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

[Fields, Christopher J]

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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