From d620e7954f3cb46d2944bda53bdc8681baa564d7 Mon Sep 17 00:00:00 2001
From: Daniel Sobral <ds19@sanger.ac.uk>
Date: Sun, 5 Jun 2011 14:28:04 +0000
Subject: [PATCH] Added update to avoid recreating analysis snpdensity
---
.../density_feature/variation_density.pl | 30 ++++++++++---------
1 file changed, 16 insertions(+), 14 deletions(-)
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index 1571342df0..7794fa1aec 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/misc-scripts/density_feature/variation_density.pl
@@ -38,7 +38,10 @@ my $variation_feature_adaptor = Bio::EnsEMBL::Registry->get_adaptor($species, "v
# TODO - variation from registry
# Clean up old features first. Also remove analysis and density type entry as these are recreated
-my $sth = $slice_adaptor->dbc->prepare("DELETE df, dt, a, ad FROM analysis_description ad, density_feature df, density_type dt, analysis a 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='snpdensity'");
+#my $sth = $slice_adaptor->dbc->prepare("DELETE df, dt, a, ad FROM analysis_description ad, density_feature df, density_type dt, analysis a 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='snpdensity'");
+
+# release 63: do not delete analysis, as this is synchronized with production!
+my $sth = $slice_adaptor->dbc->prepare("DELETE df, dt FROM analysis_description ad, density_feature df, density_type dt, analysis a 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='snpdensity'");
$sth->execute();
# Sort slices by coordinate system rank, then by length
@@ -47,19 +50,18 @@ my @sorted_slices = sort( {
|| $b->seq_region_length() <=> $a->seq_region_length()
} @{ $slice_adaptor->fetch_all('toplevel') } );
-my $analysis =
- new Bio::EnsEMBL::Analysis(
- -program => "variation_density.pl",
- -database => "ensembl",
- -gff_source => "variation_density.pl",
- -gff_feature => "density",
- -logic_name => "snpdensity",
- -description => 'Density of Single Nucleotide Polymorphisms (SNPs) calculated by variation_density.pl (see scripts at the <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/?root=ensembl">Sanger Institute CVS</a> repository).',
- -display_label => 'SNP Density',
- -displayable => 1 );
-
-$analysis_adaptor->store($analysis);
-$analysis_adaptor->update($analysis);
+my $analysis = $analysis_adaptor->fetch_by_logic_name('snpdensity');
+# new Bio::EnsEMBL::Analysis(
+# -program => "variation_density.pl",
+# -database => "ensembl",
+# -gff_source => "variation_density.pl",
+# -gff_feature => "density",
+# -logic_name => "snpdensity",
+# -description => 'Density of Single Nucleotide Polymorphisms (SNPs) calculated by variation_density.pl (see scripts at the <a rel="external" href="http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/?root=ensembl">Sanger Institute CVS</a> repository).',
+# -display_label => 'SNP Density',
+# -displayable => 1 );
+#$analysis_adaptor->store($analysis);
+#$analysis_adaptor->update($analysis);
# Create and store new density type
--
GitLab