Added commandline arguments for connecting ensembl_production db

misc-scripts/density_feature/variation_density.pl

@@ -13,6 +13,10 @@ my $max_slices = 100;
 my $bin_count  = 150;
 
 my ($host, $user, $pass, $port, $species);
+# Master database location:
+my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
+my ( $muser, $mpass ) = ( 'ensro',        undef );
+my $mdbname = 'ensembl_production';
 
 my ($block_count, $genome_size, $block_size );
 
@@ -20,6 +24,9 @@ GetOptions( "host|h=s",     \$host,
 	    "user|u=s",     \$user,
 	    "pass|p=s",     \$pass,
 	    "port=i",       \$port,
+	    "mhost=s", \$mhost,
+	    "mport=i", \$mport,
+	    "muser=s", \$muser,
 	    "species|s=s",  \$species );
 
 
@@ -56,11 +63,6 @@ my $analysis = $analysis_adaptor->fetch_by_logic_name('snpdensity');
 
 if ( !defined($analysis) ) {
 
-   # Master database location:
-   my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
-   my ( $muser, $mpass ) = ( 'ensro',        undef );
-   my $mdbname = 'ensembl_production';
-
    my $prod_dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
                      $mhost, $mport, $mdbname );
    my $prod_dbh = DBI->connect( $prod_dsn, $muser, $mpass,
@@ -196,6 +198,7 @@ Usage:
 
   $0 -h host [-port port] -u user -p password \\
   $indent -s species \\
+  $indent [-mhost ensembl_production host] [-mport ensembl_production host] [-muser ensembl_production host] \\
   $indent [-help]  \\
 
   -h|host             Database host to connect to
@@ -208,6 +211,12 @@ Usage:
 
   -s|species          Species name
 
+  -mhost              ensembl_production database host to connect to
+
+  -mport              ensembl_production database port to connect to
+
+  -muser              ensembl_production database username
+
   -help               This message