From 53f063aa5ac44eab3fbbd54fb95c8085c7986eac Mon Sep 17 00:00:00 2001
From: Damian Smedley <ds5@sanger.ac.uk>
Date: Mon, 5 Feb 2007 15:30:55 +0000
Subject: [PATCH] changed so can run on all core databases etc
---
misc-scripts/meta_coord/update_meta_coord.pl | 57 ++++++++++++--------
1 file changed, 34 insertions(+), 23 deletions(-)
diff --git a/misc-scripts/meta_coord/update_meta_coord.pl b/misc-scripts/meta_coord/update_meta_coord.pl
index 1f88488c21..879ea1f267 100755
--- a/misc-scripts/meta_coord/update_meta_coord.pl
+++ b/misc-scripts/meta_coord/update_meta_coord.pl
@@ -5,9 +5,9 @@ use Bio::EnsEMBL::DBSQL::DBConnection;
use Getopt::Long;
my $help = 0;
-my ($host, $port, $user, $pass, $dbname);
+my ($host, $port, $user, $pass, $dbpattern);
-my $usage = "\n$0 --host ecs2 --port 3364 --user ensadmin --pass ensembl --dbname homo_sapiens_core_27_35a
+my $usage = "\n$0 --host ecs2 --port 3364 --user ensadmin --pass ensembl --dbpattern core
[--help] displays this menu.
@@ -39,7 +39,7 @@ GetOptions('help' => \$help,
'port=i' => \$port,
'user=s' => \$user,
'pass=s' => \$pass,
- 'dbname=s' => \$dbname);
+ 'dbpattern=s' => \$dbpattern);
#print "help: $help argv:" . scalar(@ARGV) . "$host $port $user $pass $dbname\n";
@@ -48,13 +48,24 @@ GetOptions('help' => \$help,
# exit 0;
#}
-my $dbc = new Bio::EnsEMBL::DBSQL::DBConnection(-host => $host,
+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")};
+
+for my $dbname (@dbnames) {
+
+ next if ($dbname !~ /$dbpattern/);
+
+ my $dbc = new Bio::EnsEMBL::DBSQL::DBConnection(-host => $host,
-port => $port,
-user => $user,
-pass => $pass,
-dbname => $dbname);
-my @table_names = qw(
+ my @table_names = qw(
assembly_exception
gene
exon
@@ -76,27 +87,27 @@ my @table_names = qw(
transcript
);
-unless (system("mysql -h$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 $dbname.meta_coord.backup\n";
-}
+ unless (system("mysql -h$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";
+ }
-foreach my $table_name (@table_names) {
- print STDERR "Updating $table_name table entries...";
- my $sql = "delete from meta_coord where table_name = ? ";
- my $sth = $dbc->prepare($sql);
- $sth->execute($table_name);
- $sth->finish;
+ foreach my $table_name (@table_names) {
+ print STDERR "Updating $table_name table entries...";
+ 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 ".
+ $sql = "insert into meta_coord ".
"select '$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";
+ $sth = $dbc->prepare($sql);
+ $sth->execute;
+ $sth->finish;
+ print STDERR "Done\n";
+ }
}
-
--
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