From a167d612e4d41906e80ac892356295ffa92d8752 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 11 Nov 2014 09:39:52 +0000
Subject: [PATCH] added grch37 and verbose options default port is now 3306
---
misc-scripts/ping_ensembl.pl | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/ping_ensembl.pl b/misc-scripts/ping_ensembl.pl
index 58b8751063..c21e7653c7 100755
--- a/misc-scripts/ping_ensembl.pl
+++ b/misc-scripts/ping_ensembl.pl
@@ -69,8 +69,10 @@ use Getopt::Long;
my $help = 0;
my $host = 'ensembldb.ensembl.org';
my $user = 'anonymous';
-my $port = 5306;
+my $port = 3306;
+my $verbose = 0;
my $db_version = -1;
+my $grch37;
my $useast = 0;
my $ensembl_genomes = 0;
@@ -86,6 +88,8 @@ my $options_ok =
"eg" => \$ensembl_genomes,
"species=s" => \$species,
"db_version=i" => \$db_version,
+ "verbose" => \$verbose,
+ "grch37" => \$grch37,
"help" => \$help);
($help or !$options_ok) && usage();
@@ -95,6 +99,10 @@ $useast and $ensembl_genomes and
$useast and $host = "useastdb.ensembl.org";
+$verbose and $verbose = 1;
+
+$grch37 and $port = 3337;
+
if ($ensembl_genomes) {
$host = "mysql.ebi.ac.uk";
$port = 4157;
@@ -116,6 +124,7 @@ eval {
-port => $port,
-user => $user,
-db_version => $db_version,
+ -verbose => $verbose,
);
$species = "human" unless defined $species;
my $species_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("$species", 'core');
@@ -212,6 +221,8 @@ sub usage {
print " -eg Ping Ensembl Genomes (can't be used together with \"ue\")\n";
print " -species <species> Use species <species> (use double quotes if species name contains spaces)\n";
print " -db_version <version> Use the specified version of Ensembl not the API version\n";
+ print " -grch37 Use human assembly GRCh37 rather than the default GRCh38 version\n";
+ print " -verbose Ping output is more verbose. Not recommended for Ensembl genomes\n";
print " -help Print this message\n";
print "\n\n";
--
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