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Summary

Bio::Map::TranscriptionFactor - A transcription factor modelled as a mappable
element

Package variables

Inherit

Bio::Map::Mappable

Synopsis

  use Bio::Map::TranscriptionFactor;
  use Bio::Map::GeneMap;
  use Bio::Map::Position;

  # model a TF that binds 500bp upstream of the BRCA2 gene in humans and
  # 250bp upstream of BRCA2 in mice
  my $tf = Bio::Map::TranscriptionFactor->get(-universal_name => 'tf1');
  my $map1 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
                                    -species => "human");
  my $map2 = Bio::Map::GeneMap->get(-universal_name => "BRCA2",
                                    -species => "mouse");
  Bio::Map::Position->new(-map => $map1,
                          -element => $tf,
                          -start => -500,
                          -length => 10);
  Bio::Map::Position->new(-map => $map2,
                          -element => $tf,
                          -start => -250,
                          -length => 10);

  # Find out where the transcription factor binds
  foreach $pos ($tf->get_positions) {
    print $tf->universal_name, " binds at position " $pos->value, " relative to ",
          $pos->relative->description, " of gene ",
          $pos->map->universal_name, " in species ", $pos->map->species, "\n";
  }

Description

A transcription factor modelled as a mappable element. It can have mulitple
binding sites (positions) near multiple genes (maps).

Methods

Methods description

 Title   : new
 Usage   : my $tf = Bio::Map::TranscriptionFactor->new();
 Function: Builds a new Bio::Map::TranscriptionFactor object
 Returns : Bio::Map::TranscriptionFactor
 Args    : -universal_name => string name of the TF (in a form common to all
                              species that have the TF, but unique amongst
                              non-orthologous TFs), REQUIRED
           -description    => string, free text description of the TF

 Title   : get
 Usage   : my $obj = Bio::Map::TranscriptionFactor->get();
 Function: Builds a new Bio::Map::TranscriptionFactor object (like new()), or
           gets a pre-existing one that shares the same universal_name.
 Returns : Bio::Map::TranscriptionFactor
 Args    : -universal_name => string name of the TF (in a form common to all
                              species that have the TF, but unique amongst
                              non-orthologous TFs), REQUIRED
           -description    => string, free text description of the TF

 Title   : universal_name
 Usage   : my $name = $obj->universal_name
 Function: Get/Set TF name, corresponding to the name of the TF in a form shared
           by orthologous versions of the TF in different species, but otherwise
           unique.
 Returns : string
 Args    : none to get, OR string to set

 Title   : description
 Usage   : my $desc = $obj->description
 Function: Get/Set a description of the TF.
 Returns : string
 Args    : none to get, OR string to set

Methods code

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    my ($u_name, $desc) = $self->_rearrange([qw(UNIVERSAL_NAME DESCRIPTION)], @args);
    $u_name || $self->throw("You must supply a -universal_name");
    $self->universal_name($u_name);
    
    defined $desc && $self->description($desc);
    
    return $self;

}

sub get {

    my ($class, @args) = @_;
    my ($u_name) = Bio::Root::Root->_rearrange([qw(UNIVERSAL_NAME)], @args);
    
    if ($u_name && defined $TFS->{$u_name}) {
        return $TFS->{$u_name};
    }
    
    return $class->new(@args);

}

sub universal_name {

    my ($self, $value) = @_;
    if (defined $value) {
        delete $TFS->{$self->{'_uname'}} if $self->{'_uname'};
        $self->{'_uname'} = $value;
        $TFS->{$value} = $self;
    }
    return $self->{'_uname'};

}

sub description {

    my $self = shift;
    if (@_) { $self->{desc} = shift }
    return $self->{desc} || '';
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
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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/

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