Greetings monks! I come in seek of help regarding a perl module from bioperl tools, Primer3. Whenever I run it normally get something such as "unallowed parameter". It calls all the modules correctly though, seen in:

#!/usr/local/bin/perl
use warnings;
use strict;
use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Primer3;
use Data::Dumper;

[download]

However, when I call something such as $primer3->arguments to see the list of arguments, it doesn't work. Code within the program:

my $seqio = new Bio::SeqIO( 
   -file => "<(PRIVATE)/fastaUplist.fa",                              
+  
   -format =>'fasta');

my $seq = $seqio->next_seq;

my $primer3 = Bio::Tools::Primer3->new(    
   -seq=>$seq,
   -path=>"(PRIVATE)/primer3_core"
);

my $argref = $primer3->arguments();
print Dumper($argref);

[download]

Any ideas as to why this is not working?? Could there be an error due to the .pm file often referring to itself as Bio::Tools::Run::Primer3 instead of Bio::Tools::Primer3 as it's packaged now? Thanks!

UPDATE: Whenever I run it now I get 0 results back seen in the $results section via data dumper where:

 'maximum_primers_returned' => -1,

Also, if running it a different way I get nonsense about "thermodynamic approach chosen, but path to thermodynamic parameters not specified". Meh? It's weird since it can be ran from the command line with the example in the primer3 manual seen here: http://umbc.rnet.missouri.edu/resources/primer3_manual.htm#example However, when running with our own file there were errors (thermodynamic approach... as mentioned above). This was just to test the executable primer3_core though, because we want to use the module for development elsewhere. Any suggestions?

In reply to Primer3 - BioPerl by blarsen20

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