examples/tools/run_primer3.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5 run_primer3.pl - run primer3 and parse its output
   6
   7 =head1 SYNOPSIS
   8
   9   ./run_primer3.pl -i test.fa
  10
  11   #or
  12
  13   ./run_primer3.pl --input=test.fa
  14
  15 =head1 DESCRIPTION
  16
  17 Example of how to run primer3 and parse its output, essentially taken from an
  18 email written by Paul Wiersma to bioperl-l.
  19
  20 =head1 FEEDBACK
  21
  22 User feedback is an integral part of the evolution of this and other
  23 Bioperl scripts. Send your comments and suggestions to the Bioperl
  24 mailing list.  Your participation is much appreciated.
  25
  26   bioperl-l@bioperl.org                  - General discussion
  27   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  28
  29 =head2 Reporting Bugs
  30
  31 Report bugs to the Bioperl bug tracking system to help us keep track
  32 of the bugs and their resolution. Bug reports can be submitted via the
  33 web:
  34
  35   https://github.com/bioperl/bioperl-live/issues
  36
  37 =head1 AUTHOR
  38
  39 Brian Osborne, bosborne at alum.mit.edu
  40
  41 =cut
  42
  43 use strict;
  44 use Getopt::Long;
  45 use Bio::Tools::Run::Primer3;
  46 use Bio::SeqIO;
  47
  48 my $in_file;
  49
  50 GetOptions("i|input:s" => \$in_file );
  51
  52 usage() unless $in_file;
  53
  54 my $seqio = Bio::SeqIO->new(-file => $in_file);
  55
  56 while (my $seq = $seqio->next_seq) {
  57         my $primer3 = Bio::Tools::Run::Primer3->new(-seq => $seq);
  58         $primer3->program_name('primer3_core') unless $primer3->executable;
  59
  60         $primer3->add_targets('PRIMER_MIN_TM' => 56, 'PRIMER_MAX_TM' => 90);
  61
  62         my $results = $primer3->run;
  63
  64         unless ($results->number_of_results) {
  65                 print "No results for ",$seq->display_id;
  66                 next;
  67         }
  68
  69         my @out_keys_part = qw(START
  70                                                                     LENGTH
  71                                                                     TM
  72                                                                          GC_PERCENT
  73                                                                          SELF_ANY
  74                                                                          SELF_END
  75                                                                          SEQUENCE );
  76
  77         print "\n", $seq->display_id, "\n";
  78
  79         for (my $i = 0 ; $i < $results->number_of_results ; $i++){
  80                 my $result = $results->primer_results($i);
  81
  82                 print "\n", $i + 1;
  83                 for my $key qw(PRIMER_LEFT PRIMER_RIGHT){
  84                         my ($start, $length) = split /,/, $result->{$key};
  85                         $result->{$key . "_START"} = $start;
  86                         $result->{$key . "_LENGTH"} = $length;
  87                         foreach my $partkey (@out_keys_part) {
  88                                 print "\t", $result->{$key . "_" . $partkey};
  89                         }
  90                         print "\n";
  91                 }
  92                 print "\tPRODUCT SIZE: ", $result->{'PRIMER_PRODUCT_SIZE'}, ", PAIR ANY COMPL: ",
  93                   $result->{'PRIMER_PAIR_COMPL_ANY'};
  94                 print ", PAIR 3\' COMPL: ", $result->{'PRIMER_PAIR_COMPL_END'}, "\n";
  95         }
  96 }
  97
  98 sub usage {
  99    exec('perldoc',$0);
 100    exit(0);
 101 }
 102
 103 __END__