/usr/share/perl5/Bio/Tools/RepeatMasker.pm is in libbio-perl-perl 1.6.924-3.
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# BioPerl module for Bio::Tools::RepeatMasker
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon <shawnh@fugu-sg.org>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::RepeatMasker - a parser for RepeatMasker output
=head1 SYNOPSIS
use Bio::Tools::RepeatMasker;
my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out');
while( my $result = $parser->next_result ) {
# get some value
}
=head1 DESCRIPTION
A parser for RepeatMasker output
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
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://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::RepeatMasker;
use strict;
use Bio::SeqFeature::FeaturePair;
use base qw(Bio::Root::Root Bio::Root::IO);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::RepeatMasker->new();
Function: Builds a new Bio::Tools::RepeatMasker object
Returns : Bio::Tools::RepeatMasker
Args : -fh/-file => $val, for initing input, see Bio::Root::IO
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 next_result
Title : next_result
Usage : my $r = $rpt_masker->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::FeaturePair
Feature1 is the Query coordinates and Feature2 is the Hit
Args : none
=cut
sub next_result {
my ($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;
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