diff --git a/misc-scripts/density_feature/gene_density_calc.pl b/misc-scripts/density_feature/gene_density_calc.pl
index 736046c6446eaf2f1dade66682594c69ae684109..f9ac1c9cc2a60456452184a02e9c1e04d20c354a 100644
--- a/misc-scripts/density_feature/gene_density_calc.pl
+++ b/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",
diff --git a/misc-scripts/density_feature/percent_gc_calc.pl b/misc-scripts/density_feature/percent_gc_calc.pl
index a9c122c2d1d5fa0838a543e912405385d4f6cb96..4b1930d848f6b0e555c288bc04e3064ab28c92a5 100644
--- a/misc-scripts/density_feature/percent_gc_calc.pl
+++ b/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.
diff --git a/misc-scripts/density_feature/repeat_coverage_calc.pl b/misc-scripts/density_feature/repeat_coverage_calc.pl
index 6e2f0891877c0e373e87cfee11b2c08b67ce5539..8e947b758c4c416a45a15693307d3ec66956c0e1 100644
--- a/misc-scripts/density_feature/repeat_coverage_calc.pl
+++ b/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;
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index 3af0c7c0d739e255cc641c7ea39c827ac2544626..6e80a3e7445c228200b06a492c5f078d94db45eb 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/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);
#