Modware

Gene

   Modware::Gene - Convienent class to retrieve Modware::Feature::GENE objects.

 # USE CASE: PRINT A LIST OF DICTYBASEIDS OF RELATED FEATURES

   my $gene = new Modware::Gene( -feature_id => 4161 );

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

   This class simply provides a convenient interface to create a gene object by passing in the
   gene name as the parameter.  The name is often more useful than a feature_id.  If you pass
   in a feature_id as a parameter and this does not correspond to a gene feature you get an error.

   The object that is returned is a Modware::Feature::GENE object (see those docs for detailed
   information about what methods are available), and 'new' will throw an error
   if there is no gene with the name requested.

   See also Modware::Feature and  Modware::Feature::GENE

Methods description

 Title    : new
 Usage    : my $gene = new Modware::Gene( -name => 'eriC' );
 Function : creates a gene obejct based on either feature_id or name
 Returns  : reference to a Modware::Gene object
 Args     : named arguments
          : -feature_id => number
          : or
          : -name => string (case sensitive)
          :

Methods code

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

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

   my ( $gene_name, $feature_id, $name ) =  $self->_rearrange([qw(GENE_NAME feature_id NAME)], @args);

   $name = $gene_name if ($gene_name && !$name);

   $self->warn("-gene_name argument to Modware::Gene constructor is deprecated, use -name\n") if $gene_name;

   if ( $name ) {
      my @genes = Modware::Search::Gene->Search_by_name( $name );
      if ( scalar @genes > 1  ) { $self->throw("More than one gene names $name");   } 
      if ( scalar @genes == 0 ) { $self->throw("Could not find $name in database"); }
      return $genes[0];
   }
   $self = new Modware::Feature( -feature_id => $feature_id );

   $self->throw( "Not a valid gene name" ) if $self->type ne 'gene';


   return $self;

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.