[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.

Roy.
--
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.
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




More information about the Bioperl-l mailing list