From e6a33df5e6108614fb5c22315cb6d4aca51d6557 Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Fri, 28 Jul 2006 11:00:13 +0000
Subject: [PATCH] create cache for Id mapping one seq_region at a time
---
misc-scripts/id_mapping/dump_by_seq_region.pl | 155 ++++++++++++++++++
1 file changed, 155 insertions(+)
create mode 100755 misc-scripts/id_mapping/dump_by_seq_region.pl
diff --git a/misc-scripts/id_mapping/dump_by_seq_region.pl b/misc-scripts/id_mapping/dump_by_seq_region.pl
new file mode 100755
index 0000000000..4e5821edeb
--- /dev/null
+++ b/misc-scripts/id_mapping/dump_by_seq_region.pl
@@ -0,0 +1,155 @@
+#!/usr/local/ensembl/bin/perl
+
+=head1 NAME
+
+
+=head1 SYNOPSIS
+
+.pl [arguments]
+
+Required arguments:
+
+ --dbname, db_name=NAME database name NAME
+ --host, --dbhost, --db_host=HOST database host HOST
+ --port, --dbport, --db_port=PORT database port PORT
+ --user, --dbuser, --db_user=USER database username USER
+ --pass, --dbpass, --db_pass=PASS database passwort PASS
+
+Optional arguments:
+
+ --conffile, --conf=FILE read parameters from FILE
+ (default: conf/Conversion.ini)
+
+ --logfile, --log=FILE log to FILE (default: *STDOUT)
+ --logpath=PATH write logfile to PATH (default: .)
+ --logappend, --log_append append to logfile (default: truncate)
+
+ -v, --verbose=0|1 verbose logging (default: false)
+ -i, --interactive=0|1 run script interactively (default: true)
+ -n, --dry_run, --dry=0|1 don't write results to database
+ -h, --help, -? print help (this message)
+
+=head1 DESCRIPTION
+
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence. Please see
+http://www.ensembl.org/info/about/code_licence.html for details.
+
+=head1 AUTHOR
+
+Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
+
+=head1 CONTACT
+
+Please post comments/questions to the Ensembl development list
+<ensembl-dev@ebi.ac.uk>
+
+=cut
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use FindBin qw($Bin);
+use vars qw($SERVERROOT);
+
+BEGIN {
+ $SERVERROOT = "$Bin/../../..";
+ unshift(@INC, "$SERVERROOT/ensembl/modules");
+ unshift(@INC, "$SERVERROOT/bioperl-live");
+}
+
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConfParser;
+use Bio::EnsEMBL::Utils::Logger;
+use Bio::EnsEMBL::Utils::ScriptUtils qw(dynamic_use);
+
+$| = 1;
+
+my $conf = new Bio::EnsEMBL::Utils::ConfParser(
+ -SERVERROOT => $SERVERROOT,
+);
+
+# parse options
+$conf->param('default_conf', './default.conf');
+$conf->parse_common_options(@_);
+$conf->parse_extra_options(qw(
+ oldhost|old_host=s
+ oldport|old_port=n
+ olduser|old_user=s
+ oldpass|old_pass=s
+ olddbname|old_dbname=s
+ newhost|new_host=s
+ newport|new_port=n
+ newuser|new_user=s
+ newpass|new_pass=s
+ newdbname|new_dbname=s
+ dumppath|dump_path=s
+ biotypes=s@
+ dbtype=s
+ slice_name=s
+ cache_impl=s
+));
+$conf->allowed_params(
+ $conf->get_common_params,
+ qw(
+ oldhost oldport olduser oldpass olddbname
+ newhost newport newuser newpass newdbname
+ dumppath biotypes
+ dbtype slice_name cache_impl
+ )
+);
+
+if ($conf->param('help') or $conf->error) {
+ warn $conf->error if $conf->error;
+ pod2usage(1);
+}
+
+# ask user to confirm parameters to proceed
+$conf->confirm_params;
+
+# get log filehandle and print heading and parameters to logfile
+my $logger = new Bio::EnsEMBL::Utils::Logger(
+ -LOGFILE => $conf->param('logfile') || 'dump_by_seq_region.log',
+ -LOGPATH => $conf->param('logpath'),
+ -LOGAPPEND => $conf->param('logappend'),
+ -VERBOSE => $conf->param('verbose'),
+ -IS_COMPONENT => $conf->param('is_component'),
+);
+
+# initialise log
+$logger->init_log($conf->list_all_params);
+
+# check required parameters were set
+$conf->check_required_params(
+ qw(
+ oldhost oldport olduser olddbname
+ newhost newport newuser newdbname
+ dumppath
+ dbtype slice_name cache_impl
+ )
+);
+
+# build cache
+my $cache_impl = $conf->param('cache_impl');
+
+dynamic_use($cache_impl);
+
+my $cache = $cache_impl->new(
+ -LOGGER => $logger,
+ -CONF => $conf,
+);
+
+my $dbtype = $conf->param('dbtype');
+my $slice_name = $conf->param('slice_name');
+my $i = 0;
+my $size = 0;
+($i, $size) = $cache->build_cache($dbtype, $slice_name);
+
+# log success
+$logger->log("Done with $dbtype $slice_name (genes: $i, filesize: $size, runtime: ".$logger->runtime." ".$logger->date_and_mem."\n");
+
+
--
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