nt_contigs as slices supported

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -163,36 +163,80 @@ sub fetch_by_contig_name {
 
 sub fetch_by_fpc_name {
     my ($self,$fpc_name) = @_;
+    
+    my( $p, $f, $l ) = caller; 
+    $self->warn( "$f:$l calls deprecated method fetch_by_fpc_name. Please use fetch_by_supercontig_name instead" );
 
-    my $type = $self->db->assembly_type();
+    $self->fetch_by_supercontig_name( $fpc_name ); 
+}
 
-    my $sth = $self->db->prepare("
+sub fetch_by_supercontig_name {
+  my ($self,$supercontig_name) = @_;
+  
+  my $assembly_type = $self->db->assembly_type();
+  
+  my $sth = $self->db->prepare("
         SELECT chr.name, a.superctg_ori, MIN(a.chr_start), MAX(a.chr_end)
         FROM assembly a, chromosome chr
-        WHERE superctg_name = '$fpc_name'
-        AND type = '$type'
+        WHERE superctg_name = ?
+        AND type = ?
         AND chr.chromosome_id = a.chromosome_id
         GROUP by superctg_name
         ");
 
-    $sth->execute;
+  $sth->execute( $supercontig_name, $assembly_type );
+  
+  my ($chr, $strand, $slice_start, $slice_end) = $sth->fetchrow_array;
+  
+  my $slice;
+  
+  $slice = new Bio::EnsEMBL::Slice
+    (
+     -chr_name => $chr,
+     -chr_start =>$slice_start,
+     -chr_end => $slice_end,
+     -strand => $strand,
+     -assembly_type => $assembly_type
+    );
+  
+  return $slice;
+}
 
-    my ($chr, $strand, $slice_start, $slice_end) = $sth->fetchrow_array;
 
-    my $slice;
+=head2 list_overlapping_supercontigs
 
-    $slice = new Bio::EnsEMBL::Slice
-      (
-       -chr_name => $chr,
-       -chr_start =>$slice_start,
-       -chr_end => $slice_end,
-       -strand => $strand,
-       -assembly_type => $type
-      );
+  Arg [1]    : Bio::EnsEMBL::Slice $slice
+               overlapping given Sice
+  Example    : 
+  Description: return the names of the supercontigs that overlap given Slice.  
+  Returntype : listref string
+  Exceptions : none
+  Caller     : general
+
+=cut
 
-    return $slice;
-}
 
+sub list_overlapping_supercontigs {
+   my ($self,$slice) = @_;
+   my $sth = $self->db->prepare( "
+      SELECT DISTINCT superctg_name
+        FROM assembly a, chromosome c
+       WHERE c.chromosome_id = a.chromosome_id 
+         AND c.name = ?
+         AND a.type = ?
+         AND a.chr_end >= ?
+         AND a.chr_start <= ?
+       " );
+   $sth->execute( $slice->chr_name(), $slice->assembly_type(),
+		  $slice->chr_start(), $slice->chr_end() );
+
+   my $result = [];
+   while( my $aref = $sth->fetchrow_arrayref() ) {
+     push( @$result, $aref->[0] );
+   }
+
+   return $result;
+}
 
 
 =head2 fetch_by_clone_accession

modules/Bio/EnsEMBL/Slice.pm

@@ -192,7 +192,7 @@ sub dbID {
 
 =head2 name
 
-  Arg [1]    : none
+  Arg [1]    : optional string $name
   Example    : $name = $slice->name();
   Description: Returns the name of this slice. The name is formatted as a 
                the following string: "$chr_name.$chr_start-$chr_end". 
@@ -201,6 +201,7 @@ sub dbID {
                can also act as a hash value. This is similar to the name 
                method in RawContig so for exons which can have either type 
                of sequence attached it provides a more common interface.
+               You can as well set the slicename to something like "NT_110023" 
   Returntype : string
   Exceptions : none
   Caller     : general
@@ -208,18 +209,63 @@ sub dbID {
 =cut
 
 sub name {
-  my $self = shift;
+  my ( $self, $arg )  = @_;
+  
+  if( defined $arg ) {
+    $self->{name} = $arg;
+  } elsif(!defined $self->{name}) {
 
