From 596eead9cf49bd332367eb9927bcbf4fbd09be87 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 4 Oct 2010 10:43:14 +0000
Subject: [PATCH] go_xref is now ontology_xref
---
modules/t/dbEntries.t | 24 ++++++++++++------------
modules/t/gene.t | 2 +-
modules/t/transcript.t | 2 +-
modules/t/translation.t | 2 +-
4 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/modules/t/dbEntries.t b/modules/t/dbEntries.t
index aee1aecc36..ffab63c3d3 100644
--- a/modules/t/dbEntries.t
+++ b/modules/t/dbEntries.t
@@ -56,7 +56,7 @@ for my $gene_id ( @$all_gene_ids ) {
my $tl = $tr->translation();
my $dbentries = $dbEntryAdaptor->fetch_all_by_Translation( $tl );
$db_entry_count += scalar( @{$dbentries});
- $goxref_count += grep { $_->isa( "Bio::EnsEMBL::GoXref" )} @$dbentries;
+ $goxref_count += grep { $_->isa( "Bio::EnsEMBL::OntologyXref" )} @$dbentries;
$ident_count += grep {$_->isa( "Bio::EnsEMBL::IdentityXref" )} @$dbentries;
}
}
@@ -110,7 +110,7 @@ my $ident_xref = Bio::EnsEMBL::IdentityXref->new
$ident_xref->xref_identity( 100 );
$ident_xref->ensembl_identity( 95 );
-my $goref = Bio::EnsEMBL::GoXref->new
+my $goref = Bio::EnsEMBL::OntologyXref->new
(
-primary_id => "1",
-dbname => "GO",
@@ -121,7 +121,7 @@ $goref->add_linkage_type( "IC" ); # Linkage type on own
$goref->add_linkage_type( "ISS", $goref ); # Linkage type with source xref
-$multi->hide( "core", "object_xref", "xref", "identity_xref", "go_xref" );
+$multi->hide( "core", "object_xref", "xref", "identity_xref", "ontology_xref" );
my $gene = $ga->fetch_by_dbID( $all_gene_ids->[0] );
@@ -157,7 +157,7 @@ ok( $xref_count == 3 );
#
# 8 number of go entries right
#
-$go_count = count_rows($db, 'go_xref');
+$go_count = count_rows($db, 'ontology_xref');
debug( "Number of go_xrefs = $go_count" );
ok( $go_count == 2 );
@@ -189,7 +189,7 @@ my @syns = grep {$_ eq 'syn1' || $_ eq 'syn2'} @{$xref->get_all_synonyms};
ok(@syns == 2);
#and also 2 evidence tags, and one source_xref
-if($xref && $xref->isa('Bio::EnsEMBL::GoXref')) {
+if($xref && $xref->isa('Bio::EnsEMBL::OntologyXref')) {
my @evtags =
grep {$_ eq 'IEA' || $_ eq 'IC'} @{$xref->get_all_linkage_types()};
ok(@evtags == 2);
@@ -207,7 +207,7 @@ $translation = $ta->fetch_by_dbID(21723)->translation;
$xrefs = $dbEntryAdaptor->fetch_all_by_Translation($translation);
($xref) = grep {$_->dbID == 257} @$xrefs;
-if($xref && $xref->isa('Bio::EnsEMBL::GoXref')) {
+if($xref && $xref->isa('Bio::EnsEMBL::OntologyXref')) {
my ($evtag) = @{$xref->get_all_linkage_types()};
ok($evtag eq 'IC');
} else {
@@ -309,7 +309,7 @@ ok($xref->primary_id() eq 'IPR000010');
$multi->restore('core', 'xref');
-$multi->save('core', 'object_xref', 'identity_xref', 'go_xref');
+$multi->save('core', 'object_xref', 'identity_xref', 'ontology_xref');
#
# test the removal of dbentry associations
@@ -320,11 +320,11 @@ $translation = $ta->fetch_by_dbID(21723)->translation;
my $dbes = $translation->get_all_DBEntries();
my $all_count = @$dbes;
-$go_count = grep {$_->isa('Bio::EnsEMBL::GoXref')} @$dbes;
+$go_count = grep {$_->isa('Bio::EnsEMBL::OntologyXref')} @$dbes;
my $id_count = grep {$_->isa('Bio::EnsEMBL::IdentityXref')} @$dbes;
my $all_total = count_rows($db, 'object_xref');
-my $go_total = count_rows($db, 'go_xref');
+my $go_total = count_rows($db, 'ontology_xref');
my $id_total = count_rows($db, 'identity_xref');
print_dbEntries($dbes);
@@ -337,10 +337,10 @@ foreach my $dbe (@$dbes) {
# make sure the appropriate rows were deleted
ok($all_total - $all_count == count_rows($db, 'object_xref'));
-ok($go_total - $go_count == count_rows($db, 'go_xref'));
+ok($go_total - $go_count == count_rows($db, 'ontology_xref'));
ok($id_total - $id_count == count_rows($db, 'identity_xref'));
-$multi->restore('core', 'object_xref', 'identity_xref', 'go_xref');
+$multi->restore('core', 'object_xref', 'identity_xref', 'ontology_xref');
# new type checks
@@ -422,7 +422,7 @@ sub print_dbEntries {
foreach my $dbe (@$dbes) {
if($dbe->isa('Bio::EnsEMBL::IdentityXref')) {
debug("IDXref");
- } elsif($dbe->isa('Bio::EnsEMBL::GoXref')) {
+ } elsif($dbe->isa('Bio::EnsEMBL::OntologyXref')) {
debug("GOXref");
} elsif($dbe->isa('Bio::EnsEMBL::DBEntry')) {
debug("DBEntry");
diff --git a/modules/t/gene.t b/modules/t/gene.t
index 0baade2d6b..3566231d2a 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -511,7 +511,7 @@ $multi->save( "core", "gene", "gene_stable_id",
"transcript", "transcript_stable_id",
"translation", "translation_stable_id", "protein_feature",
"exon", "exon_stable_id", "exon_transcript", "supporting_feature",
- "object_xref", "go_xref", "identity_xref",
+ "object_xref", "ontology_xref", "identity_xref",
"dna_align_feature", "protein_align_feature");
$gene = $ga->fetch_by_stable_id( "ENSG00000171456" );
diff --git a/modules/t/transcript.t b/modules/t/transcript.t
index 05c9a5d48b..43de3cdfbc 100644
--- a/modules/t/transcript.t
+++ b/modules/t/transcript.t
@@ -325,7 +325,7 @@ $multi->save("core", "transcript", "transcript_stable_id", "translation",
"translation_stable_id", "protein_feature", "exon",
"exon_stable_id", "exon_transcript", "object_xref",
"supporting_feature", "dna_align_feature","protein_align_feature",
- "go_xref", "identity_xref");
+ "ontology_xref", "identity_xref");
$ta->remove($tr);
diff --git a/modules/t/translation.t b/modules/t/translation.t
index 9c6696dfd0..9525aa43d2 100644
--- a/modules/t/translation.t
+++ b/modules/t/translation.t
@@ -156,7 +156,7 @@ ok(length($seq) == $translation->length());
$multi->save('core', 'translation', 'translation_stable_id',
'protein_feature', 'object_xref', 'identity_xref',
- 'go_xref');
+ 'ontology_xref');
my $tl_count = count_rows($db, 'translation');
my $tlstable_count = count_rows($db, 'translation_stable_id');
--
GitLab