fixed problems with new density_type analysis_id updates

misc-scripts/density_feature/gene_density_calc.pl

@@ -94,14 +94,16 @@ if( ! $seq_region_count ) {
 # Get the adaptors needed;
 #
 
+
+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();
+
 my $dfa = $db->get_DensityFeatureAdaptor();
 my $dta = $db->get_DensityTypeAdaptor();
 my $aa  = $db->get_AnalysisAdaptor();
 my $slice_adaptor = $db->get_SliceAdaptor();
 
-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();
 
 #
 # block size estimation

misc-scripts/density_feature/percent_gc_calc.pl

@@ -52,6 +52,11 @@ 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->execute();
+
 #
 # Get the adaptors needed;
 #
@@ -64,11 +69,6 @@ my $aa  = $db->get_AnalysisAdaptor();
 my $slices = $slice_adaptor->fetch_all( "toplevel" );
 my @sorted_slices =  sort { $b->seq_region_length() <=> $a->seq_region_length()} @$slices;
 
-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->execute();
-
-
 #
 # Create new analysis object for density calculation.
 #

misc-scripts/density_feature/repeat_coverage_calc.pl

@@ -59,11 +59,6 @@ if( ! $repeat_count ) {
 # Get the adaptors needed;
 #
 
-my $slice_adaptor = $db->get_SliceAdaptor();
-my $dfa = $db->get_DensityFeatureAdaptor();
-my $dta = $db->get_DensityTypeAdaptor();
-my $aa  = $db->get_AnalysisAdaptor();
-
 #
 # Clean up old features first. Also remove analysis and density type entry as these are recreated.
 #
@@ -72,6 +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();
 
+my $slice_adaptor = $db->get_SliceAdaptor();
+my $dfa = $db->get_DensityFeatureAdaptor();
+my $dta = $db->get_DensityTypeAdaptor();
+my $aa  = $db->get_AnalysisAdaptor();
+
+
+
 #
 # Create new analysis object for density calculation.
 #