-  my $string = join '', $self->chr_name, '.', 
-                        $self->chr_start, '-', $self->chr_end();
+    my $string = join '', $self->chr_name, '.', 
+    $self->chr_start, '-', $self->chr_end();
 
-  if($self->strand == -1) {
-    return "reverse($string)";
+  
+    if($self->strand == -1) {
+      $self->{name} = "reverse($string)";
+    } else {
+      $self->{name} = $string;
+    }
   }
 
-  return $string;
+  return $self->{name};
 }
 
+=head2 get_all_supercontig_Slices
+
+  Arg [1]    : none
+  Example    : none
+  Description: Returns Slices that represent overlapping supercontigs.
+               Coordinates inside those slices are supercontig coordinates.
+               You can transfer features to this slices coordinate system with
+               the normal transform call. The returned slices hav their names
+               set to the supercontig names.
+  Returntype : listref Bio::EnsEMBL::Slice
+  Exceptions : none
+  Caller     : none
+
+=cut
+
+
+sub get_all_supercontig_Slices {
+  my $self = shift;
+  my $result = [];
+
+  if( $self->adaptor() ) {
+    my $superctg_names = $self->adaptor()->list_overlapping_supercontigs( $self );
+    
+    for my $name ( @$superctg_names ) {
+      my $slice;
+      $slice = $self->adaptor()->fetch_by_supercontig_name( $name );
+      $slice->name( $name );
+      push( @$result, $slice );
+    }
+  } else {
+    $self->warn( "Slice needs to be attached to a database to get supercontigs" );
+  }
+
+  return $result;
+}
+
+    
 
 
 

modules/t/slice.t

@@ -5,13 +5,15 @@ use lib 't';
 
 BEGIN { $| = 1;  
 	use Test;
-	plan tests => 46;
+	plan tests => 48;
 }
 
+use TestUtils qw( debug );
 
 use MultiTestDB;
 use Bio::EnsEMBL::Slice;
 
+our $verbose= 0;
 
 #
 #1 TEST - Slice Compiles
@@ -270,6 +272,16 @@ $softmasked_seq = $seq = undef;
 ok(scalar @{$slice->get_tiling_path});
 
 
+my $super_slices = $slice->get_all_supercontig_Slices();
 
 
+#
+# 47-48 get_all_supercontig_Slices()
+#
+debug( "Supercontig starts at ".$super_slices->[0]->chr_start() );
+
+ok( $super_slices->[0]->chr_start() == 29591966 );
+
+debug( "Supercontig name ".$super_slices->[0]->name() );
 
+ok( $super_slices->[0]->name() eq "NT_028392" );

modules/t/sliceAdaptor.t

@@ -5,12 +5,14 @@ use warnings;
 
 BEGIN { $| = 1;  
 	use Test;
-	plan tests => 26;
+	plan tests => 27;
 }
 
 use MultiTestDB;
 use Bio::EnsEMBL::DBSQL::SliceAdaptor;
-use TestUtils qw(test_getter_setter);
+use TestUtils qw(test_getter_setter debug);
+
+our $verbose = 1;
 
 my ($CHR, $START, $END, $FLANKING) = ("20", 30_252_000, 31_252_001, 1000);
 
@@ -68,10 +70,12 @@ ok($new_slice->chr_end   == $slice->chr_end   + $FLANKING);
 # 12-13 fetch_by_fpc_name
 #
 my $fpc_name = 'NT_011387';
-$slice = $slice_adaptor->fetch_by_fpc_name($fpc_name);
+$slice = $slice_adaptor->fetch_by_supercontig_name($fpc_name);
 ok($new_slice->chr_start);
 ok($new_slice->chr_end);
 
+
+
 #
 # 14 - 15 fetch_by_clone_accession
 #
@@ -145,4 +149,12 @@ my $chromo = $db->get_ChromosomeAdaptor->fetch_by_chr_name($CHR);
 ok($chromo->length eq $slice->chr_end);
 
 
+$slice = $slice_adaptor->fetch_by_chr_start_end("20", 29_252_000, 31_252_001 );
+my $name_list = $slice_adaptor->list_overlapping_supercontigs( $slice );
+
+for my $name ( @$name_list ) {
+  debug( "Overlapping supercontig ".$name );
+}
+
+ok( $name_list->[0] eq "NT_028392" );