From 2dc28bec455a5f65c64c57cd5325477ce4a89e61 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 6 Jun 2012 10:47:40 +0000
Subject: [PATCH] added percentgc density type to fetch_stats
---
.../Bio/EnsEMBL/DBSQL/AssemblyInfoAdaptor.pm | 23 ++++++++++++++++---
1 file changed, 20 insertions(+), 3 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/AssemblyInfoAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/AssemblyInfoAdaptor.pm
index c58d797b84..0837a2a403 100644
--- a/modules/Bio/EnsEMBL/DBSQL/AssemblyInfoAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/AssemblyInfoAdaptor.pm
@@ -141,7 +141,7 @@ sub fetch_info {
=head2 fetch_stats
Arg [1] : string $seq_region_name (optional)
- The name of a toplevel seq_region for which statistics should be fetched
+ The name of the toplevel seq_region for which statistics should be fetched
Description: Returns a hash
Returntype : hash with assembly statistics name and value pairs
@@ -174,7 +174,7 @@ sub fetch_stats {
@slices = @{$sa->fetch_all('toplevel')};
}
- my @density_types = qw(genedensity knowngenedensity snpdensity);
+ my @density_types = qw(genedensity knowngenedensity snpdensity percentgc);
my @attrib_types = qw(GeneNo% SNPCount);
@@ -182,6 +182,10 @@ sub fetch_stats {
my $dfa = $self->db()->get_adaptor('DensityFeature');
+ #used to calculate the average density value for density types represented as ratios
+
+ my %density_ft_count = ();
+
foreach my $slice (@slices) {
$assembly_stats{'Length (bps)'} += $slice->length();
@@ -189,9 +193,13 @@ sub fetch_stats {
foreach my $density_type (@density_types) {
my $density_features = $dfa->fetch_all_by_Slice($slice,$density_type);
-
+
foreach my $density_feature (@$density_features) {
+ if ($density_feature->density_type()->value_type() eq 'ratio') {
+ $density_ft_count{$density_feature->density_type()->analysis()->display_label()} += 1;
+ }
+
$assembly_stats{$density_feature->density_type()->analysis()->display_label()} += $density_feature->density_value();
}
}
@@ -206,6 +214,15 @@ sub fetch_stats {
}
}
+ foreach my $density_analysis (keys %density_ft_count) {
+
+ if ($density_ft_count{$density_analysis} > 1) {
+ $assembly_stats{$density_analysis} /= $density_ft_count{$density_analysis};
+ $assembly_stats{$density_analysis} = sprintf "%.2f", $assembly_stats{$density_analysis};
+ $assembly_stats{$density_analysis} .= '%';
+ }
+ }
+
return \%assembly_stats;
}
--
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