#
# BioPerl module for Bio::Tools::Run::Primer3Redux
#
# Copyright Chad Matsalla, Rob Edwards, Chris Fields
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# Let the code begin...
package Bio::Tools::Run::Primer3Redux;
BEGIN {
$Bio::Tools::Run::Primer3Redux::AUTHORITY = 'cpan:CJFIELDS';
}
BEGIN {
$Bio::Tools::Run::Primer3Redux::VERSION = '0.09';
}
use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
use strict;
use Bio::Tools::Primer3Redux;
use File::Spec;
use Scalar::Util qw(blessed reftype);
my $PROGRAMNAME = 'primer3_core';
my %PARAMS;
my @P1;
my @P2;
my @ALLOWED_TASKS;
# 2.0 is still in alpha (3/3/10), so fallback to v1 for determining parameters
my $DEFAULT_VERSION = '1.1.4';
BEGIN {
# $ct assigns order of parameter building
@P1 = qw(
PRIMER_SEQUENCE_ID
SEQUENCE
TARGET
EXCLUDED_REGION
INCLUDED_REGION
PRIMER_COMMENT
PRIMER_DNA_CONC
PRIMER_EXPLAIN_FLAG
PRIMER_FILE_FLAG
PRIMER_FIRST_BASE_INDEX
PRIMER_GC_CLAMP
PRIMER_DIVALENT_CONC
PRIMER_DNTP_CONC
PRIMER_LOWERCASE_MASKING
PRIMER_SALT_CORRECTIONS
PRIMER_INTERNAL_OLIGO_DNTP_CONC PRIMER_INTERNAL_OLIGO_DIVALENT_CONC
PRIMER_INTERNAL_OLIGO_DNA_CONC PRIMER_INTERNAL_OLIGO_EXCLUDED_REGION
PRIMER_INTERNAL_OLIGO_INPUT PRIMER_INTERNAL_OLIGO_MAX_GC
PRIMER_INTERNAL_OLIGO_MAX_MISHYB PRIMER_INTERNAL_OLIGO_MAX_POLY_X
PRIMER_INTERNAL_OLIGO_MAX_SIZE PRIMER_INTERNAL_OLIGO_MAX_TM
PRIMER_INTERNAL_OLIGO_MIN_GC PRIMER_INTERNAL_OLIGO_MIN_QUALITY
PRIMER_INTERNAL_OLIGO_MIN_SIZE PRIMER_INTERNAL_OLIGO_MIN_TM
PRIMER_INTERNAL_OLIGO_MISHYB_LIBRARY PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT
PRIMER_INTERNAL_OLIGO_OPT_SIZE PRIMER_INTERNAL_OLIGO_OPT_TM
PRIMER_INTERNAL_OLIGO_SALT_CONC PRIMER_INTERNAL_OLIGO_SELF_ANY
PRIMER_INTERNAL_OLIGO_SELF_END
PRIMER_IO_WT_COMPL_ANY
PRIMER_IO_WT_COMPL_END PRIMER_IO_WT_END_QUAL
PRIMER_IO_WT_GC_PERCENT_GT PRIMER_IO_WT_GC_PERCENT_LT
PRIMER_IO_WT_NUM_NS PRIMER_IO_WT_REP_SIM
PRIMER_IO_WT_SEQ_QUAL PRIMER_IO_WT_SIZE_GT
PRIMER_IO_WT_SIZE_LT PRIMER_IO_WT_TM_GT
PRIMER_IO_WT_TM_LT
PRIMER_LEFT_INPUT PRIMER_RIGHT_INPUT
PRIMER_LIBERAL_BASE
PRIMER_MAX_DIFF_TM PRIMER_MAX_END_STABILITY
PRIMER_MAX_GC PRIMER_MAX_MISPRIMING
PRIMER_MAX_POLY_X PRIMER_MAX_SIZE
PRIMER_MAX_TM
PRIMER_MIN_END_QUALITY PRIMER_MIN_GC
PRIMER_MIN_QUALITY PRIMER_MIN_SIZE
PRIMER_MIN_TM
PRIMER_MISPRIMING_LIBRARY
PRIMER_NUM_NS_ACCEPTED PRIMER_NUM_RETURN
PRIMER_OPT_GC_PERCENT PRIMER_OPT_SIZE
PRIMER_OPT_TM
PRIMER_PAIR_MAX_MISPRIMING PRIMER_PAIR_WT_COMPL_ANY
