latest state of the code (mostly adaptations due to changes in ConfParser and Logger)

misc-scripts/id_mapping/default.conf

 ; for dry runs, no data is written to the database
 dry_run = 1
 
-; verbose logging
-verbose = 1
+; log level
+loglevel = INFO
 
 ; prepend this path to your 'log' parameter
-logpath = /ecs2/work2/pm2/logs/test_20060926
+logpath = /lustre/work1/ensembl/pm2/logs/test_20070611
 
 ; old db settings
-sourcehost                  = ecs2
-sourceport                  = 3364
+sourcehost                  = ens-research
+sourceport                  = 3306
 sourceuser                  = ensro
-sourcedbname                = homo_sapiens_core_41_36c
+sourcedbname                = pm2_pan_troglodytes_core_40_3c
 
 ; new db settings
-targethost                  = ecs2
-targetport                  = 3364
+targethost                  = ens-research
+targetport                  = 3306
 targetuser                  = ensro
-targetdbname                = homo_sapiens_core_41_36c
+targetdbname                = pm2_pan_troglodytes_core_41_21
 
 ; cache
-dumppath                    = /ecs2/scratch3/pm2/data/test_20060926
-;region                     = chromosome:NCBI36:X:1:2000000:1
+dumppath                    = /lustre/scratch1/ensembl/pm2/idmapping/out_20070611
+region                     = chromosome:CHIMP1A:1:1:2000000:1
 
 ; ScoreBuilder
 min_exon_length             = 15

misc-scripts/id_mapping/dump_by_seq_region.pl

@@ -23,8 +23,8 @@ Optional arguments:
   --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)
 
-  -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)
@@ -53,84 +53,41 @@ 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::Utils::ScriptUtils qw(dynamic_use);
 
-$| = 1;
-
+# parse configuration and commandline arguments
 my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-  -SERVERROOT => $SERVERROOT,
+  -SERVERROOT => "$Bin/../../..",
+  -DEFAULT_CONF => "$Bin/default.conf"
 );
 
-# parse options
-$conf->param('default_conf', './default.conf');
-$conf->parse_common_options(@_);
-$conf->parse_extra_options(qw(
-  sourcehost|source_host=s
-  sourceport|source_port=n
-  sourceuser|source_user=s
-  sourcepass|source_pass=s
-  sourcedbname|source_dbname=s
-  targethost|target_host=s
-  targetport|target_port=n
-  targetuser|target_user=s
-  targetpass|target_pass=s
-  targetdbname|target_dbname=s
-  dumppath|dump_path=s
-  biotypes=s@
-  dbtype=s
-  slice_name=s
-  cache_impl=s
-));
-$conf->allowed_params(
-  $conf->get_common_params,
-  qw(
-    sourcehost sourceport sourceuser sourcepass sourcedbname
-    targethost targetport targetuser targetpass targetdbname
-    dumppath biotypes
-    dbtype slice_name cache_impl
-  )
+$conf->parse_options(
+  'sourcehost|source_host=s' => 1,
+  'sourceport|source_port=n' => 1,
+  'sourceuser|source_user=s' => 1,
+  'sourcepass|source_pass=s' => 0,
+  'sourcedbname|source_dbname=s' => 1,
+  'targethost|target_host=s' => 1,
+  'targetport|target_port=n' => 1,
+  'targetuser|target_user=s' => 1,
+  'targetpass|target_pass=s' => 0,
+  'targetdbname|target_dbname=s' => 1,
+  'dumppath|dump_path=s' => 1,
+  'biotypes=s@' => 0,
+  'dbtype=s' => 1,
+  'slice_name=s' => 1,
+  'cache_impl=s' => 1,
 );
 
-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') || 'dump_by_seq_region.log',
   -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(
-    sourcehost sourceport sourceuser sourcedbname
-    targethost targetport targetuser targetdbname
-    dumppath
-    dbtype slice_name cache_impl
-  )
+  -LOGAPPEND    => 1,
+  -LOGLEVEL     => $conf->param('loglevel'),
+  -IS_COMPONENT => 1,
 );
 
 # build cache
@@ -150,11 +107,11 @@ my $size = 0;
 ($i, $size) = $cache->build_cache($dbtype, $slice_name);
 
 # set flag to indicate everything went fine
-my $success_file = $conf->param('logpath')."/lsf/dump_by_seq_region.$dbtype.$slice_name.success";
+my $success_file = $conf->param('logpath')."/lsf_dump_cache/dump_by_seq_region.$dbtype.$slice_name.success";
 open(TMPFILE, '>', $success_file) and close TMPFILE
   or die "Can't open $success_file for writing: $!";
 
