Bio::Ontology
GOterm
Toolbar
Summary
GOterm - representation of GO terms
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
$term = Bio::Ontology::GOterm->new
( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
$term->add_definition_references( @refs );
$term->add_secondary_GO_ids( @ids );
$term->add_aliases( @aliases );
foreach my $dr ( $term->each_definition_reference() ) {
print $dr, "\n";
}
# etc.
Description
This is "dumb" class for GO terms (it provides no functionality related to graphs).
Implements Bio::Ontology::TermI.
Methods
Methods description
Title : GO_id
Usage : $term->GO_id( "GO:0003947" );
or
print $term->GO_id();
Function: Set/get for the goid of this GO term.
This is essentially an alias to identifier(), with added
format checking.
Returns : The goid [GO:nnnnnnn].
Args : The goid [GO:nnnnnnn] or [nnnnnnn] (nnnnnnn is a
zero-padded integer of seven digits) (optional). |
Title : add_secondary_GO_id
Usage : $term->add_secondary_GO_id( @ids );
or
$term->add_secondary_GO_id( $id );
Function: Pushes one or more secondary goids into
the list of secondary goids.
This is aliased to remove_secondary_ids().
Returns :
Args : One secondary goid [GO:nnnnnnn or nnnnnnn] or a list
of secondary goids [array of [GO:nnnnnnn or nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits). |
Title : get_secondary_GO_ids
Usage : @ids = $term->get_secondary_GO_ids();
Function: Returns a list of secondary goids of this Term.
This is aliased to remove_secondary_ids().
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args : |
Title : init()
Usage : $term->init();
Function: Initializes this GOterm to all "" and empty lists.
Returns :
Args : |
Title : new
Usage : $term = Bio::Ontology::GOterm->new( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::GOterm.
Returns : A new Bio::Ontology::GOterm object.
Args : -go_id => the goid of this GO term [GO:nnnnnnn]
or [nnnnnnn] (nnnnnnn is a zero-padded
integer of seven digits)
-name => the name of this GO term [scalar]
-definition => the definition of this GO term [scalar]
-ontology => the ontology for this term (a
Bio::Ontology::OntologyI compliant object)
-version => version information [scalar]
-is_obsolete => the obsoleteness of this GO term [0 or 1]
-comment => a comment [scalar] |
Title : remove_secondary_GO_ids()
Usage : $term->remove_secondary_GO_ids();
Function: Deletes (and returns) the secondary goids of this Term.
This is aliased to remove_secondary_ids().
Returns : A list of secondary goids [array of [GO:nnnnnnn]]
(nnnnnnn is a zero-padded integer of seven digits).
Args : |
Title : to_string()
Usage : print $term->to_string();
Function: to_string method for GO terms.
Returns : A string representation of this GOterm.
Args : |
Methods code
sub GO_id
{ my $self = shift;
my $value;
if ( @_ ) {
$value = $self->_check_go_id( shift );
unshift(@_, $value);
}
return $self->identifier( @_ );
}
} | sub _array_to_string
{ my( $self, @value ) = @_;
my $s = "";
for ( my $i = 0; $i < scalar( @value ); ++$i ) {
if ( ! ref( $value[ $i ] ) ) {
$s .= "#" . $i . "\n-- " . $value[ $i ] . "\n";
}
}
return $s;
}
*each_secondary_GO_id =\& get_secondary_GO_ids;
*add_secondary_GO_ids =\& add_secondary_GO_id;
1;} | sub _check_go_id
{ my ( $self, $value ) = @_;
unless ( $value =~ /^(GO:)?\d{7}$/ || $value eq GOID_DEFAULT ) {
$self->throw( "Found [" . $value
. "] where [GO:nnnnnnn] or [nnnnnnn] expected" );
}
unless ( $value =~ /^GO:/ ) {
$value = "GO:".$value;
}
return $value;
}
} | sub add_secondary_GO_id
{ return shift->add_secondary_id(@_);
}
} | sub get_secondary_GO_ids
{ return shift->get_secondary_ids(@_);
}
} | sub init
{
my $self = shift;
$self->SUPER::init(@_);
}
} | sub new
{
my( $class,@args ) = @_;
my $self = $class->SUPER::new( @args );
my ( $GO_id )
= $self->_rearrange( [ qw( GO_ID ) ], @args );
$GO_id && $self->GO_id( $GO_id );
return $self;
}
} | sub remove_secondary_GO_ids
{ return shift->remove_secondary_ids(@_);
}
} | sub to_string
{ my( $self ) = @_;
my $s = "";
$s .= "-- GO id:\n";
$s .= ($self->GO_id() || '')."\n";
$s .= "-- Name:\n";
$s .= ($self->name() || '') ."\n";
$s .= "-- Definition:\n";
$s .= ($self->definition() || '') ."\n";
$s .= "-- Category:\n";
if ( defined( $self->ontology() ) ) {
$s .= $self->ontology()->name()."\n";
}
else {
$s .= "\n";
}
$s .= "-- Version:\n";
$s .= ($self->version() || '') ."\n";
$s .= "-- Is obsolete:\n";
$s .= $self->is_obsolete()."\n";
$s .= "-- Comment:\n";
$s .= ($self->comment() || '') ."\n";
$s .= "-- Definition references:\n";
$s .= $self->_array_to_string( $self->get_dblinks() )."\n";
$s .= "-- Secondary GO ids:\n";
$s .= $self->_array_to_string( $self->get_secondary_GO_ids() )."\n";
$s .= "-- Aliases:\n";
$s .= $self->_array_to_string( $self->get_synonyms() );
return $s;
}
} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
The rest of the documentation details each of the object
methods.