add fetch_attributes only

modules/Bio/EnsEMBL/Lite/SNPAdaptor.pm

@@ -84,7 +84,10 @@ sub fetch_all_by_Slice {
     }
 
     #create a snp object through a fast (hacky) constructor
-    my $snp = Bio::EnsEMBL::SNP->new_fast(
+    my $STATUS = $arrayref->[6];
+    $STATUS =~s/-/ /;
+    $STATUS = ( $STATUS && $STATUS ne 'no info' ) ? "proven $STATUS" : 'suspected';
+	my $snp = Bio::EnsEMBL::SNP->new_fast(
 		  { 'dbID'       => $arrayref->[0], 
 		   '_gsf_start'  => $arrayref->[1] - $slice_start + 1,
 		    '_gsf_end'    => $arrayref->[2] - $slice_start + 1,
@@ -93,11 +96,13 @@ sub fetch_all_by_Slice {
 		    '_type'       => $arrayref->[4],
                     '_range_type' => $arrayref->[5],
                     '_validated'  => $arrayref->[6],
-                    'alleles'    => $arrayref->[7],
+                    'status'     => $STATUS,
+					'alleles'    => $arrayref->[7],
                     '_ambiguity_code' => $arrayref->[10],
                     '_snpclass'   => $arrayref->[8],
                     '_mapweight'  => $arrayref->[9],
-		    '_source_tag' => $arrayref->[11],
+		    '_source' => $arrayref->[11],
+			'_source_tag' => $arrayref->[11],
 		    'link'        => \@links });
     push @snps, $snp;
   }
@@ -105,5 +110,63 @@ sub fetch_all_by_Slice {
   return \@snps;
 }
 
+sub fetch_attributes_only{
+  my $self = shift;
+
+  my $refsnp_id = shift;
+  my $source = shift || 'dbSNP';
+
+  my $WHERE = $source eq 'dbSNP' ? "id_refsnp = ? and source='dbSNP'" : "id_ano=? and source='non-dbSNP'";
+  my %SNPS = qw( 12 dbSNP 13 WI 14 HGBASE 15 TSC-CSHL 16 ANO );
+  my $QUERY = "select internal_id, chr_start, chr_end, chr_strand, type, range_type,
+                      validated, alleles, snpclass, mapweight, ambiguity, source,
+                      id_refsnp, id_wi, id_hgbase, id_tsc, id_ano, chr_name
+                 FROM snp
+                WHERE $WHERE";
+
+  my $sth = $self->prepare( $QUERY );
+  eval { $sth->execute($refsnp_id);};
+  return [] if $@;
+  my @snps = ();
+
+  my %link_hash;
+  my $link;
+
+  while(my $arrayref = $sth->fetchrow_arrayref()) {
+    my @links = ();
+    foreach( sort keys %SNPS ) {
+       my $V = $arrayref->[ $_ ];
+       if( $V && $V ne '' ) {
+         unless($link = $link_hash{"$SNPS{$_}:$V"}) {
+           $link_hash{"$SNPS{$_}:$V"} = $link = Bio::EnsEMBL::DBEntry->new_fast( {'_dbname'     => $SNPS{$_}, '_primary_id' => $V });
+         }
+         push @links, $link;
+       }
+    }
+
+    #create a snp object through a fast (hacky) constructor
+    my $STATUS = $arrayref->[6];
+    $STATUS =~s/-/ /;
+    $STATUS = ( $STATUS && $STATUS ne 'no info' ) ? "proven $STATUS" : 'suspected';
+    my $snp = Bio::EnsEMBL::SNP->new_fast(
+                  { 'dbID'       => $arrayref->[0],
+                    '_snp_strand' => $arrayref->[3],
+                    '_gsf_score'  => 1,
+                    '_type'       => $arrayref->[4],
+                    '_range_type' => $arrayref->[5],
+                    '_validated'  => $arrayref->[6],
+                    'status'     => $STATUS,
+                    'alleles'    => $arrayref->[7],
+                    '_ambiguity_code' => $arrayref->[10],
+                    '_snpclass'   => $arrayref->[8],
+                    '_mapweight'  => $arrayref->[9],
+                    '_source' => $arrayref->[11],
+                    '_source_tag' => $arrayref->[11],
+                    'link'        => \@links });
+    return $snp;
+  }
+  return undef;
+}
+
 1;