constitutive exon analysis added to the pipeline

modules/Bio/EnsEMBL/Pipeline/Production/ConstitutiveExons.pm

+package Bio::EnsEMBL::Pipeline::Production::ConstitutiveExons;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Pipeline::Base/;
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use Bio::EnsEMBL::Utils::ConversionSupport;
+use Bio::EnsEMBL::DensityType;
+use Bio::EnsEMBL::DensityFeature;
+
+
+## Default run method
+## For a given species, generates the required density features in the core database
+sub run {
+  my ($self) = @_;
+  my $species  = $self->param('species');
+  my $dba      = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');
+  my $helper   = $dba->dbc()->sql_helper();
+  my $ga       = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'Gene');
+
+  my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice')->fetch_all('toplevel');
+
+  my @gene_dbIDs = sort { $a <=> $b } @{ $ga->list_dbIDs() };
+  my $bin = scalar(@gene_dbIDs)/1000;
+  my @gene_list;
+  for (my $i = 0; $i < $bin; $i++) {
+    push(@gene_list, @{ $ga->fetch_all_by_dbID_list([splice(@gene_dbIDs, 0, 1000)]) });
+  }
+
+  while ( my $gene = shift(@gene_list) ){
+    my @transcripts = @{ $gene->get_all_Transcripts() };
+    my $transcript_count = scalar(@transcripts);
+    my %exon_count;
+    my %exon_object;
+
+    foreach my $transcript (@transcripts) {
+      my @exons = @{ $transcript->get_all_Exons() };
+      while (my $exon = shift(@exons) ) {
+        my $key = $exon->dbID();
+        ++$exon_count{$key};
+        $exon_object{$key} = $exon;
+      }
+    }
+
+    foreach my $exon_key ( keys(%exon_count) ) {
+      my $exon = $exon_object{$exon_key};
+      my $is_constitutive = $exon->is_constitutive();
+      if ( $exon_count{$exon_key} == $transcript_count ) {
+        if ( !$exon->is_constitutive() ) {
+          $is_constitutive = 1;
+        }
+      } else {
+        if ( $exon_object{$exon_key}->is_constitutive() ) {
+          $is_constitutive = 0;
+        }
+      }
+      $ga->dbc()->sql_helper()->execute_update(
+        -SQL => 'update exon set is_constitutive = ? where exon_id =?',
+        -PARAMS => [$is_constitutive, $exon->dbID()]
+      );
+    }
+  }
+}
+
+
+
+1;