script modified to generate Vega stats and densities

misc-scripts/density_feature/vega_densities_multi_db.pl

+#
+# These script runs all density creation scripts on all
+# databases that match input pattern. It calls all configured
+# scripts of this directory with host, user,pass,port and dbname 
+# parameter.
+#
+use strict;
+use Getopt::Long;
+use DBI;
+
+#
+# configure this hash and command line parameter section for 
+#  adding new scripts
+#
+
+my %density_scripts = 
+  ( "gene"   => "vega_gene_density_calc.pl",
+    "gc"     => "percent_gc_calc.pl", 
+    "repeat" => "repeat_coverage_calc.pl",
+    "stats"  => "vega_seq_region_stats.pl",
+    "snp"    => "snp_lite_density.pl" );
+
+my @density_scripts = ();
+
+my ( $host, $user, $pass, $port, $dbpattern );
+
+GetOptions( "host=s", \$host,
+	    "user=s", \$user,
+	    "pass=s", \$pass,
+	    "port=i", \$port,
+	    "gene", sub { push( @density_scripts, $density_scripts{'gene'} ); },
+	    "gc", sub { push( @density_scripts, $density_scripts{'gc'} ); },
+	    "repeat", sub { push( @density_scripts, $density_scripts{'repeat'} ); },
+	    "stats", sub { push( @density_scripts, $density_scripts{'stats'} ); },
+	    "snp", sub { push( @density_scripts, $density_scripts{'snp'} ); },
+	    "dbpattern=s", \$dbpattern
+	  );
+
+if( !$host || !$user ) {
+  usage();
+}
+
+my $dsn = "DBI:mysql:host=$host";
+my $args = "-host $host ";
+if( $user ) {
+  $args .= "-user $user ";
+}
+
+if( $port ) {
+  $args .= "-port $port ";
+  $dsn .= ";port=$port";
+}
+
+if( $pass ) {
+  $args .= "-pass $pass ";
+}
+
+if( $host ) {
+  $args .= "-host $host ";
+}
+
+
+my $db = DBI->connect( $dsn, $user, $pass );
+
+my @dbnames = map {$_->[0] } @{ $db->selectall_arrayref( "show databases" ) };
+
+for my $dbname ( @dbnames ) {
+  if( $dbpattern ) {
+    if( $dbname !~ /$dbpattern/ ) {
+      next;
+    }
+  } else {
+    print STDERR "$dbname\n";
+    next;
+  }
+
+  if( ! @density_scripts ) {
+    print "Matches $dbname.\n";
+  } else {
+    for my $scriptname ( @density_scripts ) {
+      print( "/usr/local/ensembl/bin/perl $scriptname $args -dbname $dbname\n" );
+      system( "/usr/local/ensembl/bin/perl $scriptname $args -dbname $dbname" );
+    }
+  }
+}
+
+
+sub usage {
+  print STDERR "densities_multi_db.pl runs \n  ";
+  print STDERR <<EOF;
+
+ with parameters -host [hostname] -user [username with write permit] 
+                 -pass [password] -port [portnumber]
+ on all databases that match -dbpattern [some_db_regexp]
+ on -gene, -repeat, -stats, -gc.
+
+ Without -dbpattern it lists all available databases and does nothing.
+
+EOF
+  exit();
+}