diff variant_effect_predictor/Bio/Tools/Seg.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Seg.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,186 @@
+# $Id: Seg.pm,v 1.6 2002/10/22 07:45:22 lapp Exp $
+#
+# BioPerl module for Bio::Tools::Seg
+#
+# Copyright Balamurugan Kumarasamy
+#
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation - main docs before the code
+#
+# Copyright 
+#
+# You may distribute this module under the same terms as perl itself
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Seg - parse Seg output (filter low complexity protein sequence)
+
+=head1 SYNOPSIS
+
+  use Bio::Tools::Seg;
+  my $parser = new Bio::Tools::Seg(-fh =>$filehandle );
+  while( my $seg_feat = $parser->next_result ) {
+        #do something
+        #eg
+        push @seg_feat, $seg_feat;
+  }
+
+=head1 DESCRIPTION
+
+Parser for Seg 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 - Bala
+
+Email [e-mail]
+
+
+=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
+
+package Bio::Tools::Seg;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::SeqFeature::FeaturePair;
+use Bio::Root::IO;
+use Bio::SeqFeature::Generic;
+@ISA = qw(Bio::Root::Root Bio::Root::IO);
+
+
+
+
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Seg();
+ Function: Builds a new Bio::Tools::Seg object
+ Returns : Bio::Tools::Seg
+ 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 $feat = $seg->next_result
+ Function: Get the next result set from parser data
+ Returns : Bio::SeqFeature::Generic
+ Args    : none
+
+
+=cut
+
+sub next_result {
+        my ($self) = @_;
+
+        my $line;
+        # parse
+        my $id;
+        while ($_=$self->_readline()) {
+         $line = $_;
+         chomp $line;
+
+          next if /^$/;
+           if ($line=~/^\>/) { #if it is a line starting with a ">"
+               $line=~/^\>\s*(\S+)\s*\((\d+)\-(\d+)\)\s*complexity=(\S+)/;
+               my $id = $1;
+               my $start = $2;
+               my $end = $3;
+               my $score = $4;
+
+               #for example in this line test_prot(214-226) complexity=2.26 (12/2.20/2.50)
+               #$1 is test_prot  $2 is 214 $3 is 226 and $4 is 2.26
+
+               my (%feature);
+               $feature{name} = $id;
+               $feature{score} = $score;
+               $feature{start} = $start;
+               $feature{end} = $end;
+               $feature{source} = "Seg";
+               $feature{primary} = 'low_complexity';
+               $feature{program} = "Seg";
+               $feature{logic_name} = 'low_complexity';
+               my $new_feat =  $self->create_feature (\%feature);
+               return $new_feat;
+            }
+          next;
+        }
+
+}
+
+
+=head2 create_feature 
+
+ Title   : create_feature
+ Usage   : obj->create_feature(\%feature)
+ Function: Internal(not to be used directly)
+ Returns : 
+ Args    :
+
+
+=cut
+
+sub create_feature {
+       my ($self, $feat) = @_;
+
+
+       # create feature object
+       my $feature = Bio::SeqFeature::Generic->new(-seq_id => $feat->{name},
+                                                   -start  => $feat->{start},
+                                                   -end    => $feat->{end},
+                                                   -score  => $feat->{score},
+                                                   -source => $feat->{source},
+                                                   -primary => $feat->{primary},
+                                                   -logic_name  => $feat->{logic_name}, 
+                                               );
+
+          return $feature;
+
+}
+
+1;
+
+