GenOO::GenomicRegion - Object that corresponds to a region on a genome
# 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, );
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
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>
To install GenOO, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GenOO
CPAN shell
perl -MCPAN -e shell install GenOO
For more information on module installation, please visit the detailed CPAN module installation guide.