db->prepare() => db->dbc()->prepare()

misc-scripts/density_feature/gene_density_calc.pl

@@ -32,7 +32,7 @@ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
 					    -pass => $pass,
 					    -dbname => $dbname);
 
-my $sth = $db->prepare( "select count(*) from gene" );
+my $sth = $db->dbc()->prepare( "select count(*) from gene" );
 $sth->execute();
 
 my ( $gene_count )  = $sth->fetchrow_array();
@@ -48,7 +48,7 @@ if( ! $gene_count ) {
 # Could be database without seq_regions
 #  Then have to try and attach core db
 #
-$sth = $db->prepare( "select count(*)  from seq_region" );
+$sth = $db->dbc()->prepare( "select count(*)  from seq_region" );
 $sth->execute();
 my ( $seq_region_count ) = $sth->fetchrow_array();
 if( ! $seq_region_count ) {

misc-scripts/density_feature/percent_gc_calc.pl

@@ -43,7 +43,7 @@ my $small_blocksize = 500;
 #
 # Check wether the script should run on given database
 #
-my $sth = $db->prepare( "select count(*) from dna" );
+my $sth = $db->dbc->prepare( "select count(*) from dna" );
 $sth->execute();
 my ( $dna_count )  = $sth->fetchrow_array();
 if( ! $dna_count ) {

misc-scripts/density_feature/repeat_coverage_calc.pl

@@ -38,7 +38,7 @@ my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host => $host,
 
 
 
-my $sth = $db->prepare( "select count(*) from repeat_feature" );
+my $sth = $db->dbc()->prepare( "select count(*) from repeat_feature" );
 $sth->execute();
 
 my ( $repeat_count )  = $sth->fetchrow_array();

misc-scripts/density_feature/seq_region_stats.pl

@@ -33,7 +33,7 @@ $genestats = $snpstats = 1 if(!$genestats && !$snpstats);
 my $genes_present;
 
 if($genestats) {
-  my $sth = $db->prepare( "select count(*) from gene" );
+  my $sth = $db->dbc()->prepare( "select count(*) from gene" );
   $sth->execute();
 
   my ( $gene_count )  = $sth->fetchrow_array();
@@ -46,7 +46,7 @@ if($genestats) {
 #
 # and seq_regions
 #
-my $sth = $db->prepare( "select count(*) from seq_region" );
+my $sth = $db->dbc()->prepare( "select count(*) from seq_region" );
 $sth->execute();
 my ( $seq_region_count ) = $sth->fetchrow_array();
 if( ! $seq_region_count ) {
@@ -146,7 +146,7 @@ sub lite_attach {
   #
   # get a lost of all databases on that server
   #
-  my $sth = $db->prepare( "show databases" );
+  my $sth = $db->dbc()->prepare( "show databases" );
   $sth->execute();
   my $all_db_names = $sth->fetchall_arrayref();
   my %all_db_names = map {( $_->[0] , 1)} @$all_db_names;

misc-scripts/density_feature/snp_lite_density.pl

@@ -137,7 +137,7 @@ sub lite_attach {
   #
   # get a lost of all databases on that server
   #
-  my $sth = $db->prepare( "show databases" );
+  my $sth = $db->dbc->prepare( "show databases" );
   $sth->execute();
   my $all_db_names = $sth->fetchall_arrayref();
   my %all_db_names = map {( $_->[0] , 1)} @$all_db_names;