File: README

package info (click to toggle)
libbio-primerdesigner-perl 0.07-3
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 252 kB
  • ctags: 69
  • sloc: perl: 1,378; makefile: 84
file content (130 lines) | stat: -rw-r--r-- 3,664 bytes parent folder | download | duplicates (5)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
NAME
    Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr

SYNOPSIS
      use Bio::PrimerDesigner;

      my $pd = Bio::PrimerDesigner->new;

      #
      # Define the DNA sequence, etc.
      #
      my $dna   = "CGTGC...TTCGC";
      my $seqID = "sequence 1";

      #
      # Define design parameters (native primer3 syntax)
      #
      my %params = ( 
          PRIMER_NUM_RETURN   => 2,
          PRIMER_SEQUENCE_ID  => $seqID,
          SEQUENCE            => $dna,
          PRIMER_PRODUCT_SIZE => '500-600'
      );

      #
      # Or use input aliases
      #
      %param = ( 
          num                 => 2,
          id                  => $seqID,
          seq                 => $dna,
          sizerange           => '500-600'
      ); 

      #
      # Design primers
      #
      my $results = $pd->design( %params ) or die $pd->error;

      #
      # Make sure the design was successful
      #
      if ( !$results->left ) {
          die "No primers found\n", $results->raw_data;
      }

      #
      # Get results (single primer set)
      #
      my $left_primer  = $results->left;
      my $right_primer = $results->right;
      my $left_tm      = $results->lefttm;

      #
      # Get results (multiple primer sets)
      #
      my @left_primers  = $results->left(1..3);
      my @right_primers = $results->right(1..3);
      my @left_tms      = $results->lefttm(1..3);

DESCRIPTION
    Bio::PrimerDesigner provides a low-level interface to the primer3 and
    epcr binary executables and supplies methods to return the results.
    Because primer3 and e-PCR are only available for Unix-like operating
    systems, Bio::PrimerDesigner offers the ability to accessing the primer3
    binary via a remote server. Local installations of primer3 or e-PCR on
    Unix hosts are also supported.

METHODS
  binary_path
    Gets/sets path to the primer3 binary.

  design
    Makes the primer design or e-PCR request. Returns an
    Bio::PrimerDesigner::Result object.

  epcr_example
    Run test e-PCR job. Returns an Bio::PrimerDesigner::Results object.

  list_aliases
    Lists aliases for primer3 input/output options

  list_params
    Lists input options for primer3 or epcr, depending on the context

  method
    Gets/sets method of accessing primer3 or epcr binaries.

  os_is_unix
    Returns 1 if it looks like the operating system is a Unix variant,
    otherwise returns 0.

  primer3_example
    Runs a sample design job for primers. Returns an
    Bio::PrimerDesigner::Results object.

  program
    Gets/sets which program to use.

  run
    Alias to "design."

  url
    Gets/sets the URL for accessing the remote binaries.

  verify
    Tests local installations of primer3 or e-PCR to ensure that they are
    working properly.

AUTHORS
    Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken
    Youens-Clark <kclark@cpan.org>.

LICENSE
    This program is free software; you can redistribute it and/or modify it
    under the terms of the GNU General Public License as published by the
    Free Software Foundation; version 3 or any later version.

    This program is distributed in the hope that it will be useful, but
    WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
    Public License for more details.

    You should have received a copy of the GNU General Public License along
    with this program; if not, write to the Free Software Foundation, Inc.,
    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

SEE ALSO
    Bio::PrimerDesigner::primer3, Bio::PrimerDesigner::epcr.