diff --git a/misc-scripts/ping_ensembl.pl b/misc-scripts/ping_ensembl.pl index 58b8751063522e80faac1f4d72fa8e2188f8389d..c21e7653c7a9bfcfca316cfe42f15bd1569749a9 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";