lsf wrapper for align_nonident_regions.pl

misc-scripts/assembly/align_nonident_regions_wrapper.pl

+#!/usr/local/bin/perl
+
+=head1 NAME
+
+align_nonident_regions_wrapper.pl - lsf wrapper for align_nonident_regions.pl
+
+=head1 SYNOPSIS
+
+align_nonident_regions_wrapper.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
+    --assembly=ASSEMBLY                 assembly version ASSEMBLY
+
+    --altdbname=NAME                    alternative database NAME
+    --altassembly=ASSEMBLY              alternative assembly version ASSEMBLY
+
+Optional arguments:
+
+    --chromosomes, --chr=LIST           only process LIST chromosomes
+    --bindir=DIR                        look for program binaries in DIR
+    --tmpfir=DIR                        use DIR for temporary files (useful for
+                                        re-runs after failure)
+
+    --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
+
+This script is a wrapper around align_nonident_regions.pl to run one chromosome
+at a time via lsf. See documentation in align_nonident_regions.pl for details.
+
+=head1 RELATED FILES
+
+The whole process of creating a whole genome alignment between two assemblies
+is done by a series of scripts. Please see
+
+  ensembl/misc-scripts/assembly/README
+
+for a high-level description of this process, and POD in the individual scripts
+for the details.
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/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, ".");
+    unshift(@INC, "$SERVERROOT/ensembl/modules");
+    unshift(@INC, "$SERVERROOT/bioperl-live");
+}
+
+use Getopt::Long;
+use Pod::Usage;
+use Bio::EnsEMBL::Utils::ConversionSupport;
+use AssemblyMapper::BlastzAligner;
+
+$| = 1;
+
+my $support = new Bio::EnsEMBL::Utils::ConversionSupport($SERVERROOT);
+
+# parse options
+$support->parse_common_options(@_);
+$support->parse_extra_options(
+    'assembly=s',
+    'altdbname=s',
+    'altassembly=s',
+    'bindir=s',
+    'tmpdir=s',
+    'chromosomes|chr=s@',
+);
+$support->allowed_params(
+    $support->get_common_params,
+    'assembly',
+    'altdbname',
+    'altassembly',
+    'bindir',
+    'tmpdir',
+    'chromosomes',
+);
+
+if ($support->param('help') or $support->error) {
+  warn $support->error if $support->error;
+  pod2usage(1);
+}
+
+$support->comma_to_list('chromosomes');
+
+# ask user to confirm parameters to proceed
+$support->confirm_params;
+
+# get log filehandle and print heading and parameters to logfile
+$support->init_log;
+
+$support->check_required_params(
+    'assembly',
+    'altdbname',
+    'altassembly'
+);
+
+#####
+# connect to database and get adaptors
+#
+my $R_dba = $support->get_database('ensembl');
+
+# loop over chromosomes
+$support->log_stamped("Looping over chromosomes...\n");
+
+foreach my $chr ($support->sort_chromosomes) {
+    $support->log_stamped("Chromosome $chr...\n", 1);
+
+    # run align_nonident_regions.pl via lsf
+    my $options = $support->create_commandline_options({
+        'allowed_params' => 1,
+        'replace' => {
+            logfile     => "align_nonident_regions.chr.$chr.log",
+            chromosomes => $chr,
+            interactive => 0,
+        },
+    });
+    $support->log("Running align_nonident_regions.pl via lsf...\n", 2);
+
+    my $logpath = $support->param('logpath').'/lsf';
+    unless (-d $logpath) {
+        system("mkdir $logpath") == 0 or
+            $support->log_error("Can't create lsf log dir $logpath: $!\n");
+    }
+
+    my $cmd = qq(bsub -o $logpath/align_nonident_regions.$chr.%J.out -e $logpath/align_nonident_regions.$chr.%J.err ./align_nonident_regions.pl $options
+    );
+
+    system("$cmd") == 0
+        or $support->log_error("Error running align_nonident_regions.pl: $!");
+
+    $support->log_stamped("Done.\n", 2);
+
+    $support->log_stamped("Done with chromosome $chr.\n", 1);
+}
+
+$support->log_stamped("Done.\n");
+
+# finish logfile
+$support->finish_log;
+
+