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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Signalp.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,251 @@
+# Parser module for SignalP Bio::Tools::Signalp
+#
+# Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
+# originally written by Marc Sohrmann ([e-mail])
+# Written in BioPipe by Balamurugan Kumarasamy <[e-mail]>
+# Cared for by the Fugu Informatics team ([e-mail])
+
+# You may distribute this module under the same terms as perl itself
+#
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::SignalP
+
+=head1 SYNOPSIS
+
+ use Bio::Tools::SignalP;
+ my $parser = new Bio::Tools::SignalP(-fh =>$filehandle );
+ while( my $sp_feat = $parser->next_result ) {
+       #do something
+       #eg
+       push @sp_feat, $sp_feat;
+ }
+
+=head1 DESCRIPTION
+
+ Parser for SignalP 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
+
+ Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
+ originally written by Marc Sohrmann ([e-mail])
+ Written in BioPipe by Balamurugan Kumarasamy <[e-mail]>
+ Cared for by the Fugu Informatics team ([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::Signalp;
+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::SignalP();
+ Function: Builds a new Bio::Tools::SignalP object
+ Returns : Bio::Tools::SignalP
+ 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 = $signalp->next_result
+ Function: Get the next result set from parser data
+ Returns : Bio::SeqFeature::Generic
+ Args    : none
+
+
+=cut
+
+sub next_result {
+        my ($self) = @_;
+        
+        my $line;
+        # parse
+        my $id;
+        my ( $fact1, $fact2, $end);
+        while ($_=$self->_readline()) {
+           $line = $_;
+           chomp $line;
+           
+           if ($line=~/^\>(\S+)/) {
+              $id = $1;
+              $self->seqname($id);
+              next;
+           }
+           elsif ($line=~/max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
+              $fact1 = $2;
+              $self->fact1($fact1);
+              next;
+           }
+           elsif ($line=~/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
+              $fact2 = $2;
+                 $fact1 = $self->fact1;
+                 $id = $self->seqname;
+              
+              if ($fact1 eq "YES" && $fact2 eq "YES") {
+                  
+                  my $line = $self->_readline();
+              
+                  if ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) {
+                      $end = $1;
+                  }
+                  else {
+                      $self->throw ("parsing problem in signalp");
+                  }
+                  my (%feature);
+                  $feature{name} = $id;
+                  $feature{start} = 1;
+                  $feature{end} = $end;
+                  $feature{source} = 'Signalp';
+                  $feature{primary}= 'signal_peptide';
+                  $feature{program} = 'Signalp';
+                  $feature{logic_name} = 'signal_peptide';
+                  
+                  my $new_feat = $self->create_feature (\%feature);
+                  return $new_feat;
+                  
+              }
+               next;
+               
+           }
+        
+           next;
+        
+        }
+        
+}
+
+=head2 create_feature
+
+ Title   : create_feature
+ Usage   : obj->create_feature(\%feature)
+ Function: Internal(not to be used directly)
+ Returns :
+ Args    :
+
+
+=cut
+
+sub create_feature {
+       my ($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}, 
+                                               );
+           
+
+          $feature->add_tag_value('evalue',0);
+          $feature->add_tag_value('percent_id','NULL');
+          $feature->add_tag_value("hid",$feat->{primary});
+          
+          return $feature; 
+
+}
+=head2 seqname
+
+ Title   : seqname
+ Usage   : obj->seqname($name)
+ Function: Internal(not to be used directly)
+ Returns :
+ Args    :
+
+
+=cut
+
+sub seqname{
+    my ($self,$seqname)=@_;
+
+    if (defined$seqname){
+
+        $self->{'seqname'}=$seqname;
+    }
+
+    return $self->{'seqname'};
+
+}
+
+=head2 fact1
+
+ Title   : fact1
+ Usage   : obj->fact1($fact1)
+ Function: Internal(not to be used directly)
+ Returns :
+ Args    :
+
+
+=cut
+
+sub fact1{
+    my ($self,$fact1)=@_;
+
+    if (defined$fact1){
+
+       $self->{'fact1'}=$fact1;
+    }
+
+    return $self->{'fact1'};
+
+}
+
+
+
+1;
+
+