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

[Frank Schwach]

I also haven't had the time yet to work on this again but, yes, we need
to make sure we don't loose track of where we are. 


On Thu, 2011-09-15 at 14:13 +0000, Fields, Christopher J wrote:
> I mentioned off-list that this should be filed as a github issue so we don't lose track.  Unfortunately I can't get to it until next week (grant deadline). 
> 
> chris
> 
> On Sep 15, 2011, at 8:44 AM, Frank Schwach wrote:
> 
> > 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
> > 
> > 
> > 
> > -- 
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> > Limited, a charity registered in England with number 1021457 and a 
> > company registered in England with number 2742969, whose registered 
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> 



-- 
 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.