script to run synteny rescoring in parallel on the farm

misc-scripts/id_mapping/synteny_rescore.pl

+#!/software/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)
+  --loglevel=LEVEL                    define log level (default: INFO)
+
+  -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 Bio::EnsEMBL::Utils::ConfParser;
+use Bio::EnsEMBL::Utils::Logger;
+use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
+use Bio::EnsEMBL::IdMapping::Cache;
+use Bio::EnsEMBL::IdMapping::SyntenyFramework;
+use Bio::EnsEMBL::IdMapping::ScoredMappingMatrix;
+
+# parse configuration and commandline arguments
+my $conf = new Bio::EnsEMBL::Utils::ConfParser(
+  -SERVERROOT => "$Bin/../../..",
+  -DEFAULT_CONF => "$Bin/default.conf"
+);
+
+$conf->parse_options(
+  'dumppath|dump_path=s' => 1,
+  'index|i=n' => 1,
+);
+
+# append job index to logfile name
+my $index = $conf->param('index');
+my $logautobase = ($conf->param('logautobase') || 'synteny_rescore_') . $index;
+
+# get log filehandle and print heading and parameters to logfile
+my $logger = new Bio::EnsEMBL::Utils::Logger(
+  -LOGFILE      => $conf->param('logfile'),
+  -LOGAUTO      => $conf->param('logauto'),
+  -LOGAUTOBASE  => $logautobase,
+  -LOGAUTOID    => $conf->param('logautoid'),
+  -LOGPATH      => $conf->param('logpath'),
+  -LOGAPPEND    => $conf->param('logappend'),
+  -LOGLEVEL     => $conf->param('loglevel'),
+  -IS_COMPONENT => 1,
+);
+
+# loading cache from file
+my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
+  -LOGGER       => $logger,
+  -CONF         => $conf,
+);
+$cache->read_instance_from_file;
+
+# load SyntenyFramework and gene ScoredMappingMatrix from files
+my $dump_path = $conf->param('dumppath');
+
+my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
+  -DUMP_PATH    => path_append($dump_path, 'mapping'),
+  -CACHE_FILE   => 'synteny_framework.ser',
+  -LOGGER       => $logger,
+  -CONF         => $conf,
+  -CACHE        => $cache,
+);
+$sf->read_from_file;
+
+my $gene_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
+  -DUMP_PATH   => path_append($dump_path, 'matrix/synteny_rescore'),
+  -CACHE_FILE  => "gene_matrix_synteny$index.ser",
+  -AUTO_LOAD   => 1,
+);
+
+# synteny rescore and serialise results to file
+$gene_scores = $sf->rescore_gene_matrix($gene_scores);
+$gene_scores->write_to_file;
+
+# set flag to indicate everything went fine
+my $success_file = $conf->param('logpath')."/synteny_rescore_$index.success";
+open(TMPFILE, '>', $success_file) and close TMPFILE
+  or die "Can't open $success_file for writing: $!";
+
+# log success
+$logger->finish_log;
+