Bio::Tools RepeatMasker
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Summary
Bio::Tools::RepeatMasker - a parser for RepeatMasker output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
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
newDescriptionCode
next_resultDescriptionCode
Methods description
newcode    nextTop
 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
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $r = $rpt_masker->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::FeaturePair
Feature1 is the Query coordinates and Feature2 is the Hit
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

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

  return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($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
FEEDBACKTop
Mailing ListsTop
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
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Shawn HoonTop
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _