added a quick_check to enable quick heuristic check to allow rapid processing...

added a quick_check to enable quick heuristic check to allow rapid processing of genomes where there are no alternative transcripts

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

@@ -10,61 +10,77 @@ use Bio::EnsEMBL::Utils::ConversionSupport;
 use Bio::EnsEMBL::DensityType;
 use Bio::EnsEMBL::DensityFeature;
 
-
 # default run method
 # For a given databases of dbtype, flags exons which are constitutive
 sub run {
-  my ($self) = @_;
-  my $species  = $self->param('species');
-  my $dbtype   = $self->param('dbtype');
-  my $dba      = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $dbtype);
-  my $helper   = $dba->dbc()->sql_helper();
-  my $ga       = Bio::EnsEMBL::Registry->get_adaptor($species, $dbtype, 'Gene');
+  my ($self)      = @_;
+  my $species     = $self->param('species');
+  my $dbtype      = $self->param('dbtype');
+  my $quick_check = $self->param('quick_check');
+  my $ga = Bio::EnsEMBL::Registry->get_adaptor($species, $dbtype, 'Gene');
+
+  if ($quick_check) {
+	print "Carrying out quick check...\n";
+	my $splice_count = $ga->dbc()->sql_helper()->execute_single_result(
+	  -SQL => q/select count(*) from 
+  (select distinct(g.gene_id) as id from gene g 
+  join transcript t using (gene_id) 
+  join seq_region s on (s.seq_region_id=t.seq_region_id) 
+  join coord_system using (coord_system_id) 
+  where species_id=? group by g.gene_id having count(*)>1) x;/,
+	  -PARAMS => [$ga->species_id()]);
 
-  my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, $dbtype, 'slice')->fetch_all('toplevel');
+	if ($splice_count == 0) {
+	  print "No splices detected - setting all exons as constitutive...\n";
+	  $ga->dbc()->sql_helper()->execute_update(
+		-SQL => q/update exon e, seq_region s, coord_system c 
+	set e.is_constitutive=1 
+	where e.seq_region_id=s.seq_region_id 
+	and c.coord_system_id=s.coord_system_id and c.species_id=?/,
+		-PARAMS => [$ga->species_id()]);
+	  return;
+	}
+  }
 
-  my @gene_dbIDs = sort { $a <=> $b } @{ $ga->list_dbIDs() };
+  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, @{ $ga->fetch_all_by_dbID_list([splice(@gene_dbIDs, 0, 1000)]) });
+	push(@gene_list, @{$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()]
-      );
-    }
-  }
-}
+  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()]);
+	}
+  } ## end while (my $gene = shift(@gene_list...))
+  return;
+} ## end sub run
 
 1;