NAME

GenOO::Gene - Gene object

SYNOPSIS

    # This object represents a gene (collection of transcripts)
    # It extends the L<GenOO::GenomicRegion> object
    
    # To initialize 
    my $gene = GenOO::Gene->new(
        name        => undef,    #required
        species     => undef,
        strand      => undef,    #can be inferred from transcripts
        chromosome  => undef,    #can be inferred from transcripts
        start       => undef,    #can be inferred from transcripts
        stop        => undef,    #can be inferred from transcripts
        copy_number => undef,    #defaults to 1
        sequence    => undef,
        description => undef,
        transcripts => reference to an array of L<GenOO::Transcript> objects
    );

DESCRIPTION

    GenOO::Gene describes a gene. A gene is defined as a genomic region (it has the strand, chromosome, start and stop
    attributes required by L<GenOO::GenomicRegion>) as well as collection of L<GenOO::Transcript> objects. The genomic
    location attributes can be inferred by the locations of the contained transcripts. The start position of the gene
    will be the smallest coordinate of all the contained transcripts etc.
    Whenever a transcript is added to a gene object the genomic coordinates of the gene are automatically updated.
    It is a good idea NOT to set the genomic location of the gene directly but to let it be inferred by the transcripts.

EXAMPLES # Create a new gene object my $gene = GenOO::Gene->new( name => '2310016C08Rik', description => 'hypoxia-inducible gene 2 protein isoform 2', transcripts => [ GenOO::Transcript->new( id => 'uc012eiw.1', strand => 1, chromosome => 'chr6', start => 29222487, stop => 29225448, coding_start => 29222571, coding_stop => 29224899, biotype => 'coding', splice_starts => [29222487,29224649], splice_stops => [29222607,29225448] ), GenOO::Transcript->new( id => 'uc009bdd.2', strand => 1, chromosome => 'chr6', start => 29222625, stop => 29225448, coding_start => 29224705, coding_stop => 29224899, biotype => 'coding', splice_starts => [29222625,29224649], splice_stops => [29222809,29225448] ) ], );

    # Get gene information
    $gene->strand;     # 1
    $gene->chromosome; # chr6
    $gene->start;      # 29222487
    $gene->stop;       # 29225448