Emmanouil "Manolis" Maragkakis
and 1 contributors

NAME

GenOO::GenomicRegion - Object that corresponds to a region on a genome

SYNOPSIS

    # This object represents a genomic region (location on the genome)
    # It extends the L<GenOO::Region> object
    
    # Instantiate 
    my $genomic_region = GenOO::GenomicRegion->new(
        name         => undef,
        species      => undef,
        strand       => undef,    #required
        chromosome   => undef,    #required
        start        => undef,    #required
        stop         => undef,    #required
        copy_number  => undef,    #defaults to 1
        sequence     => undef,
    );

DESCRIPTION

    A genomic region object is an area on a reference genome. It has a
    specific start and stop position and specific strand and chromosome.
    The main difference from the the L<GenOO::Region> role is that it has the
    "chromosome" attribute instead of the generic "rname". The copy number
    attribute is useful when counting aligned reads so that the number of
    reads in this specific location can be collapsed. It defaults to 1.
    See L<GenOO::Region> and for more available methods

EXAMPLES

    my $genomic_region = GenOO::GenomicRegion->new(
        name        => 'test_object_0',
        species     => 'human',
        strand      => '+',
        chromosome  => 'chr1',
        start       => 3,
        stop        => 10,
        copy_number => 7,
        sequence    => 'AGCTAGCU'
    );
    # Get the genomic location information
    $genomic_region->start;      # 3
    $genomic_region->stop;       # 10
    $genomic_region->strand;     # 1
    $genomic_region->chromosome; # chr1
    $genomic_region->rname;      # chr1 - this is always the same as chromosome
    
    # Get the head (5p) position on the reference sequence
    $genomic_region->head_position;  # 3 - this method comes from L<GenOO::Region>