From e148443a31c5f04f8b4c04ef008fb3f240ba05ac Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 15 Dec 2014 17:24:29 +0000
Subject: [PATCH] ENSCORESW-1120: added is_high_coverage flag for genome
container
---
modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm | 33 ++++++++++++++++++++
modules/t/genomeContainer.t | 14 +++++++--
2 files changed, 45 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
index 527527c4af..c49a1c82c8 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GenomeContainer.pm
@@ -1189,6 +1189,39 @@ sub has_karyotype {
return 1;
}
+
+=head2 is_high_coverage
+
+ Arg : None
+ Example : $is_high_coverage = $genome->is_high_coverage();
+ Description: Boolean indicating whether an assembly is high coverage
+ or not
+ Returntype : integer
+ Exceptions : none
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub is_high_coverage {
+ my $self = shift;
+
+ my $coverage_depth = $self->_meta_container->single_value_by_key('assembly.coverage_depth');
+
+ return 0 if !$coverage_depth;
+ $coverage_depth = lc($coverage_depth);
+
+ if ($coverage_depth eq 'high') {
+ return 1;
+ } elsif (($coverage_depth eq 'low') or ($coverage_depth eq 'medium')) {
+ return 0;
+ } elsif ($coverage_depth =~ /^([0-9]+)x$/) {
+ return $1<6 ? 0 : 1;
+ }
+
+ return 0;
+}
+
=head2 is_polyploid
Arg : None
diff --git a/modules/t/genomeContainer.t b/modules/t/genomeContainer.t
index 37c979dc31..d91b0a3c25 100644
--- a/modules/t/genomeContainer.t
+++ b/modules/t/genomeContainer.t
@@ -15,6 +15,7 @@
use strict;
use warnings;
+use Test::Warnings;
use Bio::EnsEMBL::DBSQL::GenomeContainer;
use Bio::EnsEMBL::Test::TestUtils;
use Bio::EnsEMBL::Registry;
@@ -154,15 +155,24 @@ my $alt_transcript_count = $sql_helper->execute_single_result(-SQL => $alt_trans
is($alt_transcript_count, $genome->get_alt_transcript_count(), "Number of alt transcripts is correct");
-#
+#
# Test karyotype flag
#
-is(1, $genome->has_karyotype, "Human has some chromosomes");
my $empty_db = $multi->get_DBAdaptor("empty");
my $empty_genome = $empty_db->get_adaptor('GenomeContainer');
+
+is(1, $genome->has_karyotype, "Human has some chromosomes");
is(0, $empty_genome->has_karyotype, "Empty db does not have chromosomes");
+
+#
+# Test high coverage flag
+#
+
+is(1, $genome->is_high_coverage, "Human genebuild is high coverage");
+is(0, $empty_genome->is_high_coverage, "Empty db is not high coverage");
+
#
# Test polyploid genome support
#
--
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