## $Id: prova_primer3.pl,v 1.1 2005/05/19 17:00:24 AndreaSterbini Exp apache $

# test for Bio::Tools::Run::Primer3
# written by Rob Edwards

use strict;

use Bio::Tools::Run::Primer3;
use Bio::SeqIO;

my ($seqio, $seq, $primer3, $args, $results, $num_results);
$seqio=Bio::SeqIO->new(-file=>'bioperl-run-1.4/t/data/Primer3.fa');
$seq=$seqio->next_seq;
# ref($seq) eq "Bio::Seq", 1, "Couldn't read the sequence in t/data/dna1.fa";
$primer3 = Bio::Tools::Run::Primer3->new( -seq => $seq );

$args=$primer3->arguments;

# $$args{'PRIMER_SEQUENCE_ID'} eq "(string, optional) an id. Optional. Note must be present if PRIMER_FILE_FLAG is set";

$primer3->add_targets('PRIMER_SEQUENCE_ID'=>'test seq');

$results=$primer3->run;

$num_results=$results->number_of_results;

print "Ho trovato $num_results risultati\n";

my $primer;

while ($primer = $results->next_primer) {

my $lprimer = $primer->get_primer('-left-primer')->seq->seq;
my $rprimer = $primer->get_primer('-right-primer')->seq->seq;

print $primer->seq->seq, "\n";
print "Left : '$lprimer'\n";
print "Right: '$rprimer'\n";

my $out = new Bio::SeqIO ( -file => '>-' , -format => 'genbank' ) ;

$out -> write_seq( $primer->seq );

}