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Summary

Bio::Tools::RepeatMasker - DESCRIPTION of Object

Package variables

Included modules

Inherit

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

Synopsis

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

    }

Description

A parser for RepeatMasker output

Methods

Methods description

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

          my ($hit_start,$hit_end);
          if ($strand eq '+') {
            ($hit_start, $hit_end) = (split)[11, 12];
            $strand = 1;
          }
          elsif ($strand eq 'C') {
            ($hit_start, $hit_end) = (split)[12, 13];
            $strand = -1;
          }
          my $rf = Bio::SeqFeature::Generic->new;
          $rf->seq_id          ($query_name);
          $rf->score            ($score);
          $rf->start            ($query_start);
          $rf->end              ($query_end);
          $rf->strand           ($strand);
          $rf->source_tag       ("RepeatMasker");
          $rf->primary_tag      ($repeat_class);
          my $rf2 = Bio::SeqFeature::Generic->new;
          $rf2->seq_id         ($repeat_name);
          $rf2->score           ($score);
          $rf2->start           ($hit_start);
          $rf2->end             ($hit_end);
          $rf2->strand          ($strand);
          $rf2->source_tag      ("RepeatMasker");
          $rf->primary_tag      ($repeat_class);
          my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$rf,
                                                     -feature2=>$rf2);

          return $fp;                                                     
        }
    }
}

1;

}

General documentation

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