From 0273c1cd68b53258efe1ecf37b500d03c8179361 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 8 Feb 2011 12:54:22 +0000
Subject: [PATCH] All analysis logic_names should be lower case.
---
misc-scripts/density_feature/gene_density_calc.pl | 8 ++++----
misc-scripts/density_feature/glovar_snp_density.pl | 2 +-
misc-scripts/density_feature/logicname_density_calc.pl | 4 ++--
3 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/misc-scripts/density_feature/gene_density_calc.pl b/misc-scripts/density_feature/gene_density_calc.pl
index df455dcbe5..2d1550ed50 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 38f7e4be36..5992491ec4 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 e0dcde2287..5d38197873 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');
--
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