GO::Utils::General - provides some general utilities for clients of other GO classes

GO-TermFinder documentation Contained in the GO-TermFinder distribution.

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GO::Utils::General - provides some general utilities for clients of other GO classes

SYNOPSIS

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  use GO::Utils::General qw (CategorizeGenes);

  CategorizeGenes(annotation  => $annotation,
		  genes       => \@genes,
		  ambiguous   => \@ambiguous,
		  unambiguous => \@unambiguous,
		  notFound    => \@notFound);

CategorizeGenes

CategorizeGenes categorizes a set of genes into three categories, whether they are ambiguous, whether they are not found, or whether they are unambiguous. The category to which they belong is determined by using an annotation provider.

Usage:

  use GO::Utils::General qw (CategorizeGenes);

  CategorizeGenes(annotation  => $annotation,
		  genes       => \@genes,
		  ambiguous   => \@ambiguous,
		  unambiguous => \@unambiguous,
		  notFound    => \@notFound);

All the above named arguments are required:

annotation : A GO::AnnotationProvider concrete subclass instance genes : A reference to an array of gene names

The remaining arguments should be empty arrays, passed in by reference, that will be populated by this function.

GO-TermFinder documentation Contained in the GO-TermFinder distribution. 
package GO::Utils::General;


use strict;
use warnings;
use diagnostics;

use vars qw (@ISA @EXPORT_OK $VERSION);
use Exporter;
@ISA = ('Exporter');
@EXPORT_OK = qw (CategorizeGenes);

$VERSION = 0.11;

my @kRequiredArgs = qw (annotation genes ambiguous unambiguous notFound);

##########################################################################
sub CategorizeGenes{
##########################################################################


##########################################################################

    my (%args) = @_;

    foreach my $arg (@kRequiredArgs){

	if (!exists $args{$arg} || !defined $args{$arg}){

	    die "You must provide a $arg argument to CategorizeGenes";

	}

    }

    my $annotation     = $args{'annotation'};
    my $genesRef       = $args{'genes'};
    my $ambiguousRef   = $args{'ambiguous'};
    my $unambiguousRef = $args{'unambiguous'};
    my $notFoundRef    = $args{'notFound'};

    foreach my $gene (@{$genesRef}){

	if ($annotation->nameIsAmbiguous($gene)){

	    push(@{$ambiguousRef}, $gene);
	    next;

	}

	my $name = $annotation->standardNameByName($gene);

	if (defined $name){

	    push(@{$unambiguousRef}, $gene);

	}else{

	    push(@{$notFoundRef}, $gene);

	}

    }

}

1; # keep Perl happy