From 956d986ea02651084af273ae258cda2b6227a530 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 24 May 2004 12:50:57 +0000
Subject: [PATCH] added some tests for creation of slices sans db and coord
system
---
modules/t/slice.t | 27 +++++++++++++++++++++++++--
1 file changed, 25 insertions(+), 2 deletions(-)
diff --git a/modules/t/slice.t b/modules/t/slice.t
index 5444fd7a41..8cdc1418b3 100644
--- a/modules/t/slice.t
+++ b/modules/t/slice.t
@@ -5,7 +5,7 @@ use lib 't';
BEGIN { $| = 1;
use Test;
- plan tests => 48;
+ plan tests => 53;
}
use TestUtils qw( debug );
@@ -14,7 +14,7 @@ use MultiTestDB;
use Bio::EnsEMBL::Slice;
use Bio::EnsEMBL::ProjectionSegment;
-our $verbose= 0;
+our $verbose = 0;
#
# TEST - Slice Compiles
@@ -97,6 +97,27 @@ $subseq = $test_slice->subseq(2,6,-1);
ok($subseq eq 'ATGCA');
debug("subseq = $subseq");
+# test that subslice works correctly with attached sequence
+
+my $sub_slice = $test_slice->sub_Slice(2, 6);
+ok($sub_slice->seq eq 'TGCAT');
+
+# test that invert works correctly with attached sequence
+ok($sub_slice->invert()->seq() eq 'ATGCA');
+
+
+# test that slice can be created without db, seq or coord system
+$test_slice = Bio::EnsEMBL::Slice->new('-seq_region_name' => 'test',
+ '-start' => 1,
+ '-end' => 3);
+
+ok($test_slice);
+ok($test_slice->seq() eq 'NNN');
+
+debug("\$test_slice->name = " . $test_slice->name());
+
+ok($test_slice->name() eq '::test:1:3:1');
+
$slice = new Bio::EnsEMBL::Slice
(-seq_region_name => $CHR,
@@ -340,3 +361,5 @@ my $sr_slice = $slice->seq_region_Slice();
ok($sr_slice->start() == 1 &&
$sr_slice->end() == $slice->seq_region_length() &&
$sr_slice->strand() == 1);
+
+
--
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