Modware::Feature

GENE

   Modware::Feature::GENE - Modware representation of a gene

 # USE CASE: PRINT A LIST OF FEATURES ASSOCIATED WITH THIS GENE

   my $gene = new Modware::Gene( -gene_name => 'test_CURATED' );

   foreach $feature ( @{ $gene->features() } ) {
      print $feature->primary_id()."\n";
   }

  This object attempts to group together all information about a gene
  Most of this information is returned as references to arrays of other objects.  For example
  the features array is one such association.

  The features method returns all non-deleted features which are associated with this gene.

Methods description

 Title    : _database_object
 Usage    : my $ids = $self->_database_object($database_object);
 Function : gets/sets the Chado::Feature object
            used to read/write from the database
 Returns  : Chado::Feature object
 Args     : optional: reference to a Chado::Feature object

 Title    : _get_features
 Usage    : $gene->_get_features();
 Function : gets the features array for this gene (called from features)
 Returns  : nothing
 Args     : none

 Title    : _init
 Note     : sets attributes specific to gene
 Usage    : called internally by new
 Function :
 Returns  : nothing
 Args     : none

 Title    : _insert_feature
 Function : put gene_name into name field.  Uniquename
          : is a special identifier which is usually equal to the gene_name
          : unless the gene_name is a primary_id.  THen its not globally unique
          : so make it unique by prepending 'Gene:' to the front.
 Returns  : nothing
 Args     : none

 Title    : _update_feature
 Function : put gene_name into name field.  Uniquename
          : is a special identifier which is usually equal to the gene_name
          : unless the gene_name is a primary_id.  THen its not globally unique
          : so make it unique by prepending Gene: to the front.
 Returns  : nothing
 Args     : none

 Title    : deleted_features
 Note     : Read only, cannot set
 Usage    : To print the primary_id of all deleted features associated with this feature
          : print map { print $_->primary_id()."\n" } @{ $self->deleted_features() };
 Function : gets the deleted features array of the gene
 Returns  : string
 Args     : optional: features object

 Title    : end
 Usage    : $gene->end();
 Function : gets hightest coord from primary feature(s)
 Returns  : nothing
 Args     : none
 NOTE     : CANNOT SET -- COMPLETELY DERIVED

 Title    : features
 Note     : Fetches the features array associated with this gene
          : This is lazy evaluated so as to avoid an infinite loop
          : of creating a gene which gets its features which gets its gene
          : which gets its features .....
          : May make feature and genes singletons, then use circular refs and 'weaken'
 Usage    : To print the primary_id of all features associated with this feature
          : print map { print $_->primary_id()."\n" } @{ $self->features() };
 Function : gets/sets the features array of the gene
 Returns  : string
 Args     : optional: features object

 Title    : gene_name
 Usage    : print $gene->gene_name()
 Function : returns gene name
 Returns  : string
 Args     : string ( optional )
 Note     : will possibly be deprecated in favor of more generic 'name' method

 Title    : insert
 Usage    : $gene->insert();
 Function : writes data in object to the database;
 Returns  : nothing
 Args     : none

 Title    : name
 Usage    : $self->name( $some_name );
          : or 
          : print $self->name();
 Function : gets/sets name
 Returns  : name string
 Args     : name ( optional )

 Title    : name_description
 Note     : Brief description of gene name origin
 Usage    : $self->name_description( 'Strctural maintenance of Chromosome 1' );
          : or
          : print $self->name_description();
 Function : gets/sets the name_description attribute of the feature
 Returns  : string
 Args     : optional: name_description string

 Title    : reference_feature
 Usage    : $gene->reference_feature();
 Function : returns the reference featyre of the primary feature
 Returns  : contig or chromosome object
 Args     : none
 NOTE     : CANNOT SET -- COMPLETELY DERIVED

 Title    : start
 Usage    : $gene->start();
 Function : gets lowest start coord from primary feature(s)
 Note     : this method relies on the fact that the primary features array
          : is sorted by absolute start position
 Returns  : nothing
 Args     : none
 NOTE     : CANNOT SET -- COMPLETELY DERIVED

 Title    : strand
 Usage    : $gene->strand();
 Function : gets strand from primary feature(s)
 Returns  : nothing
 Args     : none
 NOTE     : CANNOT SET -- COMPLETELY DERIVED

 Title    : update
 Usage    : $gene->update();
 Function : writes data in object to the database;
          : CURRENTLY ONLY UPDATES THE LOCUS TABLE !!!!
 Returns  : nothing
 Args     : none

Methods code

   my ($self, $obj) = @_;
   if($obj) {
      $self->{_database_object} = $obj;
   }
   return $self->{_database_object};

   my ($self) = @_;

   my @feature_rows =  $self->_relationship_subjects( 'part_of' );

  #
  # grep is necessary because we return undef for features with no adapter yet
  #
   my @features = grep {$_} map { new Modware::Feature( -feature_id => $_->feature_id ) } @feature_rows;

   my @live_features = grep { !$_->is_deleted } @features;
   my @dead_features = grep {  $_->is_deleted } @features;


