view release on metacpan or  search on metacpan

lib/Bio/Tools/Run/Primer3.pm  view on Meta::CPAN

#
# This is the original copyright statement. I have relied on Chad's module
# extensively for this module.
#
# Copyright (c) 1997-2001 bioperl, Chad Matsalla. All Rights Reserved.
#           This module is free software; you can redistribute it and/or
#           modify it under the same terms as Perl itself. 
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
#
# But I have modified lots of it, so I guess I should add:
#
# Copyright (c) 2003 bioperl, Rob Edwards. All Rights Reserved.
#           This module is free software; you can redistribute it and/or
#           modify it under the same terms as Perl itself. 
#
# Copyright Rob Edwards
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::Primer3 - Create input for and work with the output 
from the program primer3

=head1 SYNOPSIS

Bio::Tools::Primer3 creates the input files needed to design primers
using primer3 and provides mechanisms to access data in the primer3
output files.

This module provides a bioperl interface to the program primer3. See
http://frodo.wi.mit.edu/primer3/primer3_code.html for
details and to download the software. This module only works for
primer3 release 1 but is not guaranteed to work with earlier versions.

  # design some primers.
  # the output will be put into temp.out
  use Bio::Tools::Run::Primer3;
  use Bio::SeqIO;

  my $seqio = Bio::SeqIO->new(-file=>'data/dna1.fa');
  my $seq = $seqio->next_seq;
  my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq,
                                              -outfile => "temp.out",
                                              -path => "/usr/bin/primer3_core");

  # or after the fact you can change the program_name
  $primer3->program_name('my_suprefast_primer3');

  unless ($primer3->executable) {
    print STDERR "primer3 can not be found. Is it installed?\n";
    exit(-1)
  }

  # what are the arguments, and what do they mean?
  my $args = $primer3->arguments;

  print "ARGUMENT\tMEANING\n";
  foreach my $key (keys %{$args}) {print "$key\t", $$args{$key}, "\n"}

  # 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::Run::Primer3 object with the results
  $results = $primer3->run;

  # see the Bio::Tools::Run::Primer3 pod for
  # things that you can get from this. For example: