From 623b61b24e5bc76ea466edb725d73c970656fa62 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Thu, 17 Jul 2003 14:25:49 +0000
Subject: [PATCH] added more/updated tests for go_xrefs
---
modules/t/dbEntries.t | 47 +++++++++++++++++++++++++++++++++++++++----
1 file changed, 43 insertions(+), 4 deletions(-)
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index b89cb79b22..60eb5617d7 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -4,7 +4,7 @@ use warnings;
BEGIN { $| = 1;
use Test;
- plan tests => 9;
+ plan tests => 12;
}
use MultiTestDB;
@@ -50,7 +50,7 @@ $sth->finish();
my $ga = $db->get_GeneAdaptor();
-my $all_gene_ids = $ga->list_geneIds();
+my $all_gene_ids = $ga->list_dbIDs();
for my $gene_id ( @$all_gene_ids ) {
my $gene = $ga->fetch_by_dbID( $gene_id );
@@ -99,7 +99,7 @@ my $goref = Bio::EnsEMBL::GoXref->new
-release => "1",
-display_id => "Ens related GO"
);
-$goref->linkage_type( "experimental" );
+$goref->add_linkage_type( "IC" );
my $ident_xref = Bio::EnsEMBL::IdentityXref->new
(
@@ -183,9 +183,48 @@ debug( "Number of identity_xrefs = $ident_count" );
ok( $ident_count == 2 );
+$multi->restore();
+
+
+#
+# 10-12 Test that external synonyms and go evidence tags are retrieved
+#
+my $ta = $db->get_TranscriptAdaptor();
+my $translation = $ta->fetch_by_dbID(21737)->translation;
+
+#pull out an xref that should 2 external synonyms
+my $xrefs = $dbEntryAdaptor->fetch_all_by_Translation($translation);
+($xref) = grep {$_->dbID == 315} @$xrefs;
+my @syns = grep {$_ eq 'syn1' || $_ eq 'syn2'} @{$xref->get_all_synonyms};
+ok(@syns == 2);
+
+#and also 2 evidence tags
+if($xref && $xref->isa('Bio::EnsEMBL::GoXref')) {
+ my @evtags =
+ grep {$_ eq 'IEA' || $_ eq 'IC'} @{$xref->get_all_linkage_types()};
+ ok(@evtags == 2);
+} else {
+ ok(0);
+}
+
+
+$translation = $ta->fetch_by_dbID(21723)->translation;
+
+$xrefs = $dbEntryAdaptor->fetch_all_by_Translation($translation);
+($xref) = grep {$_->dbID == 257} @$xrefs;
+
+if($xref && $xref->isa('Bio::EnsEMBL::GoXref')) {
+ my ($evtag) = @{$xref->get_all_linkage_types()};
+ ok($evtag eq 'IC');
+} else {
+ ok(0);
+}
+
+
#
# Need more tests here ...
#
-$multi->restore();
+
+
--
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