main ID mapping script

misc-scripts/id_mapping/id_mapping.pl

+#!/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::IdMapping::Cache;
+use Bio::EnsEMBL::Gene;
+use Bio::EnsEMBL::Transcript;
+use Bio::EnsEMBL::Translation;
+use Bio::EnsEMBL::Exon;
+
+#use Devel::Size qw(size total_size);
+
+$| = 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(
+  dumppath|dump_path=s
+  chromosomes|chr=s@
+  region=s
+  biotypes=s@
+));
+$conf->allowed_params(
+  $conf->get_common_params,
+  qw(
+    dumppath
+    chromosomes region biotypes
+  )
+);
+
+if ($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(
+    dumppath
+  )
+);
+
+my $cache = new Bio::EnsEMBL::IdMapping::Cache(
+  -LOGGER       => $logger,
+  -CONF         => $conf,
+);
+
+use Data::Dumper;
+$Data::Dumper::Indent = 1;
+
+# loading cache from file
+foreach my $dbtype (qw(old new)) {
+  foreach my $slice_name (@{ $cache->slice_names($dbtype) }) {
+    $logger->log("\n");
+    $cache->read_from_file('exons_by_id', "$dbtype.$slice_name");
+  }
+}
+
+$cache->merge('exons_by_id');
+
+
+=cut
+# log stats
+$logger->log("\nCache memory usage:\n\n");
+
+my $s;
+my %keys;
+
+$keys{'_cache'} = size($cache->{'_cache'});
+
+foreach my $name (keys %{ $cache->{'_cache'} }) {
+  $keys{$name} = size($cache->{'_cache'}->{$name});
+  foreach my $type (keys %{ $cache->{'_cache'}->{$name} }) {
+    $keys{$type} = size($cache->{'_cache'}->{$name}->{$type});
+    $s += size($cache->{'_cache'}->{$name}->{$type});
+  }
+}
+
+my $ts = total_size($cache->{'_cache'});
+
+my $fmt = "%-50s%12.0f\n";
+
+foreach my $k (sort { $keys{$a} <=> $keys{$b} } keys %keys) {
+  $logger->log(sprintf($fmt, $k, $keys{$k}), 1);
+}
+$logger->log(sprintf($fmt, "total overhead", $s), 1);
+$logger->log(sprintf($fmt, "data", ($ts-$s)), 1);
+$logger->log(sprintf($fmt, "total", $ts)."\n", 1);
+
+# test
+my $i = 0;
+foreach my $eid (keys %{ $cache->get_by_name('exons_by_id', 'new') }) {
+  last if ($i++ > 0);
+  
+  $logger->log("\nData object memory usage:\n\n");
+  
+  my $exon = $cache->get_by_key('exons_by_id', 'new', $eid);
+  my $s1 = size($exon);
+  my $ts1 = total_size($exon);
+
+  $logger->log(sprintf($fmt, "object", $s1), 1);
+  $logger->log(sprintf($fmt, "data", ($ts1-$s1)), 1);
+  $logger->log(sprintf($fmt, "total", $ts1)."\n", 1);
+
+  print $exon->stable_id."\n";
+  #warn Data::Dumper::Dumper($exon);
+}
+=cut
+
+
+# finish logfile
+$logger->finish_log;
+
+
+### END main ###
+