From 351f862acb58105bbc3027123100ab201b7e2378 Mon Sep 17 00:00:00 2001
From: Arne Stabenau <stabenau@sanger.ac.uk>
Date: Tue, 19 Nov 2002 11:52:43 +0000
Subject: [PATCH] all genes were known bug fixed
---
modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm | 8 +++++--
modules/Bio/EnsEMBL/Gene.pm | 17 +++++++++------
modules/t/gene.t | 24 +++++++++++++++------
3 files changed, 33 insertions(+), 16 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
index aa35ed4cfe..79104cd74d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm
@@ -442,7 +442,7 @@ sub _fetch_by_object_type {
my $sth = $self->prepare("
SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
xref.description,
- exDB.db_name, exDB.release,
+ exDB.db_name, exDB.release, exDB.status,
oxr.object_xref_id,
es.synonym,
idt.query_identity, idt.target_identity
@@ -462,7 +462,7 @@ sub _fetch_by_object_type {
while ( my $arrRef = $sth->fetchrow_arrayref() ) {
my ( $refID, $dbprimaryId, $displayid, $version,
- $desc, $dbname, $release, $objid,
+ $desc, $dbname, $release, $exDB_status, $objid,
$synonym, $queryid, $targetid ) = @$arrRef;
my $exDB;
@@ -502,6 +502,10 @@ sub _fetch_by_object_type {
$exDB->description( $desc );
}
+ if( $exDB_status ) {
+ $exDB->status( $exDB_status );
+ }
+
push( @out, $exDB );
} # if (!$seen{$refID})
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index 4189d8ba69..b8076380ca 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -288,15 +288,18 @@ sub source {
sub is_known{
my ($self) = @_;
- my @array;
- @array = $self->get_all_DBLinks();
- if( scalar(@array) > 0 ) {
- return 1;
+
+ for my $entry ( @{$self->get_all_DBLinks()} ) {
+ if( $entry->status eq "KNOWN" ) {
+ return 1;
+ }
}
+
foreach my $trans ( @{$self->get_all_Transcripts} ) {
- @array = $trans->get_all_DBLinks();
- if( scalar(@array) > 0 ) {
- return 1;
+ for my $entry ( @{$trans->get_all_DBLinks()} ) {
+ if( $entry->status eq "KNOWN" ) {
+ return 1;
+ }
}
}
diff --git a/modules/t/gene.t b/modules/t/gene.t
index fab85816d7..c1beace343 100644
--- a/modules/t/gene.t
+++ b/modules/t/gene.t
@@ -4,10 +4,12 @@ use warnings;
BEGIN { $| = 1;
use Test;
- plan tests => 22;
+ plan tests => 23;
}
use MultiTestDB;
+use TestUtils qw ( debug );
+
use Bio::EnsEMBL::Gene;
# switch on the debug prints
@@ -189,7 +191,7 @@ foreach my $trans( @{$gene_out->get_all_Transcripts()} ){
my $pep = $trans->translate();
debug( "Peptide: ".$pep->seq() );
- if($pep->seq !~ /\*\./){
+ if($pep->seq !~ /\*./){
$translate = 1;
} else {
$translate = 0;
@@ -211,17 +213,25 @@ debug( "Pep phase 1: $pep2" );
ok( $pep1 ne $pep2 );
-
$multi->restore();
+$slice = $db->get_SliceAdaptor()->fetch_by_chr_start_end("20", 30_252_000, 31_252_001 );
+
+my ( $known, $unknown );
-sub debug {
- my $txt = shift;
- if( $verbose ) {
- print STDERR $txt,"\n";
+my $genes = $slice->get_all_Genes();
+for my $gene ( @$genes ) {
+ if( $gene->is_known() ) {
+ $known++;
+ } else {
+ $unknown++;
}
}
+debug( "known: $known Unknown: $unknown\n" );
+
+ok( $known==17 );
+
--
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