Hello,
I am trying to use this module to pick primers and am receiving the error:
Uncaught exception from user code:
No alias for 'PRIMER_PRODUCT_SIZE' at
/home/radon00/amr/sandbox/alpha/primer_PBO.pl line 277.
I am using the synopsis on the cpan listing for the module as a template
as follows. In this case, $probe_key holds a FASTA header and
$probe_value contains sequence. I am not sure if this is a bug in the
module or if I am doing something wrong since I am new to perl and even
newer to using modules.
my $pd = Bio::PrimerDesigner->new;
while ((my $probe_key, my $probe_value)=each(%probe_hash))
{
#
# Define the DNA sequence, etc.
#
my $dna = $probe_value;
my $seqID = $probe_key;
#
# Define design parameters (native primer3 syntax)
#
my %params = (
PRIMER_NUM_RETURN => 2,
PRIMER_SEQUENCE_ID => $seqID,
SEQUENCE => $dna,
PRIMER_PRODUCT_SIZE => '500-600'
);
#
# Design primers
#
my $results = $pd->design( %params ) or die $pd->error;
#
# Make sure the design was successful
#
if ( !$results->left ) {
die "No primers found\n", $results->raw_data;
}
#
# Get results (single primer set)
#
my $left_primer = $results->left;
my $right_primer = $results->right;
my $left_tm = $results->lefttm;
#
# Get results (multiple primer sets)
#
my @left_primers = $results->left(1..3);
my @right_primers = $results->right(1..3);
my @left_tms = $results->lefttm(1..3);
}
RT for rt.cpan.org