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Summary

Bio::Tools::RepeatMasker - a parser for RepeatMasker output

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

    use Bio::Tools::RepeatMasker;
    my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out');
    while( my $result = $parser->next_result ) {
      # get some value
    }

Description

A parser for RepeatMasker output

Methods

Methods description

 Title   : new
 Usage   : my $obj = Bio::Tools::RepeatMasker->new();
 Function: Builds a new Bio::Tools::RepeatMasker object
 Returns : Bio::Tools::RepeatMasker
 Args    : -fh/-file => $val, for initing input, see Bio::Root::IO

 Title   : next_result
 Usage   : my $r = $rpt_masker->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::FeaturePair
           Feature1 is the Query coordinates and Feature2 is the Hit
 Args    : none

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);

  return $self;

}

sub next_result {

    my ($self) = @_;
    local $_;
    while (defined($_=$self->_readline()) ) {
	if (/no repetitive sequences detected/) {
	    $self->warn( "RepeatMasker didn't find any repetitive sequences\n");
	    return ;
	}
	#ignore introductory lines
	if (/\d+/) {
	    my @element = split;
	    # ignore features with negatives
	    next if ($element[11-13] =~ /-/);
	    my (%feat1, %feat2);
	    my @line = split;
	    my ($score, $query_name, $query_start, $query_end, $strand,
		$repeat_name, $repeat_class ) = @line[0, 4, 5, 6, 8, 9, 10];

	    my ($hit_start,$hit_end);

	    if ($strand eq '+') {
		($hit_start, $hit_end) = @line[11, 12];
		$strand = 1;
	    } elsif ($strand eq 'C') {
		($hit_end, $hit_start) = @line[12, 13];
		$strand = -1;
	    }
	    my $rf = Bio::SeqFeature::Generic->new
		(-seq_id      => $query_name,
		 -score       => $score,
		 -start       => $query_start,
		 -end         => $query_end,
		 -strand      => $strand,
		 -source_tag  => 'RepeatMasker',
		 -primary_tag => $repeat_class,
		 -tag => { 'Target'=> [$repeat_name, $hit_start, $hit_end]},
		);

	    my $rf2 = Bio::SeqFeature::Generic->new
		(-seq_id         => $repeat_name,
		 -score          => $score,
		 -start          => $hit_start,
		 -end            => $hit_end,
		 -strand         => $strand,
		 -source_tag     => "RepeatMasker",
		 -primary_tag    => $repeat_class,
		 -tag => { 'Target'=> [$query_name,$query_start,$query_end] },
		);

	    my $fp = Bio::SeqFeature::FeaturePair->new(-feature1 => $rf,
						       -feature2 => $rf2);
	    return $fp;
	}
    }
}

1;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
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Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  https://redmine.open-bio.org/projects/bioperl/

Email shawnh@fugu-sg.org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _