diff variant_effect_predictor/Bio/Tools/RepeatMasker.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/RepeatMasker.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,157 @@
+# BioPerl module for Bio::Tools::RepeatMasker
+#
+# Cared for by Shawn Hoon <[e-mail]>
+#
+# 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.
+
+  [e-mail]              - 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:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Shawn Hoon 
+
+Email [e-mail] 
+
+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;