From 7d4b1943dc9ad459fc87a6d9f0f322faa14b1bd6 Mon Sep 17 00:00:00 2001
From: Philip Lijnzaad <lijnzaad@sanger.ac.uk>
Date: Thu, 11 Oct 2001 15:00:13 +0000
Subject: [PATCH] added a mega dump option and some docu.
---
.../utilities/satellite_dbdump_bychr.pl | 59 +++++++++++++++----
1 file changed, 48 insertions(+), 11 deletions(-)
diff --git a/misc-scripts/utilities/satellite_dbdump_bychr.pl b/misc-scripts/utilities/satellite_dbdump_bychr.pl
index e035a64119..850f00b282 100755
--- a/misc-scripts/utilities/satellite_dbdump_bychr.pl
+++ b/misc-scripts/utilities/satellite_dbdump_bychr.pl
@@ -24,12 +24,22 @@
(4) Usage:
- satellite_dbdump_bychr -<dbtype> <dbinstance>
+ satellite_dbdump_bychr -litedb <litedbinstance> -<dbtype> <dbinstance>
+ [ -<anotherdb> <anotherdb instance> ... ] [ -chr <a-chromosome> ]
e.g
satellite_dbdump_bychr -disease homo_sapiens_disease_110
+ Alternatively, dump all things in one go, relying on the consistent
+ naming scheme, as
+
+ satellite_dbdump_bychr -litedb <litedbinstance> \
+ -mega 'homo_sapiens_\%s_110' [ -chr <a-chromosome> ]
+
+ In this case, the %s will be replaced by all the known database
+ types, and all will be dumped. Is the theory.
+
Known types are: (see source code)
=head1 DESCRIPTION
@@ -45,6 +55,7 @@ Based on make_dbdumpk_bychr (which should be used for the core database)
;
use strict;
+use Carp;
use Bio::EnsEMBL::DBLoader;
use Getopt::Long;
@@ -60,6 +71,7 @@ my $litedb = ''; # 'homo_sapiens_lite_110'; # force user to provide it
my $dumplite = 0;
my $chr = 'chr21'; # smaller than chr22
+my $template = undef; # when dumping all
my $lim;
@@ -97,6 +109,7 @@ my $estdb;
'snp:s' => \$snpdb,
'embl:s' => \$embldb,
'est:s' => \$estdb,
+ 'mega:s' => \$template, #dump all known ones, using $template
);
die "need a litedb; use -litedb something " unless $litedb;
@@ -108,14 +121,40 @@ if ($lim) {
$limit = "limit $lim";
}
-&dump_lite($litedb) if $dumplite;
-&dump_family($famdb);
-&dump_disease($diseasedb);
-&dump_maps($mapsdb);
-&dump_expression($expressiondb);
-&dump_snp($snpdb);
-&dump_embl($embldb);
-&dump_est($estdb);
+if ($template) { #
+ # dump all, using naming
+ my $db;
+
+ &dump_lite( template_fill($template, 'lite'));
+ &dump_family( template_fill($template, 'family'));
+ &dump_disease( template_fill($template, 'disease'));
+ &dump_maps( template_fill($template, 'maps'));
+ &dump_expression( template_fill($template, 'expression'));
+ &dump_snp( template_fill($template, 'snp'));
+ &dump_embl( template_fill($template, 'embl'));
+ &dump_est( template_fill($template, 'est'));
+
+} else {
+
+ &dump_lite($litedb) if $dumplite;
+ &dump_family($famdb);
+ &dump_disease($diseasedb);
+ &dump_maps($mapsdb);
+ &dump_expression($expressiondb);
+ &dump_snp($snpdb);
+ &dump_embl($embldb);
+ &dump_est($estdb);
+
+}
+
+sub template_fill {
+ my ($tpl, $actual) = @_;
+ confess "template should look like 'prefix\%ssuffix'\n"
+ unless $template =~ /%s/;
+ my $result = $tpl;
+ $result =~ s/%s/$actual/;
+ $result;
+}
sub dump_lite {
# needed for a few things
@@ -280,7 +319,6 @@ sub dump_expression {
return unless $satdb;
warn "ignoring any non-ENSG aliases";
- my $dumpdir = "$workdir/$satdb";
dump_schema($satdb);
my $sql;
@@ -332,7 +370,6 @@ sub dump_snp {
return unless $satdb;
warn "ignoring any non-ENSG aliases";
- my $dumpdir = "$workdir/$satdb";
dump_schema($satdb);
my $sql;
--
GitLab