PRIMER_PAIR_WT_COMPL_END PRIMER_PAIR_WT_DIFF_TM
PRIMER_PAIR_WT_IO_PENALTY PRIMER_PAIR_WT_PRODUCT_SIZE_GT
PRIMER_PAIR_WT_PRODUCT_SIZE_LT PRIMER_PAIR_WT_PRODUCT_TM_GT
PRIMER_PAIR_WT_PRODUCT_TM_LT PRIMER_PAIR_WT_PR_PENALTY
PRIMER_PAIR_WT_REP_SIM
PRIMER_PICK_ANYWAY PRIMER_PICK_INTERNAL_OLIGO
PRIMER_PRODUCT_MAX_TM PRIMER_PRODUCT_MIN_TM
PRIMER_PRODUCT_OPT_SIZE PRIMER_PRODUCT_OPT_TM
PRIMER_PRODUCT_SIZE_RANGE
PRIMER_QUALITY_RANGE_MAX PRIMER_QUALITY_RANGE_MIN
PRIMER_SALT_CONC
PRIMER_SELF_ANY PRIMER_SELF_END
PRIMER_SEQUENCE_QUALITY
PRIMER_START_CODON_POSITION
PRIMER_TASK
PRIMER_TM_SANTALUCIA
PRIMER_WT_COMPL_ANY PRIMER_WT_COMPL_END
PRIMER_WT_END_QUAL PRIMER_WT_END_STABILITY
PRIMER_WT_GC_PERCENT_GT PRIMER_WT_GC_PERCENT_LT
PRIMER_WT_NUM_NS PRIMER_WT_POS_PENALTY
PRIMER_WT_REP_SIM PRIMER_WT_SEQ_QUAL
PRIMER_WT_SIZE_GT PRIMER_WT_SIZE_LT
PRIMER_WT_TM_GT PRIMER_WT_TM_LT
PRIMER_WT_TEMPLATE_MISPRIMING
PRIMER_DEFAULT_PRODUCT PRIMER_DEFAULT_SIZE
PRIMER_INSIDE_PENALTY
PRIMER_INTERNAL_OLIGO_MAX_TEMPLATE_MISHYB
PRIMER_OUTSIDE_PENALTY
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS
PRIMER_MAX_TEMPLATE_MISPRIMING
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING PRIMER_PAIR_WT_TEMPLATE_MISPRIMING
);
@P2 = qw(
SEQUENCE_EXCLUDED_REGION
SEQUENCE_INCLUDED_REGION
SEQUENCE_QUALITY
SEQUENCE_FORCE_LEFT_END
SEQUENCE_INTERNAL_EXCLUDED_REGION
SEQUENCE_START_CODON_POSITION
SEQUENCE_FORCE_LEFT_START
SEQUENCE_INTERNAL_OLIGO
SEQUENCE_TARGET
SEQUENCE_FORCE_RIGHT_END
SEQUENCE_PRIMER
SEQUENCE_TEMPLATE
SEQUENCE_FORCE_RIGHT_START
SEQUENCE_PRIMER_OVERLAP_POS
SEQUENCE_ID
SEQUENCE_PRIMER_REVCOMP
SEQUENCE_OVERLAP_JUNCTION_LIST
SEQUENCE_PRIMER_PAIR_OK_REGION_LIST
PRIMER_DNA_CONC
PRIMER_LIBERAL_BASE
PRIMER_PAIR_WT_PR_PENALTY
PRIMER_DNTP_CONC
PRIMER_LIB_AMBIGUITY_CODES_CONSENSUS
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING
PRIMER_EXPLAIN_FLAG
PRIMER_LOWERCASE_MASKING
PRIMER_PICK_ANYWAY
PRIMER_FIRST_BASE_INDEX
PRIMER_MAX_END_GC
PRIMER_PICK_INTERNAL_OLIGO
PRIMER_GC_CLAMP
PRIMER_MAX_END_STABILITY
PRIMER_PICK_LEFT_PRIMER
PRIMER_INSIDE_PENALTY
PRIMER_MAX_GC
PRIMER_PICK_RIGHT_PRIMER
PRIMER_INTERNAL_DNA_CONC
PRIMER_MAX_LIBRARY_MISPRIMING
PRIMER_POS_OVERLAP_TO_END_DIST
PRIMER_INTERNAL_DNTP_CONC
PRIMER_MAX_NS_ACCEPTED
PRIMER_PRODUCT_MAX_TM
PRIMER_INTERNAL_MAX_GC
PRIMER_MAX_POLY_X
PRIMER_PRODUCT_MIN_TM
PRIMER_INTERNAL_MAX_LIBRARY_MISHYB
PRIMER_MAX_SELF_ANY
PRIMER_PRODUCT_OPT_SIZE
