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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Tmhmm.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,213 @@
+# $Id: Tmhmm.pm,v 1.6 2002/10/22 07:45:22 lapp Exp $
+#
+# BioPerl module for Bio::Tools::Tmhmm
+#
+# 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
+
+=head1 NAME
+
+Bio::Tools::Tmhmm - parse TmHMM output (transmembrane HMM)
+
+=head1 SYNOPSIS
+
+  use Bio::Tools::Tmhmm;
+  my $parser = new Bio::Tools::Tmhmm(-fh =>$filehandle );
+  while( my $tmhmm_feat = $parser->next_result ) {
+     #do something
+     #eg
+     push @tmhmm_feat, $tmhmm_feat;
+  }
+
+=head1 DESCRIPTION
+
+Parser for Tmhmm 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 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+package Bio::Tools::Tmhmm;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Tools::AnalysisResult;
+use Bio::Root::Root;
+use Bio::SeqFeature::FeaturePair;
+use Bio::Root::IO;
+use Bio::SeqFeature::Generic;
+@ISA = qw(Bio::Root::Root Bio::Root::IO Bio::Tools::AnalysisResult);
+
+
+
+=head2 new
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Tmhmm();
+ Function: Builds a new Bio::Tools::Tmhmm object
+ Returns : Bio::Tools::Tmhmm
+ 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 = $Tmhmm->next_result
+ Function: Get the next result set from parser data
+ Returns : Bio::SeqFeature::Generic
+ Args    : none
+
+
+=cut
+
+sub next_result {
+        my ($self) = @_;
+
+        my $line;
+
+        # parse
+        my $id;
+        while ($_=$self->_readline()) { 
+           $line = $_;
+           chomp $line;
+
+
+           next if /^$/;
+           if ($line=~/^#\s+(\S+)/) { 
+                   #if the line starts with a '#' for example in # 13 Length: 522 
+                   #assign 13 as the id.
+
+                    $id = $1;
+                    my ($junk, $values) = split /:/;
+                   $self->_seqname($id);
+                    next;
+           }
+
+           elsif ($line=~/^(\S+)\s+(\S+)\s+(\w+)\s+(\d+)\s+(\d+)/) {
+
+                    # Example :-  13      TMHMM2.0        inside       1   120
+                    # assign $orien(inside) $start(1) and $end(120)
+
+
+                    my $orien = $3;
+                    my $start = $4;
+                    my $end = $5;
+                    $orien = uc ($orien);
+
+                    if ($orien eq "TMHELIX") {
+                         my (%feature);
+                         $feature{name} = $self->_seqname;
+                         $feature{start} = $start;
+                         $feature{end} = $end;
+                         $feature{source} ='tmhmm';
+                         $feature{primary}= 'transmembrane';
+                         $feature{program} ='tmhmm';
+                         $feature{logic_name} = 'TMHelix';
+                         my $new_feat= $self->create_feature(\%feature);
+                         return $new_feat;
+                    }
+                    next;
+           }
+           next;
+        }
+}
+
+=head2 create_feature
+
+ Title   : create_feature
+ Usage   : obj->create_feature(\%feature)
+ Function: Internal(not to be used directly)
+ Returns : A Bio::SeqFeature::Generic object
+ Args    :
+
+=cut
+
+sub create_feature {
+       my ($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 $feature;
+   }
+
+=head2 _seqname
+
+ Title   :   _seqname
+ Usage   :   obj->_seqname($seqname)
+ Function:   Internal(not to be used directly)
+ Returns :
+ Args    :   seqname
+
+=cut
+
+sub _seqname{
+    my ($self,$seqname)=@_;
+
+    if (defined $seqname){
+
+        $self->{'seqname'}=$seqname;
+    }
+
+    return $self->{'seqname'};
+
+}
+
+
+1;
+
+