From a2ccb53124d0c4e132cf83db2f66a0e5b961cf82 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 22 Sep 2011 16:31:51 +0000
Subject: [PATCH] Adding a new method for describing a region's assembly
exception type
---
modules/Bio/EnsEMBL/Slice.pm | 28 +++++++++++++++++++
modules/t/slice.t | 16 +++++++----
.../homo_sapiens/core/attrib_type.txt | 1 +
.../homo_sapiens/core/seq_region_attrib.txt | 1 +
4 files changed, 41 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index a3b05713aa..e0d2aeb250 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -673,6 +673,34 @@ sub subseq {
return $subseq;
}
+=head2 assembly_exception_type
+
+ Example : $self->assembly_exception_type();
+ Description : Returns the type of slice this is. If it is reference then you
+ will get 'REF' back. Otherwise you will get the first
+ element from C<get_all_AssemblyExceptionFeatures()>. If no
+ assembly exception exists you will get an empty string back.
+ Returntype : String
+ Exceptions : None
+ Caller : Public
+ Status : Beta
+
+=cut
+
+sub assembly_exception_type {
+ my ($self) = @_;
+ my $type = q{};
+ if($self->is_reference()) {
+ $type = 'REF';
+ }
+ else {
+ my $assembly_exceptions = $self->get_all_AssemblyExceptionFeatures();
+ if(@{$assembly_exceptions}) {
+ $type = $assembly_exceptions->[0]->type();
+ }
+ }
+ return $type;
+}
=head2 get_base_count
diff --git a/modules/t/slice.t b/modules/t/slice.t
index 13e454ce7c..4d88439ca5 100644
--- a/modules/t/slice.t
+++ b/modules/t/slice.t
@@ -1,11 +1,7 @@
use strict;
use warnings;
-
-BEGIN { $| = 1;
- use Test;
- plan tests => 60;
-}
+use Test::More tests => 63;
use Bio::EnsEMBL::Test::TestUtils;
@@ -153,6 +149,8 @@ ok($name eq "chromosome:NCBI33:$CHR:$START:$END:$STRAND");
#
ok($slice->length == ($END-$START + 1));
+# Test exception name
+is($slice->assembly_exception_type(), 'REF', 'Type of region is REF');
#
# Test get_attributes
@@ -437,3 +435,11 @@ $slice = $slice_adaptor->fetch_by_region('chromosome', 1, 1, 10);
ok(@alt_names == 1);
$multi->restore();
+
+
+#Test assembly exception type on HAP
+my $hap_slice = $slice_adaptor->fetch_by_region(undef, '20_HAP1');
+is($hap_slice->assembly_exception_type(), 'HAP', 'Ensuring haplotype regions are HAP');
+my $chr_one_slice = $slice_adaptor->fetch_by_region('chromosome', '1', 1, 10);
+is($chr_one_slice->assembly_exception_type(), 'REF', 'Ensuring reference regions are REF');
+
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt b/modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
index e23310e017..a6cee5d90f 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt
@@ -15,3 +15,4 @@
15 _rna_edit RNA editing \N
16 _selenocysteine Selenocysteine \N
17 codon_table Codon Table Alternate codon table
+18 non_ref Non Reference Non Reference Sequence Region
\ No newline at end of file
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt b/modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt
index 58dd00b5e8..a4eff7fd65 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt
@@ -13,3 +13,4 @@
469283 14 1
965899 17 2
965888 17 2
+469351 18 1
\ No newline at end of file
--
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