PRIMER_INTERNAL_MAX_NS_ACCEPTED
PRIMER_MAX_SELF_END
PRIMER_PRODUCT_OPT_TM
PRIMER_INTERNAL_MAX_POLY_X
PRIMER_MAX_SIZE
PRIMER_PRODUCT_SIZE_RANGE
PRIMER_INTERNAL_MAX_SELF_ANY
PRIMER_MAX_TEMPLATE_MISPRIMING
PRIMER_QUALITY_RANGE_MAX
PRIMER_INTERNAL_MAX_SELF_END
PRIMER_MAX_TM
PRIMER_QUALITY_RANGE_MIN
PRIMER_INTERNAL_MAX_SIZE
PRIMER_MIN_END_QUALITY
PRIMER_SALT_CORRECTIONS
PRIMER_INTERNAL_MAX_TEMPLATE_MISHYB
PRIMER_MIN_GC
PRIMER_SALT_DIVALENT
PRIMER_INTERNAL_MAX_TM
PRIMER_MIN_QUALITY
PRIMER_SALT_MONOVALENT
PRIMER_INTERNAL_MIN_GC
PRIMER_MIN_SIZE
PRIMER_SEQUENCING_ACCURACY
PRIMER_INTERNAL_MIN_QUALITY
PRIMER_MIN_THREE_PRIME_DISTANCE
PRIMER_SEQUENCING_INTERVAL
PRIMER_INTERNAL_MIN_SIZE
PRIMER_MIN_TM
PRIMER_SEQUENCING_LEAD
PRIMER_INTERNAL_MIN_TM
PRIMER_MISPRIMING_LIBRARY
PRIMER_SEQUENCING_SPACING
PRIMER_INTERNAL_MISHYB_LIBRARY
PRIMER_NUM_RETURN
PRIMER_TASK
PRIMER_INTERNAL_OPT_GC_PERCENT
PRIMER_OPT_GC_PERCENT
PRIMER_TM_FORMULA
PRIMER_INTERNAL_OPT_SIZE
PRIMER_OPT_SIZE
PRIMER_WT_END_QUAL
PRIMER_INTERNAL_OPT_TM
PRIMER_OPT_TM
PRIMER_WT_END_STABILITY
PRIMER_INTERNAL_SALT_DIVALENT
PRIMER_OUTSIDE_PENALTY
PRIMER_WT_GC_PERCENT_GT
PRIMER_INTERNAL_SALT_MONOVALENT
PRIMER_PAIR_MAX_COMPL_ANY
PRIMER_WT_GC_PERCENT_LT
PRIMER_INTERNAL_WT_END_QUAL
PRIMER_PAIR_MAX_COMPL_END
PRIMER_WT_LIBRARY_MISPRIMING
PRIMER_INTERNAL_WT_GC_PERCENT_GT
PRIMER_PAIR_MAX_DIFF_TM
PRIMER_WT_NUM_NS
PRIMER_INTERNAL_WT_GC_PERCENT_LT
PRIMER_PAIR_MAX_LIBRARY_MISPRIMING
PRIMER_WT_POS_PENALTY
PRIMER_INTERNAL_WT_LIBRARY_MISHYB
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING
PRIMER_WT_SELF_ANY
PRIMER_INTERNAL_WT_NUM_NS
PRIMER_PAIR_WT_COMPL_ANY
PRIMER_WT_SELF_END
PRIMER_INTERNAL_WT_SELF_ANY
PRIMER_PAIR_WT_COMPL_END
PRIMER_WT_SEQ_QUAL
PRIMER_INTERNAL_WT_SELF_END
PRIMER_PAIR_WT_DIFF_TM
PRIMER_WT_SIZE_GT
PRIMER_INTERNAL_WT_SEQ_QUAL
PRIMER_PAIR_WT_IO_PENALTY
PRIMER_WT_SIZE_LT
PRIMER_INTERNAL_WT_SIZE_GT
PRIMER_PAIR_WT_LIBRARY_MISPRIMING
PRIMER_WT_TEMPLATE_MISPRIMING
PRIMER_INTERNAL_WT_SIZE_LT
PRIMER_PAIR_WT_PRODUCT_SIZE_GT
PRIMER_WT_TM_GT
PRIMER_INTERNAL_WT_TEMPLATE_MISHYB
PRIMER_PAIR_WT_PRODUCT_SIZE_LT
PRIMER_WT_TM_LT
PRIMER_INTERNAL_WT_TM_GT
PRIMER_PAIR_WT_PRODUCT_TM_GT
PRIMER_INTERNAL_WT_TM_LT
PRIMER_PAIR_WT_PRODUCT_TM_LT
PRIMER_THERMODYNAMIC_ALIGNMENT
PRIMER_THERMODYNAMIC_PARAMETERS_PATH
PRIMER_MAX_SELF_ANY_TH
PRIMER_MAX_SELF_ANY_TH
PRIMER_INTERNAL_MAX_SELF_ANY_TH
PRIMER_PAIR_MAX_COMPL_ANY_TH
