From 0d3d16f699bbab975719b5b14cafa6607320bb29 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Tue, 15 Jun 2004 10:53:19 +0000
Subject: [PATCH] added tests for mapping of inserts
---
modules/t/mapper.t | 33 ++++++++++++++++++++++++++++++---
1 file changed, 30 insertions(+), 3 deletions(-)
diff --git a/modules/t/mapper.t b/modules/t/mapper.t
index 63ee548c90..73cf98c5f2 100644
--- a/modules/t/mapper.t
+++ b/modules/t/mapper.t
@@ -25,7 +25,7 @@
## We start with some black magic to print on failure.
BEGIN { $| = 1;
use Test;
- plan tests => 10; # 5 tests total
+ plan tests => 14; # 5 tests total
use vars qw($loaded); }
END { print "not ok 1\n" unless $loaded; }
@@ -134,14 +134,13 @@ test_transform( $mapper,
$mapper = Bio::EnsEMBL::Mapper->new( "asm1", "asm2" );
-$mapper = Bio::EnsEMBL::Mapper->new( "asm1", "asm2" );
-
$mapper->add_map_coordinates( "1", 1, 10, 1, "1", 101, 110 );
$mapper->add_map_coordinates( "1", 11, 20, 1, "1", 111, 120 );
$mapper->add_map_coordinates( "1", 22, 30, 1, "1", 132, 140 );
$mapper->add_map_coordinates( "1", 51, 70, 1, "1", 161, 180 );
$mapper->add_map_coordinates( "1", 31, 35, 1, "1", 141, 145 );
+
test_transform( $mapper,
[ "1", 5, 45, 1, "asm1" ],
[ "1", 105, 120, 1 ],
@@ -151,6 +150,34 @@ test_transform( $mapper,
);
+#
+# test tranformation of 'insertion' coordinates where end = start -1
+#
+
+$mapper = Bio::EnsEMBL::Mapper->new('asm1', 'asm2');
+
+$mapper->add_map_coordinates('1', 1, 10, 1, 'X', 101, 110);
+$mapper->add_map_coordinates('1', 11, 20, -1, 'Y', 1, 10);
+
+# boundary insert, expect 2 edge inserts back
+test_transform($mapper, ['1', 11, 10, 1, 'asm1'],
+ ['X', 111, 110, 1],
+ ['Y', 11, 10, -1]);
+
+# edge insert, negative strand, expect edge insert negative strand
+test_transform($mapper, ['1', 1, 0, -1, 'asm1'],
+ ['X', 101, 100, -1]);
+
+# normal case, expect single insert in middle
+test_transform($mapper, ['1', 2, 1, 1, 'asm1'],
+ ['X', 102, 101, 1]);
+
+# expect a gap
+test_transform($mapper, ['1', 100, 200, 1, 'asm1'],
+ ['1', 100, 200, 0]);
+
+
+
# the following subroutine tests that a given source co-ordinate range
# transforms into a given set of destination co-ordinates
#
--
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