Formatting and slight change to startup logic to be able to see info

about how to run the script.

misc-scripts/meta_coord/update_meta_coord.pl

@@ -5,109 +5,132 @@ use Bio::EnsEMBL::DBSQL::DBConnection;
 use Getopt::Long;
 
 my $help = 0;
-my ($host, $port, $user, $pass, $dbpattern);
-
-my $usage = "\n$0 --host ecs2 --port 3364 --user ensadmin --pass ensembl --dbpattern core
-
-[--help] displays this menu.
-
-This script will dump the current meta_coord table in homo_sapiens_core_27_35a.meta_coord file.
-Then it will update the meta_coord table for all the following table names one by one
-                     assembly_exception
-                     gene
-                     exon
-                     density_feature
-                     ditag
-                     ditag_feature
-                     dna_align_feature
-                     karyotype
-                     marker_feature
-                     misc_feature
-                     qtl_feature
-                     oligo_feature
-                     prediction_exon
-                     prediction_transcript
-                     protein_align_feature
-                     regulatory_feature
-                     regulatory_search_region
-                     repeat_feature
-                     simple_feature
-                     transcript\n";
-
-GetOptions('help'     => \$help,
-           'host=s'   => \$host,
-           'port=i'   => \$port,
-           'user=s'   => \$user,
-           'pass=s'   => \$pass,
-           'dbpattern=s' => \$dbpattern);
-
-#print "help: $help argv:" . scalar(@ARGV) . "$host $port $user $pass $dbname\n";
-
-#if ($help || scalar @ARGV == 0) {
-#  print $usage,"\n";
-#  exit 0;
-#}
+my ( $host, $port, $user, $pass, $dbpattern );
+
+my $usage = qq(
+  $0 --host ens-staging --port 3306 --user ensadmin \\
+    --pass XXX --dbpattern core
+
+  [--help] displays this menu.
+
+This script will dump the current meta_coord table in the latest
+homo_sapiens_core.meta_coord file.  Then it will update the meta_coord
+table for all the following table names one by one
+
+  assembly_exception
+  gene
+  exon
+  density_feature
+  ditag
+  ditag_feature
+  dna_align_feature
+  karyotype
+  marker_feature
+  misc_feature
+  qtl_feature
+  oligo_feature
+  prediction_exon
+  prediction_transcript
+  protein_align_feature
+  regulatory_feature
+  regulatory_search_region
+  repeat_feature
+  simple_feature
+  transcript
+  );
+
+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) {
+  print $usage, "\n";
+  exit 0;
+}
+
+#print "help: $help argv:"
+  #. scalar(@ARGV)
+  #. "$host $port $user $pass $dbname\n";
 
 my $dsn = "DBI:mysql:host=$host";
 $dsn .= ";port=$port" if ($port);
 
 my $db = DBI->connect( $dsn, $user, $pass );
 
-my @dbnames = map {$_->[0] } @{$db->selectall_arrayref("show databases")};
+my @dbnames =
+  map { $_->[0] } @{ $db->selectall_arrayref("show databases") };
 
 for my $dbname (@dbnames) {
 
-  next if ($dbname !~ /$dbpattern/);
-  
-  my $dbc = new Bio::EnsEMBL::DBSQL::DBConnection(-host   => $host,
-                                                -port   => $port,
-                                                -user   => $user,
-                                                -pass   => $pass,
-                                                -dbname => $dbname);
+  next if ( $dbname !~ /$dbpattern/ );
+
+  my $dbc =
+    new Bio::EnsEMBL::DBSQL::DBConnection( -host   => $host,
+                                           -port   => $port,
+                                           -user   => $user,
+                                           -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
-                     oligo_feature
-                     prediction_exon
-                     prediction_transcript
-                     protein_align_feature
-                     regulatory_feature
-                     regulatory_search_region
-                     repeat_feature
-                     simple_feature
-                     transcript
-                    );
-
-  unless (system("mysql -h$host -P$port -u$user -p$pass -N -e 'select * from meta_coord' $dbname > $dbname.meta_coord.backup") ==0) {
+    assembly_exception
+    gene
+    exon
+    density_feature
+    ditag_feature
+    dna_align_feature
+    karyotype
+    marker_feature
+    misc_feature
+    qtl_feature
+    oligo_feature
+    prediction_exon
+    prediction_transcript
+    protein_align_feature
+    regulatory_feature
+    regulatory_search_region
+    repeat_feature
+    simple_feature
+    transcript
+  );
+
+  unless (
+           system(     "mysql -h$host -P$port -u$user -p$pass -N "
+                     . "-e 'SELECT * FROM meta_coord' $dbname "
+                     . "> $dbname.meta_coord.backup"
+           ) == 0 )
+  {
     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 $dbname.meta_coord.backup\n";
+    print STDERR "Original meta_coord table backed up in "
+      . "$dbname.meta_coord.backup\n";
   }
 
   foreach my $table_name (@table_names) {
     print STDERR "Updating $table_name table entries...";
-    my $sql = "delete from meta_coord where table_name = ? ";
+    my $sql = "DELETE FROM meta_coord WHERE table_name = ?";
     my $sth = $dbc->prepare($sql);
     $sth->execute($table_name);
     $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";
+    $sql =
+        "INSERT INTO meta_coord "
+      . "SELECT '$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";
     $sth = $dbc->prepare($sql);
     $sth->execute;
     $sth->finish;
     print STDERR "Done\n";
   }
-}
+} ## end for my $dbname (@dbnames)