Added some sanity checks to ChromosomeAdaptor, Fixed some more bugs in...

Added some sanity checks to ChromosomeAdaptor, Fixed some more bugs in SliceAdaptor in which chromosome id was being used as chromosome name

modules/Bio/EnsEMBL/DBSQL/ChromosomeAdaptor.pm

@@ -69,6 +69,10 @@ sub fetch_by_dbID {
 
   my $chr = (); 
 
+  unless(defined $id) {
+    $self->throw("Chromosome dbID argument required\n");
+  }
+
   unless(defined $self->{'_chr_cache'} ) {
     $self->{'_chr_cache'} = {};
   }
@@ -129,6 +133,11 @@ sub fetch_by_chr_name{
 
    #Convert the name to the dbID
    my $dbID = $self->get_dbID_by_chr_name($chr_name);
+
+   unless(defined $dbID) {
+     $self->warn("chromosome with name $chr_name not in database");
+     return undef;
+   } 
    
    return $self->fetch_by_dbID($dbID);
 }
@@ -202,7 +211,6 @@ sub get_landmark_MarkerFeatures_old{
                        AND    sgp.chr_name='$chr_name'";
    
    $statement =~ s/\s+/ /g;
-   #print STDERR "Doing Query ... $statement\n";
    
    my $sth = $self->prepare($statement);
    $sth->execute;
@@ -262,7 +270,6 @@ sub get_landmark_MarkerFeatures{
 		";
    
    $statement =~ s/\s+/ /g;
-   #print STDERR "Doing Query ... $statement\n";
    
    my $sth = $self->prepare($statement);
    $sth->execute;

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -76,11 +76,19 @@ use Bio::EnsEMBL::DBSQL::DBAdaptor;
 sub fetch_by_chr_start_end {
     my ($self,$chr,$start,$end) = @_;
 
-    if( !defined $end ) {   # Why defined?  Is '0' a valid end?
-        $self->throw("must provide chr, start and end");
+    unless($chr) {
+      $self->throw("chromosome name argument must be defined and not ''");
     }
 
-    if( $start > $end ) {
+    unless(defined $end) {   # Why defined?  Is '0' a valid end?
+      $self->throw("end argument must be defined\n");
+    }
+
+    unless(defined $start) {
+      $self->throw("start argument must be defined\n");
+    }
+
+    if($start > $end) {
       $self->throw("start must be less than end: parameters $chr:$start:$end");
     }
     
@@ -147,10 +155,11 @@ sub fetch_by_fpc_name {
     my $type = $self->db->assembly_type();
 
     my $sth = $self->db->prepare("
-        SELECT chromosome_id, superctg_ori, MIN(chr_start), MAX(chr_end)
-        FROM assembly
+        SELECT chr.name, a.superctg_ori, MIN(a.chr_start), MAX(a.chr_end)
+        FROM assembly a, chromosome chr
         WHERE superctg_name = '$fpc_name'
         AND type = '$type'
+        AND chr.chromosome_id = a.chromosome_id
         GROUP by superctg_name
         ");
 
@@ -193,14 +202,16 @@ sub fetch_by_clone_accession{
    my $sth = $self->db->prepare("SELECT  c.name,
                         a.chr_start,
                         a.chr_end,
-                        a.chromosome_id 
+                        chr.name 
                     FROM    assembly a, 
                         contig c, 
-                        clone  cl
+                        clone  cl,
+                        chromosome chr
                     WHERE c.clone_id = cl.clone_id
                     AND cl.name = '$clone'  
                     AND c.contig_id = a.contig_id 
-                    AND a.type = '$type' 
+                    AND a.type = '$type'
+                    AND chr.chromosome_id = a.chromosome_id
                     ORDER BY a.chr_start"
                     );
    $sth->execute();
@@ -399,11 +410,12 @@ sub _get_chr_start_end_of_contig {
    my $sth = $self->db->prepare("SELECT  c.name,
                         a.chr_start,
                         a.chr_end,
-                        a.chromosome_id 
-                    FROM assembly a, contig c 
+                        chr.name 
+                    FROM assembly a, contig c, chromosome chr 
                     WHERE c.name = '$contigid' 
                     AND c.contig_id = a.contig_id 
-                    AND a.type = '$type'"
+                    AND a.type = '$type'
+                    AND chr.chromosome_id = a.chromosome_id"
                     );
    $sth->execute();
    my ($contig,$start,$end,$chr_name) = $sth->fetchrow_array;
@@ -438,21 +450,21 @@ sub _get_chr_start_end_of_gene {
                     (a.chr_start+a.contig_end-e.contig_end)),
    if(a.contig_ori=1,(e.contig_end-a.contig_start+a.chr_start),
                     (a.chr_start+a.contig_end-e.contig_start)),
-     c.name
+     chr.name
   
                     FROM    exon e,
                         transcript tr,
                         exon_transcript et,
                         assembly a,
                         gene_stable_id gsi,
-                        chromosome c
+                        chromosome chr
                     WHERE e.exon_id=et.exon_id 
                     AND et.transcript_id =tr.transcript_id 
                     AND a.contig_id=e.contig_id 
                     AND a.type = '$type' 
                     AND tr.gene_id = gsi.gene_id
                     AND gsi.stable_id = '$geneid'
-                    AND a.chromosome_id = c.chromosome_id" 
+                    AND a.chromosome_id = chr.chromosome_id" 
                     );
    $sth->execute();