Make sure the analysis_description is also deleted and properly

reinstated.  The analysis_id in the analysis table and in the
analysis_description table seems to become unsynced otherwise.

misc-scripts/density_feature/gene_density_calc.pl

@@ -99,6 +99,13 @@ print "Deleting old knownGeneDensity and geneDensity features\n";
 $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();
 
+$sth = $db->dbc()->prepare(
+  qq(
+  DELETE ad
+  FROM analysis_description ad
+  WHERE ad.display_label IN ('knownGeneDensity', 'geneDensity')) );
+$sth->execute();
+
 my $dfa = $db->get_DensityFeatureAdaptor();
 my $dta = $db->get_DensityTypeAdaptor();
 my $aa  = $db->get_AnalysisAdaptor();
@@ -112,14 +119,20 @@ my $slice_adaptor = $db->get_SliceAdaptor();
 my $top_slices = $slice_adaptor->fetch_all('toplevel');
 my @sorted_slices = sort { $b->seq_region_length() <=> $a->seq_region_length()} @$top_slices;
 
-	
-my $analysis = new Bio::EnsEMBL::Analysis (-program     => "gene_density_calc.pl",
-					   -database    => "ensembl",
-					   -gff_source  => "gene_density_calc.pl",
-					   -gff_feature => "density",
-					   -logic_name  => "knownGeneDensity");
-
-$aa->store( $analysis );
+my $analysis =
+  new Bio::EnsEMBL::Analysis(
+            -program     => "gene_density_calc.pl",
+            -database    => "ensembl",
+            -gff_source  => "gene_density_calc.pl",
+            -gff_feature => "density",
+            -logic_name  => "knownGeneDensity",
+            -description => 'Known gene density features in a database '
+              . 'as calculated by gene_density_calc.pl',
+            -display_label => 'knownGeneDensity',
+            -displayable   => 1 );
+
+$aa->store($analysis);
+$aa->update($analysis);
 
 $analysis = new Bio::EnsEMBL::Analysis (-program     => "gene_density_calc.pl",
 					-database    => "ensembl",

misc-scripts/density_feature/percent_gc_calc.pl

@@ -54,7 +54,20 @@ if( ! $dna_count ) {
 
 
 print "Deleting old PercentGC features\n";
-$sth = $db->dbc->prepare("DELETE df, dt, a FROM density_feature df, density_type dt, analysis a WHERE a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name='PercentGC'");
+$sth = $db->dbc->prepare(
+  qq(
+DELETE df, dt, a
+FROM density_feature df, density_type dt, analysis a
+WHERE a.analysis_id=dt.analysis_id
+AND dt.density_type_id=df.density_type_id
+AND a.logic_name='PercentGC') );
+$sth->execute();
+
+$sth = $db->dbc()->prepare(
+  qq(
+  DELETE ad
+  FROM analysis_description ad
+  WHERE ad.display_label = 'PercentGC') );
 $sth->execute();
 
 #
@@ -73,14 +86,19 @@ my @sorted_slices =  sort { $b->seq_region_length() <=> $a->seq_region_length()}
 # Create new analysis object for density calculation.
 #
 
-my $analysis = new Bio::EnsEMBL::Analysis (-program     => "percent_gc_calc.pl",
-					   -database    => "ensembl",
-					   -gff_source  => "percent_gc_calc.pl",
-					   -gff_feature => "density",
-					   -logic_name  => "PercentGC");
+my $analysis =
+  new Bio::EnsEMBL::Analysis(
+             -program     => "percent_gc_calc.pl",
+             -database    => "ensembl",
+             -gff_source  => "percent_gc_calc.pl",
+             -gff_feature => "density",
+             -logic_name  => "PercentGC",
+             -description => 'Percentage of G/C bases in the sequence.',
+             -display_label => 'PercentGC',
+             -displayable   => 1 );
 
 $aa->store($analysis);
-
+$aa->update($analysis);
 
 #
 # Create new density type.

misc-scripts/density_feature/repeat_coverage_calc.pl

@@ -67,6 +67,13 @@ print "Deleting old PercentageRepeat features\n";
 $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='PercentageRepeat'");
 $sth->execute();
 
+$sth = $db->dbc()->prepare(
+  qq(
+  DELETE ad
+  FROM analysis_description ad
+  WHERE ad.display_label = 'PercentageRepeat') );
+$sth->execute();
+
 my $slice_adaptor = $db->get_SliceAdaptor();
 my $dfa = $db->get_DensityFeatureAdaptor();
 my $dta = $db->get_DensityTypeAdaptor();
@@ -78,13 +85,20 @@ my $aa  = $db->get_AnalysisAdaptor();
 # Create new analysis object for density calculation.
 #
 
-my $analysis = new Bio::EnsEMBL::Analysis (-program     => "repeat_coverage_calc.pl",
-					   -database    => "ensembl",
-					   -gff_source  => "repeat_coverage_calc.pl",
-					   -gff_feature => "density",
-					   -logic_name  => "PercentageRepeat");
- 
+my $analysis =
+  new Bio::EnsEMBL::Analysis(
+       -program     => "repeat_coverage_calc.pl",
+       -database    => "ensembl",
+       -gff_source  => "repeat_coverage_calc.pl",
+       -gff_feature => "density",
+       -logic_name  => "PercentageRepeat",
+       -description =>
+         'Percentage of repetetive elements for top level seq_regions.',
+       -display_label => 'PercentageRepeat',
+       -displayable   => 1 );
+
 $aa->store($analysis);
+$aa->update($analysis);
 
 my $slices = $slice_adaptor->fetch_all( "toplevel" );
 my @sorted_slices = sort { $b->seq_region_length() <=> $a->seq_region_length() } @$slices;

misc-scripts/density_feature/variation_density.pl

@@ -53,6 +53,13 @@ if( ! variation_attach( $db )) {
 my $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='snpDensity'");
 $sth->execute();
 
+$sth = $db->dbc()->prepare(
+  qq(
+  DELETE ad
+  FROM analysis_description ad
+  WHERE ad.display_label = 'snpDensity') );
+$sth->execute();
+
 #
 # Get the adaptors needed;
 #
@@ -65,15 +72,19 @@ my $slice_adaptor = $db->get_SliceAdaptor();
 my $top_slices = $slice_adaptor->fetch_all( "toplevel" );
 my @sorted_slices =  sort { $b->seq_region_length() <=> $a->seq_region_length()} @$top_slices;
 
-
-
-my $analysis = new Bio::EnsEMBL::Analysis (-program     => "variation_density.pl",
-					   -database    => "ensembl",
-					   -gff_source  => "variation_density.pl",
-					   -gff_feature => "density",
-					   -logic_name  => "snpDensity");
-
-$aa->store( $analysis );
+my $analysis =
+  new Bio::EnsEMBL::Analysis(
+              -program     => "variation_density.pl",
+              -database    => "ensembl",
+              -gff_source  => "variation_density.pl",
+              -gff_feature => "density",
+              -logic_name  => "snpDensity",
+              -description => 'Density of SNP features on the sequence',
+              -display_label => 'snpDensity',
+              -displayable   => 1 );
+
+$aa->store($analysis);
+$aa->update($analysis);
 
 
 #