From 6e2afb3cf59dd928a765ccd5a28a00c95baca599 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Thu, 29 Nov 2012 11:15:27 +0000
Subject: [PATCH] allow for column configuration
---
misc-scripts/import/sort_feature_table.pl | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
diff --git a/misc-scripts/import/sort_feature_table.pl b/misc-scripts/import/sort_feature_table.pl
index 11ada536bc..a796b7bf0f 100644
--- a/misc-scripts/import/sort_feature_table.pl
+++ b/misc-scripts/import/sort_feature_table.pl
@@ -11,6 +11,7 @@ use POSIX qw/strftime/;
my ($db_name,$db_host,$db_user,$db_pass,$db_port,$help);
my @tables;
+my @columns;
my ($optimise, $nobackup, $nolock);
GetOptions ("db_name|dbname|database=s" => \$db_name,
@@ -22,12 +23,17 @@ GetOptions ("db_name|dbname|database=s" => \$db_name,
'optimise!' => \$optimise,
'nolock!' => \$nolock,
'nobackup!' => \$nobackup,
+ 'columns=s@' => \@columns,
"h|help!" => \$help,
);
if ($help) {&usage; exit 0;}
unless ($db_name and $db_host) {print "Insufficient arguments\n"; &usage; exit 1;}
+if(!@columns) {
+ @columns = qw/seq_region_id seq_region_start seq_region_end/;
+}
+
sub get_adaptor {
my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-species => 'tmp',
@@ -67,7 +73,8 @@ sub sort_table {
}
info("Re-ordering table");
- $dba->dbc()->do("ALTER TABLE ${table} ORDER BY seq_region_id, seq_region_start, seq_region_end");
+ my $cols = join(',', @columns);
+ $dba->dbc()->do("ALTER TABLE ${table} ORDER BY $cols");
if(!$nolock) {
info("Unlocking table %s", $table);
@@ -166,6 +173,10 @@ Options:
-nolock Stop the code from applying for table locks
+ -columns Specify the columns to sort on. Defaults to
+ seq_region_id, seq_region_start and seq_region_end.
+ Multiple parameters allowed
+
-help
";
}
--
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