/usr/share/perl5/Bio/DB/TFBS.pm is in libbio-perl-perl 1.6.923-1.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 | # $Id: TFBS.pm,v 1.11 2006/08/12 11:00:03 sendu Exp $
#
# BioPerl module for Bio::DB::TFBS
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Sendu Bala <bix@sendu.me.uk>
#
# Copyright Sendu Bala
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::DB::TFBS - Access to a Transcription Factor Binding Site database
=head1 SYNOPSIS
use Bio::DB::TFBS;
my $db = Bio::DB::TFBS->new(-source => 'transfac');
my ($factor_id) = $db->get_factor_ids('PPAR-gamma1');
my ($matrix_id) = $db->get_matrix_ids('PPAR-gamma1');
# get a Bio::Map::TranscriptionFactor with all the positions of a given factor
my $factor = $db->get_factor(-factor_id => $factor_id);
# get a Bio::Map::GeneMap containing all the factors that bind near a given gene
my $gene_map = $db->get_gene_map(-gene_name => 'AQP 7');
# get a PSM (Bio::Matrix::PSM) of a given matrix
my $psm = $db->get_matrix(-matrix_id => $matrix_id);
# get the aligned sequences (Bio::SimpleAlign) that were used to build a given
# matrix
my $align = $db->get_alignment(-matrix_id => $matrix_id);
# get a specific instance sequence (Bio::LocatableSeq)
my $seq = $db->get_seq($id);
=head1 DESCRIPTION
This is a front end module for access to a Transcription Factor Binding Site
database.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Sendu Bala
Email bix@sendu.me.uk
=head1 CONTRIBUTORS
Based on Bio::DB::Taxonomy by Jason Stajich
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::TFBS;
use strict;
use Bio::Root::Root;
use base qw(Bio::Root::Root);
our $DefaultSource = 'transfac';
=head2 new
Title : new
Usage : my $obj = Bio::DB::TFBS->new(-source => 'transfac');
Function: Builds a new Bio::DB::TFBS object.
Returns : an instance of Bio::DB::TFBS
Args : -source => which database source: currently only 'transfac_pro'
=cut
sub new {
my ($class, @args) = @_;
if ($class =~ /Bio::DB::TFBS::(\S+)/) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
}
else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $source = $param{'-source'} || $DefaultSource;
$source = "\L$source"; # normalize capitalization to lower case
# normalize capitalization
return unless( $class->_load_tax_module($source) );
return "Bio::DB::TFBS::$source"->new(@args);
}
}
# empty for now
sub _initialize { }
=head2 _load_tax_module
Title : _load_tax_module
Usage : *INTERNAL Bio::DB::TFBS stuff*
Function: Loads up (like use) a module at run time on demand
=cut
sub _load_tax_module {
my ($self, $source) = @_;
my $module = "Bio::DB::TFBS::" . $source;
my $ok;
eval { $ok = $self->_load_module($module) };
if ( $@ ) {
print STDERR $@;
print STDERR <<END;
$self: $source cannot be found
Exception $@
For more information about the Bio::DB::TFBS system please see
the Bio::DB::TFBS docs. This includes ways of checking for
formats at compile time, not run time.
END
;
}
return $ok;
}
1;
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