PRIMER_WT_SELF_ANY_TH
PRIMER_INTERNAL_WT_SELF_ANY_TH
PRIMER_PAIR_WT_COMPL_ANY_TH
PRIMER_MAX_SELF_END_TH
PRIMER_INTERNAL_MAX_SELF_END_TH
PRIMER_PAIR_MAX_COMPL_END_TH
PRIMER_WT_SELF_END_TH
PRIMER_INTERNAL_WT_SELF_END_TH
PRIMER_PAIR_WT_COMPL_END_TH
PRIMER_MAX_HAIRPIN_TH
PRIMER_PAIR_MAX_HAIRPIN_TH
PRIMER_INTERNAL_MAX_HAIRPIN_TH
PRIMER_WT_HAIRPIN_TH
PRIMER_INTERNAL_WT_HAIRPIN_TH
PRIMER_MAX_TEMPLATE_MISPRIMING_TH
PRIMER_INTERNAL_MAX_TEMPLATE_MISHYB_TH
PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH
PRIMER_WT_TEMPLATE_MISPRIMING_TH
PRIMER_INTERNAL_WT_TEMPLATE_MISHYB_TH
PRIMER_PAIR_WT_TEMPLATE_MISPRIMING_TH
P3_FILE_ID
P3_FILE_FLAG
P3_COMMENT
);
# These are the allowed values for PRIMER_TASK
# A run method of the same name will be created dynamically
# in _create_run_methods for each of the tasks listed here
@ALLOWED_TASKS = qw(
pick_pcr_primers
pick_detection_primers
check_primers
pick_primer_list
pick_sequencing_primers
pick_cloning_primers
pick_discriminative_primers
pick_pcr_primers_and_hyb_probe
pick_left_only
pick_right_only
pick_hyb_probe_only
);
}
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->io->_initialize_io();
# create the methods for the various run methods
$self->_create_run_methods;
my ($program, $outfile, $path, $p3_settings_file, $verbose) = $self->_rearrange(
[qw(PROGRAM OUTFILE PATH P3_SETTINGS_FILE VERBOSE)], @args);
$program && $self->program_name($program);
if ($outfile) {
$self->outfile_name($outfile);
}
if ($path) {
my (undef,$path,$prog) = File::Spec->splitpath($path);
$self->program_dir($path);
$self->program_name($prog);
}
if ($verbose) {
$self->{'verbose'}=1;
}
# determine the correct set of parameters to use (v1 vs v2)
my $v = eval {$self->executable; 1;} ? $self->version : $DEFAULT_VERSION;
if (($p3_settings_file)&&($v=~/^2/)){ #apply $p3_settings_file only if version>2
$self->p3_settings_file($p3_settings_file);
}
my $ct = 0;
%PARAMS = ($v && $v =~ /^2/) ? map {$_ => $ct++} @P2 :
map {$_ => $ct++} @P1;
$self->_set_from_args(\@args,
-methods => [sort keys %PARAMS],
-create => 1
);
return $self;
}
sub program_name {
my $self = shift;
# if explicitly set, use that
return $self->{'program_name'} = shift @_ if @_;
# then if previously set, use that
return $self->{'program_name'} if $self->{'program_name'};
# run a quick check to look for programm set class attribute if found
if (!$PROGRAMNAME) {
for (qw(primer3 primer3_core)) {
