From 5f3f73e8869dbf56637f5855fcfdd230eeb350c9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Wed, 16 Mar 2011 10:40:53 +0000
Subject: [PATCH] Update analysis_description for 'snpdensity' to be the same
as in the production database.
---
.../density_feature/variation_density.pl | 28 ++++++++++---------
1 file changed, 15 insertions(+), 13 deletions(-)
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index 26c866a272..1571342df0 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/misc-scripts/density_feature/variation_density.pl
@@ -42,19 +42,21 @@ my $sth = $slice_adaptor->dbc->prepare("DELETE df, dt, a, ad FROM analysis_descr
$sth->execute();
# Sort slices by coordinate system rank, then by length
-my @sorted_slices =
- sort( { $a->coord_system()->rank() <=> $b->coord_system()->rank()
- || $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 SNP features on the sequence',
- -display_label => 'SNP Density',
- -displayable => 1 );
+my @sorted_slices = sort( {
+ $a->coord_system()->rank() <=> $b->coord_system()->rank()
+ || $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);
--
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