diff --git a/misc-scripts/density_feature/gene_density_calc.pl b/misc-scripts/density_feature/gene_density_calc.pl index df455dcbe5be71fcab1d3110285645e23d761627..2d1550ed50d8815aa4fe8bd42862f9c62b0f4946 100644 --- a/misc-scripts/density_feature/gene_density_calc.pl +++ b/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'); } # diff --git a/misc-scripts/density_feature/glovar_snp_density.pl b/misc-scripts/density_feature/glovar_snp_density.pl index 38f7e4be3628e0aff0a1988cfced33cc54cd985e..5992491ec4cbe5a4a58f3ddc1a732cbaf20dd081 100755 --- a/misc-scripts/density_feature/glovar_snp_density.pl +++ b/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')); diff --git a/misc-scripts/density_feature/logicname_density_calc.pl b/misc-scripts/density_feature/logicname_density_calc.pl index e0dcde228788828ea0a64e0b9246099c5a865472..5d3819787338b02d578fe9beffea9b75a0117690 100644 --- a/misc-scripts/density_feature/logicname_density_calc.pl +++ b/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');