if ($self->io->exists_exe($_)) {
$PROGRAMNAME = $_;
last;
}
}
}
# don't set permanently, use global
return $PROGRAMNAME;
}
sub program_dir {
my ($self, $dir) = @_;
if ($dir) {
$self->{'program_dir'}=$dir;
}
# we need to stop here if we know what the answer is, otherwise we can
# never set it and then call it later
return $self->{'program_dir'} if $self->{'program_dir'};
if ($ENV{PRIMER3}) {
$self->{'program_dir'} = Bio::Root::IO->catfile($ENV{PRIMER3});
} else {
$self->{'program_dir'} = Bio::Root::IO->catfile('usr','local','bin');
}
return $self->{'program_dir'}
}
sub version {
my ($self) = @_;
return unless my $exe = $self->executable;
if (!defined $self->{'_progversion'}) {
my $string = `$exe -about 2>&1`;
my $v;
if ($string =~ m{primer3\s+release\s+([\d\.]+)}) {
$self->{'_progversion'} = $1;
}
}
return $self->{'_progversion'} || undef;
}
sub set_parameters {
my ($self, %args)=@_;
# hack around _rearrange issue to deal with lack of '-'
my ($seq) = map {
$args{$_}
}
grep { uc $_ eq 'SEQ' } keys %args;
if (defined $seq) {
my @seqs = (ref $seq && (reftype $seq eq 'ARRAY')) ? @$seq : ($seq);
for my $s (@seqs) {
$self->throw("-seq must be a single or array reference of Bio::SeqI") unless (blessed $seq &&
$seq->isa('Bio::SeqI'));
}
$self->{seq_cache} = \@seqs;
}
my $added_args = 0;
# add this back in
unless ($self->{'no_param_checks'}) {
for my $key (sort keys %args) {
my $method = uc $key; # consistency
$method =~ s/^-//; # remove possible hanging bp-like parameter prefix
if (!$self->can($method)) {
next if $method eq 'SEQ';
$self->warn("Parameter $key is not a valid Primer3 parameter");
next
}
$self->$method($args{$key});
$added_args++;
if($self->{'verbose'}){print("$key has been updated to $args{$key}.\n");};
}
}
return $added_args;
}
sub get_parameters {
my $self = shift;
my %args = map {$_->[0] => $_->[1]}
grep { defined $_->[1] }
map { [$_, $self->$_] } sort keys %PARAMS;
return %args;
}
sub reset_parameters {
my $self = shift;
my %args = map {$_ => undef} sort keys %PARAMS;
$self->_set_from_args(\%args, -methods => [sort keys %PARAMS]);
}
sub p3_settings_file{
my ($self, $file_path)=@_;
if ($self->version()=~/^2/){ #version check
if ($file_path){$self->{'p3_settings_file'}=$file_path;}
if ($self->{'p3_settings_file'}){return $self->{'p3_settings_file'};}
}
else {$self->warn("p3_settings_file is only available on primer3 release 2 or above.")}
}
