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>