Bio/DB/TFBS.pm

   1 # $Id: TFBS.pm,v 1.11 2006/08/12 11:00:03 sendu Exp $
   2 #
   3 # BioPerl module for Bio::DB::TFBS
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Sendu Bala <bix@sendu.me.uk>
   8 #
   9 # Copyright Sendu Bala
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12
  13 # POD documentation - main docs before the code
  14
  15 =head1 NAME
  16
  17 Bio::DB::TFBS - Access to a Transcription Factor Binding Site database
  18
  19 =head1 SYNOPSIS
  20
  21   use Bio::DB::TFBS;
  22
  23   my $db = Bio::DB::TFBS->new(-source => 'transfac');
  24   my ($factor_id) = $db->get_factor_ids('PPAR-gamma1');
  25   my ($matrix_id) = $db->get_matrix_ids('PPAR-gamma1');
  26
  27   # get a Bio::Map::TranscriptionFactor with all the positions of a given factor
  28   my $factor = $db->get_factor(-factor_id => $factor_id);
  29
  30   # get a Bio::Map::GeneMap containing all the factors that bind near a given gene
  31   my $gene_map = $db->get_gene_map(-gene_name => 'AQP 7');
  32
  33   # get a PSM (Bio::Matrix::PSM) of a given matrix
  34   my $psm = $db->get_matrix(-matrix_id => $matrix_id);
  35
  36   # get the aligned sequences (Bio::SimpleAlign) that were used to build a given
  37   # matrix
  38   my $align = $db->get_alignment(-matrix_id => $matrix_id);
  39
  40   # get a specific instance sequence (Bio::LocatableSeq)
  41   my $seq = $db->get_seq($id);
  42
  43 =head1 DESCRIPTION
  44
  45 This is a front end module for access to a Transcription Factor Binding Site
  46 database.
  47
  48 =head1 FEEDBACK
  49
  50 =head2 Mailing Lists
  51
  52 User feedback is an integral part of the evolution of this and other
  53 Bioperl modules. Send your comments and suggestions preferably to
  54 the Bioperl mailing list.  Your participation is much appreciated.
  55
  56   bioperl-l@bioperl.org                  - General discussion
  57   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  58
  59 =head2 Support
  60
  61 Please direct usage questions or support issues to the mailing list:
  62
  63 I<bioperl-l@bioperl.org>
  64
  65 rather than to the module maintainer directly. Many experienced and
  66 reponsive experts will be able look at the problem and quickly
  67 address it. Please include a thorough description of the problem
  68 with code and data examples if at all possible.
  69
  70 =head2 Reporting Bugs
  71
  72 Report bugs to the Bioperl bug tracking system to help us keep track
  73 of the bugs and their resolution. Bug reports can be submitted via
  74 the web:
  75
  76   https://github.com/bioperl/bioperl-live/issues
  77
  78 =head1 AUTHOR - Sendu Bala
  79
  80 Email bix@sendu.me.uk
  81
  82 =head1 CONTRIBUTORS
  83
  84 Based on Bio::DB::Taxonomy by Jason Stajich
  85
  86 =head1 APPENDIX
  87
  88 The rest of the documentation details each of the object methods.
  89 Internal methods are usually preceded with a _
  90
  91 =cut
  92
  93 # Let the code begin...
  94
  95 package Bio::DB::TFBS;
  96 use strict;
  97
  98 use Bio::Root::Root;
  99
 100 use base qw(Bio::Root::Root);
 101
 102 our $DefaultSource = 'transfac';
 103
 104 =head2 new
 105
 106  Title   : new
 107  Usage   : my $obj = Bio::DB::TFBS->new(-source => 'transfac');
 108  Function: Builds a new Bio::DB::TFBS object.
 109  Returns : an instance of Bio::DB::TFBS
 110  Args    : -source => which database source: currently only 'transfac_pro'
 111
 112 =cut
 113
 114 sub new {
 115     my ($class, @args) = @_;
 116
 117     if ($class =~ /Bio::DB::TFBS::(\S+)/) {
 118         my ($self) = $class->SUPER::new(@args);
 119         $self->_initialize(@args);
 120         return $self;
 121     }
 122     else {
 123         my %param = @args;
 124         @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
 125         my $source = $param{'-source'} || $DefaultSource;
 126
 127         $source = "\L$source";  # normalize capitalization to lower case
 128
 129         # normalize capitalization
 130         return unless( $class->_load_tax_module($source) );
 131         return "Bio::DB::TFBS::$source"->new(@args);
 132     }
 133 }
 134
 135 # empty for now
 136 sub _initialize { }
 137
 138 =head2 _load_tax_module
 139
 140  Title   : _load_tax_module
 141  Usage   : *INTERNAL Bio::DB::TFBS stuff*
 142  Function: Loads up (like use) a module at run time on demand
 143
 144 =cut
 145
 146 sub _load_tax_module {
 147     my ($self, $source) = @_;
 148     my $module = "Bio::DB::TFBS::" . $source;
 149     my $ok;
 150
 151     eval { $ok = $self->_load_module($module) };
 152     if ( $@ ) {
 153         print STDERR $@;
 154         print STDERR <<END;
 155 $self: $source cannot be found
 156 Exception $@
 157 For more information about the Bio::DB::TFBS system please see
 158 the Bio::DB::TFBS docs.  This includes ways of checking for
 159 formats at compile time, not run time.
 160 END
 161   ;
 162     }
 163     return $ok;
 164 }
 165
 166 1;