From e14eee62dbae0c80c9283826425b65a27b2c2480 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Fri, 13 Apr 2007 14:24:11 +0000
Subject: [PATCH] added test for optional info_type to
get_all_db(Entries/Links) for translation, transcript and gene
---
modules/t/dbEntries.t | 70 ++++++++++++++++++++++++++++++++++++++++++-
1 file changed, 69 insertions(+), 1 deletion(-)
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index 0ba040db67..9b1fc58ab0 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -3,7 +3,7 @@ use warnings;
BEGIN { $| = 1;
use Test;
- plan tests => 43;
+ plan tests => 58;
}
use Bio::EnsEMBL::Test::MultiTestDB;
@@ -67,6 +67,7 @@ debug( " $goxref_count GoXrefs, $ident_count identityXrefs." );
#
# 3 as many dblinks as entries in object_xref
#
+print $db_entry_count."\t".$xref_count."\n";
ok( $db_entry_count == $xref_count );
#
@@ -337,6 +338,73 @@ ok($id_total - $id_count == count_rows($db, 'identity_xref'));
$multi->restore('core', 'object_xref', 'identity_xref', 'go_xref');
+# new info type checks
+
+# fetch_all_by Gene Transcript Translation
+
+# transclation info type
+
+$translation = $ta->fetch_by_dbID(21737)->translation;
+$dbes = $translation->get_all_DBEntries(undef,"DEPENDENT");
+
+ok(@$dbes == 2); # test 44
+
+$dbes = $translation->get_all_DBLinks(undef,"DEPENDENT");
+ok(@$dbes == 2);
+
+$dbes = $translation->get_all_DBLinks(undef,"SEQUENCE_MATCH");
+ok(@$dbes == 1);
+
+$dbes = $translation->get_all_DBLinks(undef,"INFERRED_PAIR");
+ok(@$dbes == 1);
+
+$dbes = $translation->get_all_DBLinks(undef,"RUBBISH");
+ok(@$dbes == 0);
+
+
+
+# transcript info type
+
+my $transcript = $ta->fetch_by_dbID(21737);
+$dbes = $transcript->get_all_DBEntries(undef,"DEPENDENT");
+
+ok(@$dbes == 0); # test 49
+
+$dbes = $transcript->get_all_DBLinks(undef,"DEPENDENT");
+ok(@$dbes == 2);
+
+$dbes = $transcript->get_all_DBLinks(undef,"SEQUENCE_MATCH");
+ok(@$dbes == 1);
+
+$dbes = $transcript->get_all_DBLinks(undef,"INFERRED_PAIR");
+ok(@$dbes == 1);
+
+$dbes = $transcript->get_all_DBLinks(undef,"RUBBISH");
+ok(@$dbes == 0);
+
+
+
+# gene info type
+
+$gene = $ga->fetch_by_dbID(18272);
+$dbes = $gene->get_all_DBEntries(undef,"DEPENDENT");
+
+ok(@$dbes == 0); # test 54
+
+$dbes = $gene->get_all_DBLinks(undef,"DEPENDENT");
+ok(@$dbes == 2);
+
+$dbes = $gene->get_all_DBLinks(undef,"SEQUENCE_MATCH");
+ok(@$dbes == 1);
+
+$dbes = $gene->get_all_DBLinks(undef,"INFERRED_PAIR");
+ok(@$dbes == 1);
+
+$dbes = $gene->get_all_DBLinks(undef,"RUBBISH");
+ok(@$dbes == 0);
+
+
+
sub print_dbEntries {
my $dbes = shift;
--
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