Merge branch 'master' of https://github.com/Ensembl/ensembl

misc-scripts/db/dump_mysql.pl

@@ -361,10 +361,10 @@ sub checksum {
   my @files = sort { $a cmp $b } readdir($dh);
   closedir($dh) or die "Cannot close directory $dir";
 
-  my $checksum = $self->file('CHECKSUMS.gz');
+  my $checksum = $self->file('CHECKSUMS');
   unlink $checksum if -f $checksum;
 
-  my $fh = IO::Compress::Gzip->new($checksum) or croak "Cannot create gzip stream to $checksum: $GzipError";
+  open my $fh, '>', $checksum or croak "Cannot open filehandle to $checksum: $!";
   foreach my $file (@files) {
     next if $file =~ /^\./;         #hidden file or up/current dir
     next if $file =~ /^CHECKSUM/;

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -564,24 +564,13 @@ sub fetch_all_by_Slice_and_external_dbname_link {
 
   foreach my $local_external_db_id (@{$external_db_ids}) {
     my @linked_genes = $dbentry_adaptor->list_gene_ids_by_external_db_id($local_external_db_id);
-    foreach my $gene_id (@linked_genes) {
-      $linked_genes{$gene_id} = 1;
-    }
-  }
-
-  # Get all the genes on the slice.
-  my $genes = $self->SUPER::fetch_all_by_Slice_constraint($slice, 'g.is_current = 1', $logic_name);
-
-  # Create a list of those that are in the gene_ids list.
-  my @genes_passed;
-  foreach my $gene (@$genes) {
-    if (exists($linked_genes{$gene->dbID()})) {
-      push(@genes_passed, $gene);
-    }
+    $linked_genes{$_} = 1 for @linked_genes;
   }
-
-  # Return the list of those that passed.
-  return \@genes_passed;
+  
+  # Get all the genes on the slice and filter by the gene ids list
+  my $genes = $self->fetch_all_by_Slice($slice, $logic_name, $load_transcripts);
+  my $genes_passed = [ grep { exists $linked_genes{$_->dbID()} } @{$genes} ];
+  return $genes_passed;
 } ## end sub fetch_all_by_Slice_and_external_dbname_link
 
 =head2 fetch_all_by_Slice

modules/Bio/EnsEMBL/Feature.pm

@@ -1100,7 +1100,7 @@ sub seq_region_start {
   if ( defined($slice) ) {
 
     return $self->_seq_region_boundary_from_db('start')
-      if $slice->is_circular() and $self->adaptor->dbc;
+      if $slice->is_circular() and $self->adaptor() and $self->adaptor->dbc();
 
     my $start;
     if ( $slice->strand() == 1 ) {
@@ -1142,7 +1142,7 @@ sub seq_region_end {
   if ( defined($slice) ) {
 
     return $self->_seq_region_boundary_from_db('end')
-      if $slice->is_circular() and $self->adaptor->dbc;
+      if $slice->is_circular() and $self->adaptor() and $self->adaptor->dbc();
 
     my $end;
     if ( $slice->strand() == 1 ) {

modules/t/gene.t

@@ -946,4 +946,14 @@ SKIP: {
   dies_ok { $gene->get_all_homologous_Genes(); } 'No Compara DBAdaptor has been configured. No way to retrieve data';
 }
 
+# Fetching by slice and an external DB
+{
+  $ga->clear_cache(); # have to clear the cache because otherwise it gets the wrong values back!
+  my $local_slice = $sa->fetch_by_region("chromosome", "20", 30_249_935, 31_254_640);
+  my $genes = $ga->fetch_all_by_Slice_and_external_dbname_link($local_slice, undef, undef, 'HUGO'); # yes HUGO. Not HGNC. Old data
+  is(scalar(@{$genes}), 13, 'Expect 13 genes with HUGO/HGNC links');
+  # assume this will be the display xref
+  is($_->display_xref()->dbname(), 'HUGO', $_->stable_id().' has a display HUGO') for @{$genes};
+}
+
 done_testing();