[Bioperl-l] issue with Bio::Tools::Run::Primer3Redux

[Frank Schwach]

Hi Kumar,

We are currently working on this module and you might want to check out
the latest version on Chris Field's github project:

https://github.com/cjfields/Bio-Tools-Primer3Redux

There will probably be some changes again once I get some time again to
work on a few points we discussed lately. You can also check out my repo
here:
https://github.com/fschwach/Bio-Tools-Primer3Redux

but I will certainly have to make changes to that code because I used
AUTOLAD in the last version, which is probably not a good idea.
My recommendation would be to use Chris' repo and see if that works for
you. If not, feedback would be much appreciated.

Cheers,

Frank




On Thu, 2011-09-15 at 13:20 +0200, kumar Saurabh wrote:
> Hi,
> 
> I need to integrate the primer3 module in one of our pipeline. In a process,
> I was testing the initial code given on the CPAN website. But whenever I try
> to run this program its giving me error...that "Cannot locate the Object
> method add_target via the package Bio::Tools:Run::Primer3Redux...."
> 
> The line of codes I am using is as follows:
> 
> # design some primers.
>   # the output will be put into temp.out
>   use Bio::Tools::Primer3Redux;
>   use Bio::Tools::Run::Primer3Redux;
>   use Bio::SeqIO;
> 
>   my $seqio = Bio::SeqIO->new(-file=>'sample.dna');
>   my $seq = $seqio->next_seq;
> 
>   my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
>                                             -path =>
> "/home/singh/Downloads/primer3-2.2.3/src/primer3_core");
> 
>   # or after the fact you can change the program_name
>   $primer3->program_name('my_superfast_primer3');
> 
>   unless ($primer3->executable) {
>     print STDERR "primer3 can not be found. Is it installed?\n";
>     exit(-1)
>   }
> 
>   # set the maximum and minimum Tm of the primer
>   $primer3->add_targets('PRIMER_MIN_TM'=>56, 'PRIMER_MAX_TM'=>90);
> 
>   # Design the primers. This runs primer3 and returns a
>   # Bio::Tools::Primer3::result object with the results
>   # Primer3 can run in several modes (see explanation for
>   # 'PRIMER_TASK' in the primer3 doccumentation). To run a task,
>   # either call it by its PRIMER_TASK name as in these examples:
>   $pcr_primer_results = $primer3->pick_pcr_primers($seq);
>   $pcr_and_hyb_results = $primer3->pick_pcr_primers_and_hyb_probe( $seq );
>   $check_results = $primer3->check_primers();
> 
>   # Alternatively, explicitly set the PRIMER_TASK parameter and
>   # use the generic 'run' method (this is mainly here for backwards
>   # compatibility) :
>   $primer3->PRIMER_TASK( 'pick_left_only' );
>   $result = $primer3->run( $seq );
> 
>   # If no task is set and the 'run' method is called, primer3 will default
> to
>   # pick pcr primers.
> 
>   # see the Bio::Tools::Primer3Redux POD for
>   # things that you can get from this. For example:
> 
>   print "There were ", $results->num_primer_pairs, " primer pairs\n";
> 
> 
> Can anyone help me with this???
> 
> 
> Best regards,
> Kumar
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.