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Summary

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

Package variables

Included modules

Inherit

Bio::Root::Root

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);

Description

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

Methods

Methods description

 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'

 Title   : _load_tax_module
 Usage   : *INTERNAL Bio::DB::TFBS stuff*
 Function: Loads up (like use) a module at run time on demand

Methods code

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 _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;

}

General documentation

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

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.

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/

Email bix@sendu.me.uk

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

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