From 37515b040f099975daa6e7b1561787082dee994e Mon Sep 17 00:00:00 2001
From: Arnaud Kerhornou <arnaud@ebi.ac.uk>
Date: Wed, 30 Nov 2011 15:49:01 +0000
Subject: [PATCH] Added muser, mhost and mport so we can pass as command
arguments an alternative server which hosts the ensembl_production database;
updated the usage
---
.../density_feature/seq_region_stats.pl | 19 +++++++++++++------
1 file changed, 13 insertions(+), 6 deletions(-)
diff --git a/misc-scripts/density_feature/seq_region_stats.pl b/misc-scripts/density_feature/seq_region_stats.pl
index 633bec5369..1dc1df5749 100644
--- a/misc-scripts/density_feature/seq_region_stats.pl
+++ b/misc-scripts/density_feature/seq_region_stats.pl
@@ -9,6 +9,10 @@ use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
use Getopt::Long;
my ( $host, $user, $pass, $port, $dbname, $pattern, $stats );
+# Master database location:
+my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
+my ( $muser, $mpass ) = ( 'ensro', undef );
+my $mdbname = 'ensembl_production';
GetOptions( "host|h=s", \$host,
"user|u=s", \$user,
@@ -17,6 +21,9 @@ GetOptions( "host|h=s", \$host,
"dbname|d=s", \$dbname,
"pattern=s", \$pattern,
"stats|s=s", \$stats,
+ "mhost=s", \$mhost,
+ "mport=i", \$mport,
+ "muser=s", \$muser,
"help" , \&usage
);
@@ -25,12 +32,6 @@ usage() if (!$host || !$user || !$pass || (!$dbname && !$pattern) || !$stats ||
#get biotypes and attrib codes from the production database
-# Master database location:
-my ( $mhost, $mport ) = ( 'ens-staging1', '3306' );
-my ( $muser, $mpass ) = ( 'ensro', undef );
-my $mdbname = 'ensembl_production';
-
-
my $prod_dsn = sprintf( 'DBI:mysql:host=%s;port=%d;database=%s',
$mhost, $mport, $mdbname );
my $prod_dbh = DBI->connect( $prod_dsn, $muser, $mpass,
@@ -345,6 +346,12 @@ Usage:
-pattern Database name regexp
+ -mhost ensembl_production database host to connect to
+
+ -mport ensembl_production database port to connect to
+
+ -muser ensembl_production database username
+
-s|stats 'gene' or 'snp'
-help This message
--
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