Convert stray tabs to spaces

modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm

@@ -136,8 +136,8 @@ sub fetch_all_by_external_name {
   my $entry_adaptor = $self->db->get_DBEntryAdaptor();
 
   my @ids = $entry_adaptor->list_rnaproduct_ids_by_extids($external_name,
-							  $external_db_name,
-							  $override);
+                                                          $external_db_name,
+                                                          $override);
 
   my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
 
@@ -468,12 +468,12 @@ sub _fetch_direct_query {
 
   my $sql =
     sprintf("SELECT rp.rnaproduct_id, pt.code, rp.transcript_id, "
-	    . "rp.seq_start, rp.start_exon_id, rp.seq_end, rp.end_exon_id, "
+            . "rp.seq_start, rp.start_exon_id, rp.seq_end, rp.end_exon_id, "
             . "rp.stable_id, rp.version, %s, %s "
-	    . "FROM rnaproduct rp JOIN rnaproduct_type pt "
+            . "FROM rnaproduct rp JOIN rnaproduct_type pt "
             . "ON rp.rnaproduct_type_id = pt.rnaproduct_type_id "
-	    . "WHERE %s = ?",
-	    $rp_created_date, $rp_modified_date, $where_args->[0]);
+            . "WHERE %s = ?",
+            $rp_created_date, $rp_modified_date, $where_args->[0]);
   my $sth = $self->prepare($sql);
   $sth->bind_param(1, $where_args->[1], $where_args->[2]);
   $sth->execute();
@@ -501,7 +501,7 @@ sub _obj_from_sth {
   my $transcript_adaptor = $self->db()->get_TranscriptAdaptor();
   while (my $row_ref = shift @{$sql_data}) {
     my ($rnaproduct_id, $type_code, $transcript_id, $seq_start, $start_exon_id,
-	$seq_end, $end_exon_id, $stable_id, $version, $created_date,
+        $seq_end, $end_exon_id, $stable_id, $version, $created_date,
         $modified_date) = @{$row_ref};
 
     if (!defined($rnaproduct_id)) {

modules/Bio/EnsEMBL/MicroRNA.pm

@@ -134,8 +134,8 @@ sub arm {
     my $n_arms = scalar @{$arm_attrs};
     if ($n_arms > 0) {
       if ($n_arms > 1) {
-	throw("MicroRNA " . $self->display_id() .
-	      " has multiple arm attributes");
+        throw("MicroRNA " . $self->display_id() .
+              " has multiple arm attributes");
       }
       $self->{'arm'} = $arm_attrs->[0]->value();
     }

modules/Bio/EnsEMBL/RNAProduct.pm

@@ -110,7 +110,7 @@ sub new { ## no critic (Subroutines::RequireArgUnpacking)
 
   my ($seq_start, $seq_end, $start_exon, $end_exon, $stable_id, $version, $dbID,
       $adaptor, $seq, $created_date, $modified_date ) =
-	rearrange(["SEQ_START", "SEQ_END", "START_EXON", "END_EXON",
+        rearrange(["SEQ_START", "SEQ_END", "START_EXON", "END_EXON",
                    "STABLE_ID", "VERSION", "DBID", "ADAPTOR", "SEQ",
                    "CREATED_DATE", "MODIFIED_DATE"], @_);
 
@@ -356,10 +356,10 @@ sub genomic_end {
 
     if ($transcript->strand() >= 0) {
       $self->{'genomic_end'} =
-	$transcript->start() + ($self->end() - 1);
+        $transcript->start() + ($self->end() - 1);
     } else {
       $self->{'genomic_end'} =
-	$transcript->end() - ($self->start() - 1);
+        $transcript->end() - ($self->start() - 1);
     }
   }
 
@@ -388,10 +388,10 @@ sub genomic_start {
 
     if ($transcript->strand() >= 0) {
       $self->{'genomic_start'} =
-	$transcript->start() + ($self->start() - 1);
+        $transcript->start() + ($self->start() - 1);
     } else {
       $self->{'genomic_start'} =
-	$transcript->end() - ($self->end() - 1);
+        $transcript->end() - ($self->end() - 1);
     }
   }
 
@@ -733,10 +733,10 @@ sub stable_id_version {
     my $vindex = rindex($stable_id, '.');
     ($self->{stable_id},
      $self->{version}) = ($vindex > 0 ?
-			  (substr($stable_id, 0, $vindex),
-			   substr($stable_id, $vindex + 1)) :
-			  $stable_id, undef
-			 );
+                          (substr($stable_id, 0, $vindex),
+                           substr($stable_id, $vindex + 1)) :
+                          $stable_id, undef
+                         );
   }
 
   return $self->{stable_id} . ($self->{version} ? ".$self->{version}" : '');

modules/t/rnaProduct.t

@@ -57,12 +57,12 @@ subtest 'RNAProductTypeMapper tests' => sub {
   is($rpt_mapper->type_code_to_class('miRNA'), 'Bio::EnsEMBL::MicroRNA',
      'Can map existing type ID to class');
   dies_ok(sub { $rpt_mapper->type_code_to_class('semprini'); },
-	  'Exception thrown on unknown type ID');
+          'Exception thrown on unknown type ID');
 
   is($rpt_mapper->class_to_type_code('Bio::EnsEMBL::RNAProduct'), 'generic',
      'Can map existing class to type ID');
   dies_ok(sub { $rpt_mapper->class_to_type_code('Bio::EnsEMBL::Storable'); },
-	  'Exception thrown on unknown rnaproduct class name');
+          'Exception thrown on unknown rnaproduct class name');
 };
 
 
@@ -327,7 +327,7 @@ subtest 'Attribute functionality' => sub {
   is(scalar @{ $rp_nonsense }, 0, 'Get empty attribute list for nonsense code');
 
   dies_ok(sub { $rp->add_Attributes({}) },
-	  'add_Attributes() dies on invalid argument type');
+          'add_Attributes() dies on invalid argument type');
 
   my $n_attrs_before = scalar @{ $rp_all_attrs };
   my $extra_attr1 = Bio::EnsEMBL::Attribute->new(
@@ -354,7 +354,7 @@ subtest 'xref functionality' => sub {
   cmp_ok(scalar @{ $xrefs }, '>', 0, 'Got a non-empty list of DBEntries');
 
   dies_ok(sub { $rp->add_DBEntry({}) },
-	  'add_DBEntry() dies on invalid argument type');
+          'add_DBEntry() dies on invalid argument type');
 
   my $n_xrefs_before = scalar @{ $xrefs };
   my $dbe = Bio::EnsEMBL::DBEntry->new(