Bio::DB::TFBS - Access to a Transcription Factor Binding Site database

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

Top

Bio::DB::TFBS - Access to a Transcription Factor Binding Site database

SYNOPSIS

Top

  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);

DESCRIPTION

Top

This is a front end module for access to a Transcription Factor Binding Site database.

FEEDBACK

Top

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

Support

Please direct usage questions or support issues to the mailing list:

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.

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/

AUTHOR - Sendu Bala

Top

Email bix@sendu.me.uk

CONTRIBUTORS

Top

Based on Bio::DB::Taxonomy by Jason Stajich

APPENDIX

Top

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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'

_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
BioPerl documentation Contained in the BioPerl distribution. 
# $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


# Let the code begin...

package Bio::DB::TFBS;
use strict;

use Bio::Root::Root;

use base qw(Bio::Root::Root);

our $DefaultSource = 'transfac';


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 { }


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;