stable Id mapping ported to perl

misc-scripts/id_mapping/default.conf

+; for dry runs, no data is written to the database
+dry_run = 1
+
+; verbose logging
+verbose = 1
+
+; prepend this path to your 'log' parameter
+logpath = /ecs2/work2/pm2/logs/test
+
+; old db settings
+oldhost                 = ecs4
+oldport                 = 3350
+olduser                 = ensro
+olddbname               = pm2_homo_sapiens_core_39_36a
+
+; new db settings
+newhost                 = ecs4
+newport                 = 3350
+newuser                 = ensadmin
+newpass                 = ensembl
+newdbname               = pm2_homo_sapiens_core_39_36a
+
+; cache
+dumppath                = /ecs2/scratch3/pm2/data/test
+;region                  = chromosome:NCBI36:X:1000000:2000000:1
+

misc-scripts/id_mapping/dump_cache.pl

+#!/usr/local/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::IdMapping::Cache;
+
+$| = 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
+  cachefile|cache_file=s
+  chromosomes|chr=s@
+  region=s
+  biotypes=s@
+));
+$conf->allowed_params(
+  $conf->get_common_params,
+  qw(
+    oldhost oldport olduser oldpass olddbname
+    newhost newport newuser newpass newdbname
+    dumppath cachefile
+    chromosomes region biotypes
+  )
+);
+
+if ($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'),
+  -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
+  )
+);
+
+my $cache = new Bio::EnsEMBL::IdMapping::Cache(
+  -LOGGER       => $logger,
+  -CONF         => $conf,
+);
+
+unless ($cache->cache_file_exists) {
+  # load objects from database
+  $cache->build_cache;
+
+  # write cache to file
+  $cache->write_to_file;
+}
+
+# finish logfile
+$logger->finish_log;
+
+
+### END main ###
+

misc-scripts/id_mapping/run_all.pl

+#!/usr/local/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;
+
+$| = 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
+  cachefile|cache_file=s
+  chromosomes|chr=s@
+  region=s
+  biotypes=s@
+));
+$conf->allowed_params(
+  $conf->get_common_params,
+  qw(
+    oldhost oldport olduser oldpass olddbname
+    newhost newport newuser newpass newdbname
+    dumppath cachefile
+    chromosomes region biotypes
+  )
+);
+
+if ($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'),
+  -LOGPATH    => $conf->param('logpath'),
+  -LOGAPPEND  => $conf->param('logappend'),
+  -VERBOSE    => $conf->param('verbose'),
+);
+
+# initialise log
+$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
+  )
+);
+
+# create commandline options for running component scripts
+my $options = $conf->create_commandline_options(
+    -ALLOWED_PARAMS => 1,
+    -REPLACE => {
+        interactive => 0,
+        is_component => 1,
+    },
+);
+
+# dump cache files
+&run_component('dump_cache.pl', $options, 'building cache');
+
+# ID mapping
+#&run_component('id_mapping.pl', $options, 'Id mapping');
+
+# archive
+#&run_component('archive.pl', $options, 'archive');
+
+# reporting
+#&run_component('report.pl', $options, 'creating report');
+
+# QC
+#&run_component('qc.pl', $options, 'QC');
+
+
+# finish logfile
+$logger->finish_log;
+
+
+### END main ###
+
+sub run_component {
+  my $cmd = shift;
+  my $options = shift;
+  my $logtext = shift || $cmd;
+
+  $logger->log_stamped("----- $logtext -----\n");
+  
+  system("./$cmd $options") == 0
+    or $logger->log_error("Error running $cmd. Please see the respective logfile for more information.\n");
+  
+  $logger->log_stamped("----- done with $logtext -----\n\n");
+}
+