 # log success
-$logger->log("Done with $dbtype $slice_name (genes: $i, filesize: $size, runtime: ".$logger->runtime." ".$logger->date_and_mem."\n");
+$logger->info("Done with $dbtype $slice_name (genes: $i, filesize: $size, runtime: ".$logger->runtime." ".$logger->date_and_mem."\n");
 
 

misc-scripts/id_mapping/dump_cache.pl

@@ -23,8 +23,8 @@ Optional arguments:
   --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)
 
-  -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)
@@ -63,97 +63,59 @@ 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::Utils::ScriptUtils qw(dynamic_use);
 
-$| = 1;
-
+# parse configuration and commandline arguments
 my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-  -SERVERROOT => $SERVERROOT,
+  -SERVERROOT => "$Bin/../../..",
+  -DEFAULT_CONF => "$Bin/default.conf"
 );
 
-# parse options
-$conf->param('default_conf', './default.conf');
-$conf->parse_common_options(@_);
-$conf->parse_extra_options(qw(
-  sourcehost|source_host=s
-  sourceport|source_port=n
-  sourceuser|source_user=s
-  sourcepass|source_pass=s
-  sourcedbname|source_dbname=s
-  targethost|target_host=s
-  targetport|target_port=n
-  targetuser|target_user=s
-  targetpass|target_pass=s
-  targetdbname|target_dbname=s
-  dumppath|dump_path=s
-  chromosomes|chr=s@
-  region=s
-  biotypes=s@
-));
-$conf->allowed_params(
-  $conf->get_common_params,
-  qw(
-    sourcehost sourceport sourceuser sourcepass sourcedbname
-    targethost targetport targetuser targetpass targetdbname
-    dumppath
-    chromosomes region biotypes
-  )
+$conf->parse_options(
+  'sourcehost|source_host=s' => 1,
+  'sourceport|source_port=n' => 1,
+  'sourceuser|source_user=s' => 1,
+  'sourcepass|source_pass=s' => 0,
+  'sourcedbname|source_dbname=s' => 1,
+  'targethost|target_host=s' => 1,
+  'targetport|target_port=n' => 1,
+  'targetuser|target_user=s' => 1,
+  'targetpass|target_pass=s' => 0,
+  'targetdbname|target_dbname=s' => 1,
+  'dumppath|dump_path=s' => 1,
+  'chromosomes|chr=s@' => 0,
+  'region=s' => 0,
+  'biotypes=s@' => 0,
 );
 
-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'),
+  -LOGLEVEL     => $conf->param('loglevel'),
   -IS_COMPONENT => $conf->param('is_component'),
 );
 
 # initialise log
-$logger->init_log($conf->list_all_params);
-
-# check required parameters were set
-$conf->check_required_params(
-  qw(
-    sourcehost sourceport sourceuser sourcedbname
-    targethost targetport targetuser targetdbname
-    dumppath
-  )
-);
+$logger->init_log($conf->list_param_values);
 
 my %jobs;
 
 # create empty directory for logs
-my $logpath = ($conf->param('logpath')||$conf->param('dumppath')).'/lsf_dump_cache';
+my $logpath = ($conf->param('logpath') || $conf->param('dumppath')) .
+  '/lsf_dump_cache';
 system("rm -rf $logpath") == 0 or
-  $logger->log_error("Unable to delete lsf log dir $logpath: $!\n");
+  $logger->error("Unable to delete lsf log dir $logpath: $!\n");
 system("mkdir -p $logpath") == 0 or
-  $logger->log_error("Can't create lsf log dir $logpath: $!\n");
+  $logger->error("Can't create lsf log dir $logpath: $!\n");
 
 # submit jobs to lsf
 foreach my $dbtype (qw(source target)) {
   
-  $logger->log_stamped("\n".ucfirst($dbtype)." db...\n");
+  $logger->info("\n".ucfirst($dbtype)." db...\n", 0, 'stamped');
 
   my $schema = $conf->param("${dbtype}schema") || 'latest';
   my $cache_builder = "build_cache_$schema";
@@ -178,22 +140,23 @@ while (keys %jobs) {
     push @types, $type;
   }
 
