From e8aaf3139af325bf4bbb6afc714015fa4c5bcd21 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Mon, 8 Mar 2004 18:51:37 +0000
Subject: [PATCH] added tests for fetch_by_region which can now "guess"
coordinate system if one is not provided
---
modules/t/sliceAdaptor.t | 26 +++++++++++++++++++++++++-
1 file changed, 25 insertions(+), 1 deletion(-)
diff --git a/modules/t/sliceAdaptor.t b/modules/t/sliceAdaptor.t
index 500d790b30..bae3444259 100644
--- a/modules/t/sliceAdaptor.t
+++ b/modules/t/sliceAdaptor.t
@@ -5,7 +5,7 @@ use warnings;
BEGIN { $| = 1;
use Test;
- plan tests => 56;
+ plan tests => 63;
}
use MultiTestDB;
@@ -377,6 +377,30 @@ $slice = $slice_adaptor->fetch_by_region('contig', $clone_name);
ok(!defined($slice));
print_slices([$slice]);
+#make sure that you can fetch a seq_region without knowing its version
+$slice = $slice_adaptor->fetch_by_region(undef, '20');
+ok(defined($slice) && $slice->seq_region_name eq '20');
+
+$slice = $slice_adaptor->fetch_by_region('toplevel', '20');
+ok(defined($slice) && $slice->seq_region_name eq '20');
+
+$slice = $slice_adaptor->fetch_by_region('toplevel', '20', 10, 20);
+ok(defined($slice) && $slice->start == 10 && $slice->end == 20);
+
+$slice = $slice_adaptor->fetch_by_region(undef, '20', 10, 20, 1, 'NCBI33');
+ok(defined($slice) && $slice->seq_region_name eq '20');
+
+$slice = $slice_adaptor->fetch_by_region(undef, '20', 10, 20, 1, 'bogus');
+ok(!defined($slice));
+
+
+$slice = $slice_adaptor->fetch_by_region('toplevel', '20', 10, 20, 1, 'bogus');
+ok(defined($slice) && $slice->seq_region_name eq '20');
+
+# try fuzzy matching in conjunction with coord system guessing
+$clone_name = 'AL031658';
+$slice = $slice_adaptor->fetch_by_region(undef, $clone_name);
+ok($slice->seq_region_name =~ /$clone_name\.\d+/);
sub print_slices {
my $slices = shift;
--
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