diff variant_effect_predictor/Bio/Ontology/GOterm.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Ontology/GOterm.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,362 @@
+# $Id: GOterm.pm,v 1.12.2.4 2003/07/03 00:41:40 lapp Exp $
+#
+# BioPerl module for Bio::Ontology::GOterm
+#
+# Cared for by Christian M. Zmasek <[e-mail]> or <[e-mail]>
+#
+# (c) Christian M. Zmasek, [e-mail], 2002.
+# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
+#
+# You may distribute this module under the same terms as perl itself.
+# Refer to the Perl Artistic License (see the license accompanying this
+# software package, or see http://www.perl.com/language/misc/Artistic.html)
+# for the terms under which you may use, modify, and redistribute this module.
+#
+# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
+# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+
+=head1 NAME
+
+GOterm - representation of GO terms 
+
+=head1 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.
+
+=head1 DESCRIPTION
+
+This is "dumb" class for GO terms (it provides no functionality related to graphs).
+Implements Bio::Ontology::TermI.
+
+=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 one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]             - General discussion
+  http://bio.perl.org/MailList.html - About the mailing lists
+
+=head2 Reporting Bugs
+
+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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+Christian M. Zmasek
+
+Email: [e-mail]  or  [e-mail]
+
+WWW:   http://www.genetics.wustl.edu/eddy/people/zmasek/
+
+Address: 
+
+  Genomics Institute of the Novartis Research Foundation
+  10675 John Jay Hopkins Drive
+  San Diego, CA 92121
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods.
+
+=cut
+
+
+# Let the code begin...
+
+package Bio::Ontology::GOterm;
+use vars qw( @ISA );
+use strict;
+use Bio::Ontology::Term;
+
+use constant GOID_DEFAULT => "GO:0000000";
+use constant TRUE         => 1;
+use constant FALSE        => 0;
+
+@ISA = qw( Bio::Ontology::Term );
+
+
+
+
+=head2 new
+
+ 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]
+
+=cut
+
+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;
+    
+} # new
+
+
+=head2 init
+
+ Title   : init()
+ Usage   : $term->init();   
+ Function: Initializes this GOterm to all "" and empty lists.
+ Returns : 
+ Args    :
+
+=cut
+
+sub init {
+
+    my $self = shift;
+
+    # first call the inherited version to properly chain up the hierarchy
+    $self->SUPER::init(@_);
+
+    # then only initialize what we implement ourselves here
+    #$self->GO_id( GOID_DEFAULT );
+  
+} # init
+
+
+
+
+=head2 GO_id
+
+ 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).
+
+=cut
+
+sub GO_id {
+    my $self = shift;
+    my $value;
+
+    if ( @_ ) {
+        $value = $self->_check_go_id( shift );
+	unshift(@_, $value);
+    }
+
+    return $self->identifier( @_ );
+
+} # GO_id
+
+
+=head2 get_secondary_GO_ids
+
+ 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    :
+
+=cut
+
+sub get_secondary_GO_ids {
+    return shift->get_secondary_ids(@_);
+} # get_secondary_GO_ids
+
+
+=head2 add_secondary_GO_id
+
+ 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).
+
+=cut
+
+sub add_secondary_GO_id {
+    return shift->add_secondary_id(@_);
+} # add_secondary_GO_id
+
+
+=head2 remove_secondary_GO_ids
+
+ 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    :
+
+=cut
+
+sub remove_secondary_GO_ids {
+    return shift->remove_secondary_ids(@_);
+} # remove_secondary_GO_ids
+
+
+
+
+=head2 to_string
+
+ Title   : to_string()
+ Usage   : print $term->to_string();
+ Function: to_string method for GO terms.
+ Returns : A string representation of this GOterm.
+ Args    :
+
+=cut
+
+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;
+    
+} # to_string
+
+
+
+
+# Title   : _check_go_id
+# Function: Checks whether the argument is [GO:nnnnnnn].
+#           If "GO:" is not present, it adds it.
+# Returns : The canonical GO id.
+# Args    : The value to be checked.
+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;
+} # _check_go_id
+
+
+
+# Title   : _array_to_string         
+# Function:
+# Returns : 
+# Args    : 
+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;
+    
+} # _array_to_string
+
+#################################################################
+# aliases or forwards to maintain backward compatibility
+#################################################################
+
+*each_secondary_GO_id = \&get_secondary_GO_ids;
+*add_secondary_GO_ids = \&add_secondary_GO_id;
+
+1;