[Bioperl-l] Ask help for Bio::Tools::Run::Primer3

Thomas J Keller kellert at ohsu.edu
Wed Sep 29 16:45:04 EDT 2004

Hi Tony,
Jason answered this question not too long ago. I happened to have saved 
his answer (pasted below). Note that he gave the path to primer3_core

>> Hello Bioperlers
>> I have been trying to use the BioPerl-run Primer3.pm module to run
>> primer3. In doing so I think I have found 2 bugs that prevent it from
>> working properly (I hope this is the right place to ask this).
> This is exactly the right place to ask this question
>> The line
>> my $executable = $self->{'program_dir'}.$self->{'program'};
>> I think should be
>> my $executable = $self->{'program_dir'}.$self->{'program_name'};
>> otherwise the primer3 executable is never found using the -path option
>> in a call to the constructor
>> my $primer3 =
>> Bio::Tools::Run::Primer3->new(-path=>'/usr/mbin/primer3_core',-
>> seq=>$seq,
>> -outfile=>"temp.out");

and rob - I think you want to call $self->program_dir and $self->program
so they can overriden as well - that's why I set up the Base Class to 
these methods.

On Sep 29, 2004, at 1:21 PM, Fengkai Zhang (Tony) wrote:

> Hi, I am a newbie for bioperl and met the below question.
> I was trying to use Bio::Tools::Run::Primer3. When I run the example
> code in the documentation of this module, I got the following error
> message:
> --------------------------------
> <shell> $ perl -I ../primer3_1.0.0/src/ -w primer3run_test.pl
> Use of uninitialized value in concatenation (.) or string at
> /usr/lib/perl5/site_perl/5.8.0/Bio/Tools/Run/Primer3.pm line 212,
> <GEN0> line 1.
> primer3 can not be found. Is it installed?
> --------------------------------
> I already installed Primer3 according its instruction and it works
> well to run the test and example. I also noticed that the
> primer_test.pl in primer3 package calls "primer3_core" rather than
> "primer3". Does it matter for Bio::Tools::Run::Primer3 module?
> Thanks ahead for your help.
> Tony
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