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package Bio::Pipeline::Utils::MaskSeq;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
@ISA = qw(Bio::Root::Root);
=head2 new
Title : new
Usage : my $MaskSeq = Bio::Pipeline::Utils::MaskSeq->new('-module'=>$module);
Function: constructor for MaskSeq object
Returns : a new MaskSeq object
Args : module, the list of MaskSeq modules found in Bio::Pipeline::Utils::MaskSeq::*
=cut
sub new {
my ($caller ,@args) = @_;
my $class = ref($caller) || $caller;
my ($self) = $class->SUPER::new(@args);
return $self;
}
sub run {
my ($self,$contig) = @_;
$self->throw("Not an Ensembl Contig") unless ($contig->isa("Bio::EnsEMBL::RawContig") || $contig->isa("Bio::EnsEMBL::Slice"));
return $contig->get_repeatmasked_seq;
}
1;