All analysis logic_names should be lower case.

misc-scripts/density_feature/gene_density_calc.pl

@@ -114,10 +114,10 @@ foreach my $dbname (@dbnames) {
 
 
   print "Deleting old knownGeneDensity and geneDensity features\n";
-  $sth = $db->dbc->prepare("DELETE df, dt, a, ad FROM density_feature df, density_type dt, analysis a, analysis_description ad WHERE ad.analysis_id = a.analysis_id AND a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name IN ('knownGeneDensity', 'geneDensity')");
+  $sth = $db->dbc->prepare("DELETE df, dt, a, ad FROM density_feature df, density_type dt, analysis a, analysis_description ad WHERE ad.analysis_id = a.analysis_id AND a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name IN ('knowngenedensity', 'genedensity')");
   $sth->execute();
   
-  $sth = $db->dbc->prepare("DELETE df, dt, a FROM density_feature df, density_type dt, analysis a WHERE a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name IN ('knownGeneDensity', 'geneDensity')");
+  $sth = $db->dbc->prepare("DELETE df, dt, a FROM density_feature df, density_type dt, analysis a WHERE a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name IN ('knowngenedensity', 'genedensity')");
   $sth->execute();
   
 
@@ -178,9 +178,9 @@ foreach my $dbname (@dbnames) {
   #
 
     if($known) {
-      $analysis = $aa->fetch_by_logic_name('knownGeneDensity');
+      $analysis = $aa->fetch_by_logic_name('knowngenedensity');
     } else {
-      $analysis = $aa->fetch_by_logic_name('geneDensity');
+      $analysis = $aa->fetch_by_logic_name('genedensity');
     }
 
   #

misc-scripts/density_feature/glovar_snp_density.pl

@@ -153,7 +153,7 @@ my $analysis = Bio::EnsEMBL::Analysis->new(
         -database    => "vega",
         -gff_source  => "glovar_snp_density.pl",
         -gff_feature => "density",
-        -logic_name  => "snpDensity",
+        -logic_name  => "snpdensity",
 );
 $aa->store( $analysis ) unless ($support->param('dry_run'));
 

misc-scripts/density_feature/logicname_density_calc.pl

@@ -107,7 +107,7 @@ $analysis = new Bio::EnsEMBL::Analysis
      -database    => "ensembl",
      -gff_source  => "logic_name_calc.pl",
      -gff_feature => "density",
-     -logic_name  => "Density_$logic_name");
+     -logic_name  => "density_$logic_name");
 $analysis_adaptor->store( $analysis );
 
 #
@@ -115,7 +115,7 @@ $analysis_adaptor->store( $analysis );
 #
 # Create new density type.
 #
-$analysis = $analysis_adaptor->fetch_by_logic_name("Density_$logic_name");
+$analysis = $analysis_adaptor->fetch_by_logic_name("density_$logic_name");
 my $dt = Bio::EnsEMBL::DensityType->new(-analysis   => $analysis,
                                         -block_size => $block_size,
                                         -value_type => 'sum');