synteny_rescore.pl

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#!/usr/bin/env perl
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# regarding copyright ownership.
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# 
#      http://www.apache.org/licenses/LICENSE-2.0
# 
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
 
# Don't change the above line.
# Change the PATH in the myRun.ksh script if you want to use another 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 AUTHOR
 
Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team
 
=head1 CONTACT
 
Please post comments/questions to the Ensembl development list
<http://lists.ensembl.org/mailman/listinfo/dev>
 
=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(
  'basedir|basedir=s' => 1,
  'index|i=n' => 1,
  'chromosomes|chr=s@' => 0,
  'region=s' => 0,
);
 
# append job index to logfile name
my $index = $conf->param('index');
my $logautobase = $conf->param('logautobase') || 'synteny_rescore';
 
# 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,
  -LOAD_INSTANCE  => 1,
);
 
# load SyntenyFramework and gene ScoredMappingMatrix from files
my $basedir = $conf->param('basedir');
 
my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
  -DUMP_PATH    => path_append($basedir, 'mapping'),
  -CACHE_FILE   => 'synteny_framework.ser',
  -LOGGER       => $logger,
  -CONF         => $conf,
  -CACHE        => $cache,
);
$sf->read_from_file;
 
my $gene_scores = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
  -DUMP_PATH   => path_append($basedir, '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;