   $self->features(\@live_features);
   $self->deleted_features(\@dead_features);

   my ($self, @args) = @_;

   delete $self->{primary_id};

  #
  # if its coming from the database, set certain properties from the database
  #
   if ( $self->_database_object ) {
      $self->gene_name( $self->_database_object->name );
   }

   my ($self, @args) = @_;

   my ($cvterm) = Chado::Cvterm->get_single_row(
      cv_id => Modware::Constant->Sequence_ontology_id(),
      name  => $self->type
   );

   $self->throw( "cannot insert a feature with out a valid SO type.") if !$cvterm;

   my $type_id    = $cvterm->cvterm_id;

   my $feautre_row = Chado::Feature->create({
     organism_id => Modware::Constant->Organism_id(),
     dbxref_id   => undef,
     name        => $self->name(),
     uniquename  => $self->name(),
     type_id     => $type_id,
     is_obsolete => $self->is_deleted() || 0
   });

   $self->feature_id( $feautre_row->feature_id );

   my ($self, @args) = @_;

   $self->_database_object( $self->is_deleted() );
   $self->_database_object( $self->gene_name );
   $self->_database_object( $self->gene_name() );

   $self->_database_object();

   my ($self, $obj) = @_;

   exists $self->{deleted_features} || scalar @_ > 1 || $self->_get_features();

   if(scalar @_ > 1) {
      $self->{deleted_features} = $obj;
   }
   return $self->{deleted_features};

   my ($self) = @_;

   if ( @{$self->features()} ) {
      my @features = @{ $self->features() };

      if ( $features[0]->start() ) {
         @features    = sort{ $b->end() <=> $a->end() } @features;
         return $features[0]->end();
      }
      return undef;
   }
   return undef;

   my ($self, $obj) = @_;

  #
  # fetches features from database (_get_features) if features is not yet defined
  #  and the user is not attempting to set the features
  #
   exists $self->{features} || scalar @_ > 1 || $self->_get_features();

   if(scalar @_ > 1) {
      $self->{features} = $obj;
   }
   return $self->{features};

   my ($self, $obj) = @_;
   #warn "gene_name method in Modware::Feature::GENE is deprecated, use name instead\n";

   return scalar @_ > 1 ? $self->name( $obj ) : $self->name();

   my ($self) = @_;

   $self->SUPER::insert();

   my ($self) = @_;

   $self->feature_id ? $self->update() : $self->insert();

   my ($self, $obj) = @_;
   if($obj) {
      $self->{name} = $obj;
   }
   return $self->{name};

   my ($self, $obj) = @_;
  #
  # fetches name_description from database (_get_name_description) if name_description is not yet defined
  #  and the user is not attempting to set the name_description options
  #
   exists $self->{name_description} || scalar @_ > 1 || $self->name_description( $self->_get_featureprop( 'name description' )   );

   if(scalar @_ > 1) {
      $self->{name_description} = $obj;
   }
   return $self->{name_description};

   my ($type, @args) = @_;

   my $self = {};
   bless $self,$type;

   my @arglist = qw(
     GENE_NAME DESCRIPTION SOURCE NAME_DESCRIPTION NAME
   );

   my (
      $gene_name, $description, $source, $name_description, $name
    )   = $self->_rearrange( [@arglist], @args );


  #
  # Default source to dictyBase curator
  #
   $source ||= 'Curator';

   if ( $gene_name ) {
      warn "-gene_name argument to gene constructor is deprecated, please use -name instead\n";
      $name = $gene_name;
   }
   $self->source          ( $source           ) if defined $source;
   $self->type            ( 'gene'            );
   $self->description     ( $description      ) if defined $description;
   $self->gene_name       ( $name             ) if defined $name;
   $self->name_desciption ( $name_description ) if defined $name_description;
   $self->qualifiers( [] );
   $self->_init();
   return $self;

   my ($self) = @_;

   if ( @{$self->features()} ) {
      my @features = @{ $self->features() };

      if ( $features[0]->reference_feature() ) {
         return $features[0]->reference_feature();
      }
      return undef;
   }
   return undef;

   my ($self) = @_;

   if ( @{$self->features()} ) {
      my @features = @{ $self->features() };

      if ( $features[0]->start() ) {
         @features    = sort{ $a->start() <=> $b->start() } @features;
         return $features[0]->start();
      }
      return undef;
   }
   return undef;

   my ($self) = @_;

   if ( @{$self->features()} ) {
      my @features = @{ $self->features() };

      if ( $features[0]->start() ) {
         return $features[0]->strand();
      }
      return undef;
   }
   return undef;

   my ($self) = @_;

   $self->SUPER::update();

   if ( exists $self->{features} ) {
      $self->_update_featureloc();
   }
   $self->_insert_or_update_featureprop( 'name description', $self->name_description() ) if exists $self->{name_description};

General documentation

   Eric Just e-just@northwestern.edu

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

Copyright © 2006, Northwestern University All rights reserved.