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  • Committer: Bazaar Package Importer
  • Author(s): Charles Plessy
  • Date: 2008-03-18 14:44:57 UTC
  • mfrom: (4 hardy)
  • mto: This revision was merged to the branch mainline in revision 6.
  • Revision ID: james.westby@ubuntu.com-20080318144457-1jjoztrvqwf0gruk
http://bugs.debian.org/448890
* debian/control:
  - Removed MIA Matt Hope (dopey) from the Uploaders field.
    Thank you for your work, Matt. I hope you are doing well.
  - Downgraded some recommended package to the 'Suggests' priority,
    according to the following discussion on Upstream's mail list.
    http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
    (Closes: #448890)
* debian/copyright converted to machine-readable format.

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examples/tools/run_primer3.pl
 
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#!/usr/bin/perl -w
 
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# $Id: run_primer3.pl,v 1.3.4.1 2006/10/02 23:10:38 sendu Exp $
 
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=head1 NAME
 
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run_primer3.pl - run primer3 and parse its output
 
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=head1 SYNOPSIS
 
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  ./run_primer3.pl -i test.fa
 
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  #or
 
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  ./run_primer3.pl --input=test.fa
 
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=head1 DESCRIPTION
 
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Example of how to run primer3 and parse its output, essentially taken from an
 
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email written by Paul Wiersma to bioperl-l.
 
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=head1 FEEDBACK
 
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User feedback is an integral part of the evolution of this and other
 
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Bioperl scripts. Send your comments and suggestions to the Bioperl 
 
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mailing list.  Your participation is much appreciated.
 
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  bioperl-l@bioperl.org                  - General discussion
 
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  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
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=head2 Reporting Bugs
 
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Report bugs to the Bioperl bug tracking system to help us keep track
 
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of the bugs and their resolution. Bug reports can be submitted via the
 
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web:
 
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  http://bugzilla.open-bio.org/
 
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=head1 AUTHOR
 
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Brian Osborne, bosborne at alum.mit.edu
 
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=cut
 
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use strict;
 
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use Getopt::Long;
 
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use Bio::Tools::Run::Primer3;
 
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use Bio::SeqIO;
 
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my $in_file;
 
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GetOptions("i|input:s" => \$in_file );
 
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usage() unless $in_file;
 
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my $seqio = Bio::SeqIO->new(-file => $in_file);
 
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while (my $seq = $seqio->next_seq) {
 
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        my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq);
 
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        $primer3->program_name('primer3_core') unless $primer3->executable;
 
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        $primer3->add_targets('PRIMER_MIN_TM' => 56, 'PRIMER_MAX_TM' => 90);
 
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        my $results = $primer3->run;
 
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        unless ($results->number_of_results) {
 
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                print "No results for ",$seq->display_id;
 
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                next;
 
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        }
 
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        my @out_keys_part = qw(START
 
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                                                                    LENGTH
 
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                                                                    TM
 
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                                                                         GC_PERCENT
 
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                                                                         SELF_ANY
 
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                                                                         SELF_END
 
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                                                                         SEQUENCE );
 
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        print "\n", $seq->display_id, "\n";
 
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        for (my $i = 0 ; $i < $results->number_of_results ; $i++){
 
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                my $result = $results->primer_results($i);
 
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                print "\n", $i + 1;     
 
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                for my $key qw(PRIMER_LEFT PRIMER_RIGHT){       
 
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                        my ($start, $length) = split /,/, $result->{$key};
 
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                        $result->{$key . "_START"} = $start;
 
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                        $result->{$key . "_LENGTH"} = $length;
 
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                        foreach my $partkey (@out_keys_part) {
 
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                                print "\t", $result->{$key . "_" . $partkey};
 
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                        } 
 
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                        print "\n";
 
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                }
 
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                print "\tPRODUCT SIZE: ", $result->{'PRIMER_PRODUCT_SIZE'}, ", PAIR ANY COMPL: ",
 
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                  $result->{'PRIMER_PAIR_COMPL_ANY'};
 
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                print ", PAIR 3\' COMPL: ", $result->{'PRIMER_PAIR_COMPL_END'}, "\n";
 
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        }
 
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}
 
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sub usage {
 
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   exec('perldoc',$0);
 
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   exit(0);
 
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}
 
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__END__