sub run {
my($self, @seqs) = @_;
$self->_do_run(\@seqs);
}
# Create a method that calls _do_run with correct parameters
# for each of the allowed run methods (tasks)
# so we can run primer3 with calls like this:
# $primer3->pick_left_only( $seq );
sub _create_run_methods {
my $self = shift;
foreach my $task (@ALLOWED_TASKS) {
next if defined *{ __PACKAGE__ . '::' . $task };
my $code = 'my($self, @seqs) = @_; $self->_do_run(\@seqs, "'.
$task.'");';
my $sub = eval "sub { $code }";
$self->throw("Compilation error while creating method for $task: $@") if $@;
no strict 'refs';
*{ __PACKAGE__ . '::' . $task } = $sub;
}
}
sub _do_run {
my($self, $seqs, $task) = @_;
my @seqs = ref $seqs eq 'ARRAY' ? @$seqs : ($seqs);
my @exec_array;
my $executable = $self->executable;
my $arguments = ''; #variable to hole run-time arguments
my $out = $self->outfile_name;
unless ($executable && -e $executable) {
$self->throw("Executable was not found. Do not know where primer3 is!") if !$executable;
$self->throw("$executable was not found. Do not know where primer3 is!");
exit(-1);
}
push (@exec_array, $executable);
$self->PRIMER_TASK( $task ) if $task;
my %params = $self->get_parameters;
my $file = $self->_generate_input_file(\%params, \@seqs);
if($self->version=~/^2/){
if ($self->p3_settings_file()){push (@exec_array, "-p3_settings_file=". $self->p3_settings_file());}
if ($self->{'verbose'}){
push (@exec_array, "-echo_settings_file");
}
}
my $str;
foreach (@exec_array){$str.=$_." ";} #"$executable $arguments < $file";
my $obj = Bio::Tools::Primer3Redux->new(-verbose => $self->verbose);
my $status;
my @args;
# file output
if ($out) {
if($self->version=~/^2/){
$str.= "-output=".$out. " <". $file;
$status=system ($str);
}
else {
$str .= "< $file > $out";
my $status = system($str);
}
if($status || !-e $out || -z $out ) {
my $error = ($!) ? "$! Status: $status" : "Status: $status";
$self->throw( "Primer3 call crashed: $error \n[command $str]\n");
return undef;
}
if ($obj && ref($obj)) {
$obj->file($out);
@args = (-file => $out);
}
# fh-based (no outfile)
} else {
$str.=' <'. $file;
open(my $fh,$str."|") || $self->throw("Primer3 call ($str) crashed: $?\n");
if ($obj && ref($obj)) {
$obj->_fh($fh);
@args = (-fh => $fh);
} else {
# dump to debugging
my $io;
while(<$fh>) {$io .= $_;}
close($fh);
$self->debug($io);
return 1;
}
}
$obj->_initialize_io(@args) if $obj && ref($obj);
return $obj;
