Modified in line with bringing slices on-line: specfically related to

adding and debugging the get_all_Genes method on Slice.pm

modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm

@@ -181,10 +181,10 @@ sub _exon_from_sth {
     $exon->dbID($hashRef->{'exon_id'});
     # make first component exon
     my $component = $self->_new_Exon_from_hashRef($hashRef);
-
+    
     $exon->add_component_Exon($component);
     $sticky_length += $component->length;
-    $sticky_str    .= $component->seq->seq;
+    $sticky_str    .= $component->seq;
 
     $exon->phase($component->phase);
     $exon->adaptor($self);
@@ -195,7 +195,7 @@ sub _exon_from_sth {
 
       $exon->add_component_Exon($component);
       $sticky_length += $component->length;
-      $sticky_str     = $component->seq->seq . $sticky_str;
+      $sticky_str     = $component->seq . $sticky_str;
 
       if( $component->sticky_rank == 1 ) {
 	$exon->contig( $component->contig );

modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

@@ -245,7 +245,6 @@ sub fetch_by_contig_list{
    $str =~ s/\,$//g;
    $str = "($str)";
 
-
    # 
    # this is non-optimised, because we are going to make multiple
    # trips to the database. should fix here
@@ -292,18 +291,30 @@ sub fetch_by_Slice {
   my @cids = $mapper->list_contig_ids( $slice->chr_name(),
 				       $slice->chr_start(),
 				       $slice->chr_end());
-  
+
+  # no genes found so return
+  if ( scalar (@cids) == 0 ) {
+    return undef;
+  }
+
   my $str = "(".join( ",",@cids ).")";
 
-  my $sth = $self->prepare("select distinct(t.gene_id) from transcript t,exon_transcript et,exon e where e.contig_id in $str and et.exon_id = e.exon_id and et.transcript_id = t.transcript_id");
+  my $sth = $self->prepare("
+     SELECT distinct(t.gene_id) 
+     FROM   transcript t,exon_transcript et,exon e 
+     WHERE  e.contig_id in $str 
+     AND    et.exon_id = e.exon_id 
+     AND    et.transcript_id = t.transcript_id");
+
   $sth->execute;
   
-  while( my $arref = $sth->fetchrow_arrayref() ) {
-    my $gene = $self->fetch_by_dbID( $$arref );
-    my $newgene = $gene->transform( $slice );
-    
+  while( my ($geneid) = $sth->fetchrow ) {
+    my $gene = $self->fetch_by_dbID( $geneid );
+    my $newgene = $gene->transform( $slice );    
     push( @out, $newgene );
   }
+
+  return @out;
 }
 
 

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -86,8 +86,7 @@ sub fetch_by_contig_id_start_end_strand {
     $sth = $self->prepare( "SELECT c.length, SUBSTRING( d.sequence, $start, $length )
                             FROM dna d, contig c 
                             WHERE d.dna_id = c.dna_id 
-                            AND c.contig_id = $contig_id" );
-    
+                            AND c.contig_id = $contig_id" );    
   }
 
   $sth->execute();
@@ -129,6 +128,8 @@ sub fetch_by_contig_id_start_end_strand {
 sub fetch_by_Slice_start_end_strand {
    my ( $self, $slice, $start, $end, $strand ) = @_;
 
+   my $seq= "";
+
    if( !$slice ){
      $self->throw("need a slice to work\n");
    }
@@ -145,7 +146,7 @@ sub fetch_by_Slice_start_end_strand {
    # need to check the strand'edness of the slice as this
    # affects the direction in which the dna seq is grabbed
    if ( $slice->strand == 1 ) {
-     $self->fetch_by_assembly_location
+     $seq = $self->fetch_by_assembly_location
        (
 	$slice->chr_start()+$start-1,
 	$slice->chr_start()+$end-1,
@@ -155,7 +156,7 @@ sub fetch_by_Slice_start_end_strand {
        );
    }
    elsif ( $slice->strand == -1 ) {
-     $self->fetch_by_assembly_location
+     $seq = $self->fetch_by_assembly_location
        (
 	$slice->chr_end()-$end+1,
 	$slice->chr_end()-$start+1,
@@ -167,6 +168,7 @@ sub fetch_by_Slice_start_end_strand {
    else {
      $self->throw("Incorrect strand set on slice $slice");
    }
+   return $seq;
 }