried it with a sequence
consisting of just As, so no primers were designed. However the temp.out
file was not empty, it still contained lines with the input data
(PRIMER_SEQUENCE_ID and SEQUENCE), so this suggests that Primer3 is not
running correctly for you. Perhaps there is a file permissions issue? Is
primer3_core executable?

I notice that you haven't declared $results using "my". If you're not
doing so already, include "use warnings; use strict;" at the top of your
program, that might give you some more useful information on why things
are going wrong.

Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

Paola Bignone wrote:
> 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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