}
sub _generate_input_file {
# note that I write this to a temp file because we need both read
# and write access to primer3, therefore,
# we can't use a simple pipe.
my ($self, $args, $seqs) = @_;
my ($tmpfh, $tmpfile) = $self->io->tempfile();
# this is a hack to get around interface issues and conflicts when passing
# in raw sequence via PRIMER_SEQUENCE_ID and SEQUENCE (one can potentially
# have both). For now, push any explicitly set parameters on last
my ($id_tag, $seq_tag) = $self->version =~ /^2/ ? # v2 differs from v1
qw(SEQUENCE_ID SEQUENCE_TEMPLATE) : #v2
qw(PRIMER_SEQUENCE_ID SEQUENCE); #v1
my @seqdata;
for my $seq (@$seqs) {
$self->throw("Arguments to run() must be a single or array ref of Bio::SeqI")
unless (blessed $seq && $seq->isa('Bio::SeqI')) ;
push @seqdata, {$id_tag => $seq->id,
$seq_tag => $seq->seq};
}
if (exists $args->{$id_tag} || exists $args->{$seq_tag}) {
push @seqdata, {$id_tag => $args->{$id_tag},
$seq_tag => $args->{$seq_tag}};
delete $args->{$id_tag};
delete $args->{$seq_tag};
}
# generate the common BoulderIO string to be used for each sequence
my $string = '';
for my $param (sort keys %$args) {
my $tmp = $self->$param;
my @data = (ref $tmp && reftype $tmp eq 'ARRAY' ) ? @$tmp : $tmp;
for my $d (@data) {
$string .= "$param=$d\n";
}
}
$string .= "=\n";
# Print the parameters once for each sequence provided or, if
# no sequence given, just write a single block without the
# SEQUENCE_TEMPLATE but make sure we are doing a check_primers taks
# because that's the only allowed situation where no sequence is required
if (@seqdata){
for my $data (@seqdata) {
my $str = join("\n", map { "$_=".$data->{$_}} sort keys %$data)."\n$string";
if($self->{'verbose'}){$self->debug("TRYING\n$str");}
print $tmpfh $str;
}
} elsif ( $args->{PRIMER_TASK} eq 'check_primers' ){
print $tmpfh $string;
} else {
$self->throw("'run' was called without a sequence but PRIMER_TASK was not ".
"'check_primers'. All tasks except 'check_primers' must be given a sequence ".
"to design primers on");
}
close($tmpfh);
return $tmpfile;
}
1;
__END__
=pod
=encoding utf-8
=head1 NAME
Bio::Tools::Run::Primer3Redux
=head1 SYNOPSIS
# design some primers.
# the output will be put into temp.out
use Bio::Tools::Run::Primer3Redux;
use Bio::SeqIO;
my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
my $seq = $seqio->next_seq;
my $primer3 = Bio::Tools::Run::Primer3Redux->new(-outfile => "temp.out",
-path => "/usr/bin/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";
=head1 DESCRIPTION
Bio::Tools::Run::Primer3Redux creates the input files needed to design primers
using primer3 and provides mechanisms to access data in the primer3
output files.
This module a refactoring of the original BioPerl primer3 tools, themselves a
refactoring of the original Primer3 module written by Rob Edwards. See
my @ALLOWED_TASKS = qw(
pick_pcr_primers
pick_detection_primers
check_primers
pick_primer_list
pick_sequencing_primers
pick_cloning_primers
pick_discriminative_primers
pick_pcr_primers_and_hyb_probe
pick_left_only
pick_right_only
pick_hyb_probe_only
);
http://primer3.sourceforge.net for details and to download the software. This
module should work for primer3 release 1 and above but is not guaranteed to work
with earlier versions.
