Raw content of Bio::Tools::RepeatMasker # BioPerl module for Bio::Tools::RepeatMasker # # 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 - DESCRIPTION of Object =head1 SYNOPSIS use Bio::Tools::RepeatMasker; my $parser = new Bio::Tools::RepeatMasker(-file => 'seq.fa.out'); while( my $result = $parser->next_result ) { } =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/MailList.shtml - About the mailing lists =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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Shawn Hoon Email shawnh@fugu-sg.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =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 vars qw(@ISA); use strict; use Bio::Root::Root; use Bio::SeqFeature::FeaturePair; use Bio::Root::IO; @ISA = qw(Bio::Root::Root Bio::Root::IO ); =head2 new Title : new Usage : my $obj = new Bio::Tools::RepeatMasker(); Function: Builds a new Bio::Tools::RepeatMasker object Returns : Bio::Tools::RepeatMasker Args : -fh/-file => $val, # for initing input, see Bio::Root::IO =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); $self->_initialize_io(@args); return $self; } =head2 next_result Title : next_result Usage : my $r = $rpt_masker->next_result Function: Get the next result set from parser data Returns : L<Bio::SeqFeature::FeaturePair> Args : none =cut sub next_result{ my ($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;