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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Tools/Pseudowise.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,263 @@
+# BioPerl module for Bio::Tools::Pseudowise
+#
+# Copyright Fugu Team 
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Pseudowise - Results of one Pseudowise run
+
+=head1 SYNOPSIS
+
+  use Bio::Tools::Pseudowise;
+
+  my $parser = Bio::Tools::Pseudowise->new(-file=>"pw.out");
+  while(my $feat = $parser->next_result){
+      push @feat, $feat;
+  }
+
+=head1 DESCRIPTION
+
+Pseudowise is a pseudogene prediction program written by Ewan Birney as part of the 
+Wise Package. This module is the parser for the output of the program.
+
+http://www.sanger.ac.uk/software/wise2
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
+
+  [e-mail]          - General discussion
+  http://bio.perl.org/MailList.html             - About the mailing lists
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+the bugs and their resolution.  Bug reports can be submitted via email
+or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Fugu Team 
+
+Describe contact details here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods. 
+Internal methods are usually preceded with a _
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Tools::Pseudowise;
+use vars qw(@ISA);
+use strict;
+use Symbol;
+
+use Bio::Root::Root;
+use Bio::Tools::AnalysisResult;
+use Bio::SeqFeature::Generic;
+use Bio::SeqFeature::Gene::Exon;
+use Bio::Tools::Run::WrapperBase;
+use Bio::SeqFeature::FeaturePair;
+use Bio::SeqFeature::Gene::Transcript;
+use Bio::SeqFeature::Gene::GeneStructure;
+
+@ISA = qw(Bio::Tools::AnalysisResult);
+
+sub _initialize_state {
+    my ($self,@args) = @_;
+
+    # first call the inherited method!
+    $self->SUPER::_initialize_state(@args);
+
+    # our private state variables
+    $self->{'_preds_parsed'} = 0;
+    $self->{'_has_cds'} = 0;
+    # array of pre-parsed predictions
+    $self->{'_preds'} = [];
+    # seq stack
+    $self->{'_seqstack'} = [];
+}
+
+=head2 analysis_method
+
+ Usage     : $pseudowise->analysis_method();
+ Purpose   : Inherited method. Overridden to ensure that the name matches
+             /pseudowise/i.
+ Returns   : String
+ Argument  : n/a
+
+=cut
+
+#-------------
+sub analysis_method { 
+#-------------
+    my ($self, $method) = @_;  
+    if($method && ($method !~ /pseudowise/i)) {
+	$self->throw("method $method not supported in " . ref($self));
+    }
+    return $self->SUPER::analysis_method($method);
+}
+
+=head2 next_prediction
+
+ Title   : next_prediction
+ Usage   : while($gene = $pseudowise->next_prediction()) {
+                  # do something
+           }
+ Function: Returns the gene of the Pseudowise result
+           file. Call this method repeatedly until FALSE is returned.
+
+ Example :
+ Returns : a Bio::SeqFeature::Generic 
+ Args    :
+
+=cut
+
+sub next_prediction {
+    my ($self,$filehandle) = @_;
+    my $gene;
+
+    # if the prediction section hasn't been parsed yet, we do this now
+    $self->_parse_predictions($filehandle) unless $self->_predictions_parsed();
+
+    # get next gene structure
+    $gene = $self->_prediction();
+
+    return $gene;
+}
+
+=head2 _parse_predictions
+
+ Title   : _parse_predictions()
+ Usage   : $obj->_parse_predictions()
+ Function: Parses the prediction section. Automatically called by
+           next_prediction() if not yet done.
+ Example :
+ Returns : 
+
+=cut
+
+sub _parse_predictions {
+    my ($self, $filehandle) = @_;
+    my $gene;
+    my @genes;
+    #The big parsing loop - parses exons and predicted peptides
+    while (<$filehandle>)
+    {
+      if (/Gene/i)
+      {
+        $gene = new Bio::SeqFeature::Generic (
+                    -primary => 'pseudogene',
+                    -source => 'pseudowise');
+        push @genes, $gene;
+
+        while(<$filehandle>) {
+          my @gene_elements = split;
+          my $no = scalar(@gene_elements);
+          if ((/Gene/i) && $no == 3) {
+            my @element = split;
+            my $no = scalar(@element);
+            my $gene_start = $element[1];
+            my $gene_end = $element[2];
+            $gene->start($gene_start);
+            $gene->end($gene_end);
+          }
+          elsif (/Exon/i) {
+            my @element = split;
+            my $no = scalar(@element);
+            my $exon_start = $element[1];
+            my $exon_end = $element[2];
+            my $exon_phase = $element[4];
+            my $exon = new Bio::SeqFeature::Generic (
+                           -start => $exon_start,
+                           -end => $exon_end,
+                           -primary => 'exon',
+                           -source => 'pseudowise',
+                           -frame  => $exon_phase);
+            $gene->add_sub_SeqFeature($exon);
+          }
+          elsif ((/Gene/i) && $no != 3) {
+            $gene = new Bio::SeqFeature::Generic (
+                        -primary => 'pseudogene',
+                        -source => 'pseudowise');
+            push @genes, $gene;
+          }
+        }
+      }
+    }
+    $self->_add_prediction(\@genes);
+    $self->_predictions_parsed(1);
+        
+}
+
+=head1 _prediction
+
+ Title   : _prediction()
+ Usage   : $gene = $obj->_prediction()
+ Function: internal
+ Example :
+ Returns : 
+
+=cut
+
+sub _prediction {
+    my ($self) = @_;
+
+    return undef unless(exists($self->{'_preds'}) && @{$self->{'_preds'}});
+    return shift(@{$self->{'_preds'}});
+}
+
+=head2 _add_prediction
+
+ Title   : _add_prediction()
+ Usage   : $obj->_add_prediction($gene)
+ Function: internal
+ Example :
+ Returns : 
+
+=cut
+
+sub _add_prediction {
+    my ($self, $gene) = @_;
+
+    if(! exists($self->{'_preds'})) {
+	$self->{'_preds'} = [];
+    }
+    push(@{$self->{'_preds'}}, $gene);
+}
+
+=head2 _predictions_parsed
+
+ Title   : _predictions_parsed
+ Usage   : $obj->_predictions_parsed
+ Function: internal
+ Example :
+ Returns : TRUE or FALSE
+
+=cut
+
+sub _predictions_parsed {
+    my ($self, $val) = @_;
+
+    $self->{'_preds_parsed'} = $val if $val;
+    if(! exists($self->{'_preds_parsed'})) {
+	$self->{'_preds_parsed'} = 0;
+    }
+    return $self->{'_preds_parsed'};
+}
+
+1;