Allow for using dbhost, dbport etc. as options, and set default value

for port to '3306'. Some formatting.

misc-scripts/meta_coord/update_meta_coord.pl

@@ -7,6 +7,8 @@ use Getopt::Long;
 my $help = 0;
 my ( $host, $port, $user, $pass, $dbpattern );
 
+$port = '3306';
+
 my $usage = qq(
   $0 --host ens-staging --port 3306 --user ensadmin \\
     --pass XXX --dbpattern core
@@ -37,34 +39,50 @@ table for all the following table names one by one
   transcript
   );
 
-if (scalar @ARGV == 0 ) {
+if ( scalar @ARGV == 0 ) {
   print $usage, "\n";
   exit 0;
 }
 
-GetOptions( 'help'        => \$help,
-            'host=s'      => \$host,
-            'port=i'      => \$port,
-            'user=s'      => \$user,
-            'pass=s'      => \$pass,
-            'dbpattern=s' => \$dbpattern );
-
-if ($help) {
+if ( !GetOptions( 'help!'                  => \$help,
+                  'dbhost|host=s'          => \$host,
+                  'dbport|port=i'          => \$port,
+                  'dbuser|user=s'          => \$user,
+                  'dbpass|password|pass=s' => \$pass,
+                  'dbpattern=s'            => \$dbpattern
+     ) ||
+     $help )
+{
   print $usage, "\n";
-  exit 0;
+  exit;
 }
 
-#print "help: $help argv:"
-  #. scalar(@ARGV)
-  #. "$host $port $user $pass $dbname\n";
-
-my $dsn = "DBI:mysql:host=$host";
-$dsn .= ";port=$port" if ($port);
+my $dsn = "DBI:mysql:host=$host;port=$port";
 
 my $db = DBI->connect( $dsn, $user, $pass );
 
 my @dbnames =
-  map { $_->[0] } @{ $db->selectall_arrayref("show databases") };
+  map { $_->[0] } @{ $db->selectall_arrayref("SHOW DATABASES") };
+
+my @table_names = qw(
+  assembly_exception
+  gene
+  exon
+  density_feature
+  ditag_feature
+  dna_align_feature
+  karyotype
+  marker_feature
+  misc_feature
+  qtl_feature
+  prediction_exon
+  prediction_transcript
+  protein_align_feature
+  repeat_feature
+  simple_feature
+  splicing_event
+  transcript
+);
 
 for my $dbname (@dbnames) {
 
@@ -77,37 +95,16 @@ for my $dbname (@dbnames) {
                                            -pass   => $pass,
                                            -dbname => $dbname );
 
-  my @table_names = qw(
-    assembly_exception
-    gene
-    exon
-    density_feature
-    ditag_feature
-    dna_align_feature
-    karyotype
-    marker_feature
-    misc_feature
-    qtl_feature
-    prediction_exon
-    prediction_transcript
-    protein_align_feature
-    repeat_feature
-    simple_feature
-    splicing_event
-    transcript
-  );
-
-  unless (
-           system(     "mysql -h$host -P$port -u$user -p'$pass' -N "
-                     . "-e 'SELECT * FROM meta_coord' $dbname "
-                     . "> $dbname.meta_coord.backup"
-           ) == 0 )
+  if ( system( "mysql -h$host -P$port -u$user -p'$pass' -N " .
+                 "-e 'SELECT * FROM meta_coord' $dbname " .
+                 "> $dbname.meta_coord.backup" ) )
   {
     print STDERR "Can't dump the original meta_coord for back up\n";
     exit 1;
-  } else {
-    print STDERR "Original meta_coord table backed up in "
-      . "$dbname.meta_coord.backup\n";
+  }
+  else {
+    print STDERR "Original meta_coord table backed up in " .
+      "$dbname.meta_coord.backup\n";
   }
 
   foreach my $table_name (@table_names) {
@@ -118,12 +115,12 @@ for my $dbname (@dbnames) {
     $sth->finish;
 
     $sql =
-        "INSERT INTO meta_coord "
-      . "SELECT '$table_name', s.coord_system_id, "
-      . "MAX( t.seq_region_end - t.seq_region_start + 1 ) "
-      . "FROM $table_name t, seq_region s "
-      . "WHERE t.seq_region_id = s.seq_region_id "
-      . "GROUP BY s.coord_system_id";
+      "INSERT INTO meta_coord " .
+      "SELECT '$table_name', s.coord_system_id, " .
+      "MAX( t.seq_region_end - t.seq_region_start + 1 ) " .
+      "FROM $table_name t, seq_region s " .
+      "WHERE t.seq_region_id = s.seq_region_id " .
+      "GROUP BY s.coord_system_id";
     $sth = $dbc->prepare($sql);
     $sth->execute;
     $sth->finish;