[Bioperl-l] passing paramteters to primer3

[Thomas J Keller]

Greetings,
I'm trying to customize the Primer3 parameters via 
Bio::Tools::Run::Primer3.
I don't understand why my param_string  variable is not working 
(####code####):
####
use strict;
use warnings;
use Bio::Tools::Run::Primer3;
use Bio::SeqIO;

my $seqio = Bio::SeqIO->new(-file => 
'/Users/kellert/Documents/Consults/Afentoulis/X03019.fa');
my $seq = $seqio->next_seq;
my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq, -outfile => 
'/Users/kellert/Documents/Consults/Afentoulis/temp.out');

unless ($primer3->executable) { print STDERR "primer3 cannot be 
found.\n"; exit(-1) }

my %params = (
	PRIMER_TASK					=> 'pick_pcr_primers_and_hyb_probe',
	PRIMER_MIN_TM 				=> 48,
	PRIMER_MAX_TM 				=> 70,
	PRIMER_OPT_TM				=> 60,
	PRIMER_PRODUCT_SIZE_RANGE	=> '75-150',
	PRIMER_NUM_RETURN			=> 10,
	PRIMER_MAX_POLY_X			=> 3,
	);
my $arg_string = join(", ", ( map { "$_ => \'$params{$_}\'" } keys 
%params));

# set max and min of Tm
$primer3->add_targets($arg_string);

####

this runs Primer3 but I get the warning:
-------------------- WARNING ---------------------
MSG: Parameter PRIMER_MIN_TM => '48', PRIMER_MAX_POLY_X => '3', 
PRIMER_TASK => 'pick_pcr_primers_and_hyb_probe', PRIMER_MAX_TM => '70', 
PRIMER_NUM_RETURN => '10', PRIMER_PRODUCT_SIZE_RANGE => '75-150', 
PRIMER_OPT_TM => '60' is not a valid Primer3 parameter
---------------------------------------------------


I'm betting I've missed something trivial, but would appreciate your 
help.

Thanks,
Tom K

Tom Keller, Ph.D.
http://www.ohsu.edu/research/core
kellert at ohsu.edu
503-494-2442
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