=head1 NAME
Bio::Tools::Run::Primer3Redux - Create input for and work with the output
from the program primer3
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.html - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
L<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
=head1 AUTHOR
Chris Fields cjfields-at-bioperl-dot-org
Refactored from the original Primer3 parser by Rob Edwards, which in turn was
based heavily on work of Chad Matsalla.
bioinformatics1@dieselwurks.com
=head1 CONTRIBUTORS
Rob Edwards redwards@utmem.edu
Chad Matsalla bioinformatics1@dieselwurks.com
Shawn Hoon shawnh-at-stanford.edu
Jason Stajich jason-at-bioperl.org
Brian Osborne osborne1-at-optonline.net
Chris Fields cjfields-at-bioperl-dot-org
Frank Schwach fs5-at-sanger.ac.uk
=head1 SEE ALSO
L<Bio::Tools::Primer3>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=head2 new()
Title : new()
Usage : my $primer3 = Bio::Tools::Run::Primer3->new(-file=>$file) to read
a primer3 output file.
my $primer3 = Bio::Tools::Run::Primer3->new(-seq=>sequence object)
design primers against sequence
Function: Start primer3 working and adds a sequence. At the moment it
will not clear out the old sequence, but I suppose it should.
Returns : Does not return anything. If called with a filename will allow
you to retrieve the results
Args : -outfile : file name send output results to
-path : path to primer3 executable
-p3_settings_file :(optional) path to the settings file. Supported only by primer3 version 2 or above.
-verbose :(optional) boolean value to set verbose output.
=head2 program_name
Title : program_name
Usage : $primer3->program_name()
Function: holds the program name
Returns: string
Args : None
=head2 program_dir
Title : program_dir
Usage : $primer3->program_dir($dir)
Function: returns the program directory, which may also be obtained from ENV variable.
Returns : string
Args :
=head2 version
Title : version
Usage : $v = $prog->version();
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=head2 set_parameters()
Title : set_parameters()
Usage : $primer3->set_parameters(key=>value)
Function: Sets parameters for the input file
Returns : Returns the number of arguments added
Args : See the primer3 docs.
Notes : To set individual parameters use the associated method:
$primer3->PRIMER_MAX_TM(40)
=head2 get_parameters
Title : get_parameters
Usage : $obj->get_parameters
Function :
Returns :
Args :
=head2 reset_parameters()
Title : reset_parameters()
Usage : $primer3->reset_parameters()
Function: Resets all parameters to be undef
Returns : none
Args : none; to reset specific targets call the specific method for that
target (i.e. $primer3->PRIMER_MAX_TM(undef))
=head2 p3_settings_file()
Title : p3settingsfile()
Usage : $primer3->p3settingsfile($file_path);
Function : Getter/Setter for the Primer3 settings file.
Returns : A string containing the path of the named settings file.
Args : $file_path A valid file path to the settings file.
Note : This argument only works in primer3 version 2 or above.
=head2 run
Title : run
Usage : $primer3->run;
Function: Generic run method for the primer3 program. The PRIMER_TASK
must be defined either in the parameter set or it defaults to
'pick_pcr_primers'.
Returns : A Bio::Tools::Primer3 object containing the results.
See the Bio::Tools::Primer3 documentation for those functions.
Args : Bio::Seq object(s) to use as SEQUENCE_TEMPLATE(s)
=head2 _do_run
Title : _do_run
Usage : INTERNAL
Function: Generate input file and run the primer3 program.
Returns : A Bio::Tools::Primer3 object containing the results.
See the Bio::Tools::Primer3 documentation for those functions.
Args : sequence or ref to array of sequences, [task]
If 'task' given, parameter 'PRIMER_TASK' is set to the given task,
otherwise, the 'PRIMER_TASK' parameter is used to detmine what to do.
If that too isn't set the primer3 will default to pick_pcr_primers
=head1 AUTHOR
cjfields <cjfields@bioperl.org>
=head1 COPYRIGHT AND LICENSE
This software is copyright (c) 2011 by Chris Fields.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.
=cut