-  $logger->log("Jobs waiting: ".scalar(keys %jobs)."/$total.\r");
+  $logger->info("Jobs waiting: ".scalar(keys %jobs)."/$total.\r");
 
   sleep(3) if (scalar(keys %jobs));
 }
 
-$logger->log("\n\n");
+$logger->info("\n\n");
 
 # check if anything went wrong
 foreach my $type (@types) {
+  warn "$logpath/dump_by_seq_region.$type.success\n";
   $err++ unless (-e "$logpath/dump_by_seq_region.$type.success");
 }
 
 my $retval = 0;
 if ($err) {
-  $logger->log("At least one of your jobs failed.\n");
-  $logger->log("Please check $logpath and ".$conf->param('logpath')."/dump_by_seq_region.log for errors.\n");
+  $logger->warning("At least one of your jobs failed.\n");
+  $logger->warning("Please check $logpath and ".$conf->param('logpath')."/".$conf->param('logfile')." for errors.\n");
   $retval = 1;
 }
 
@@ -221,7 +184,7 @@ sub build_cache_latest {
   my $dba = $cache->get_DBAdaptor($dbtype);
   my $sa = $dba->get_SliceAdaptor;
   
-  $logger->log("Submitting jobs to lsf...\n", 1);
+  $logger->info("Submitting jobs to lsf...\n", 1);
 
   foreach my $slice_name (@{ $cache->slice_names($dbtype) }) {
     &bsubmit($dbtype, $slice_name, $cache, $logpath);
@@ -236,22 +199,18 @@ sub bsubmit {
   my $cache = shift;
   my $logpath = shift;
   
-  $logger->log("$slice_name\n", 2);
+  $logger->info("$slice_name\n", 2);
   
   my $type = "$dbtype.$slice_name";
 
   unless ($cache->all_cache_files_exist($type)) {
     my $options = $conf->create_commandline_options(
-        -ALLOWED_PARAMS => 1,
-        -REPLACE => {
-            interactive   => 0,
-            is_component  => 1,
-            dbtype        => $dbtype,
-            slice_name    => $slice_name,
-            cache_impl    => ref($cache),
-            log_append    => 1,
-        },
-        -EXCLUDE => [qw(region chromosomes)]
+        interactive   => 0,
+        is_component  => 1,
+        dbtype        => $dbtype,
+        slice_name    => $slice_name,
+        cache_impl    => ref($cache),
+        log_append    => 1,
     );
     
     my $cmd = "bsub ".
@@ -260,7 +219,7 @@ sub bsubmit {
                 "./dump_by_seq_region.pl $options";
 
     system("$cmd") == 0
-      or $logger->log_error("Error running dump_by_seq_region.pl: $!");
+      or $logger->error("Error running dump_by_seq_region.pl: $!");
 
     # mark job as submitted
     $jobs{$type} = 1;

misc-scripts/id_mapping/id_mapping.pl

@@ -23,8 +23,8 @@ Optional arguments:
   --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)
 
-  -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)
@@ -53,85 +53,47 @@ 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::IdMapping::ExonScoreBuilder;
 use Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder;
+use Bio::EnsEMBL::IdMapping::GeneScoreBuilder;
 
 #use Devel::Size qw(size total_size);
 #use Data::Dumper;
 #$Data::Dumper::Indent = 1;
 
-
-$| = 1;
-
+# parse configuration and commandline arguments
 my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-  -SERVERROOT => $SERVERROOT,
+  -SERVERROOT => "$Bin/../../..",
+  -DEFAULT_CONF => "$Bin/default.conf"
 );
 
-# parse options
-$conf->param('default_conf', './default.conf');
-$conf->parse_common_options(@_);
-$conf->parse_extra_options(qw(
-  mode=s
-  dumppath|dump_path=s
-  chromosomes|chr=s@
-  region=s
-  biotypes=s@
-  min_exon_length|minexonlength=i
-  exonerate_path|exoneratepath=s
-  exonerate_threshold|exoneratethreshold=i
-  exonerate_jobs|exoneratejobs=i
-  exonerate_bytes_per_job|exoneratebytesperjob=i
-));
-$conf->allowed_params(
-  $conf->get_common_params,
-  qw(
-    mode dumppath
-    chromosomes region biotypes
-    min_exon_length
-    exonerate_path exonerate_threshold exonerate_jobs exonerate_byte_per_job
-  )
+$conf->parse_options(
+  'mode=s' => 0,
+  'dumppath|dump_path=s' => 1,
+  'chromosomes|chr=s@' => 0,
+  'region=s' => 0,
+  'biotypes=s@' => 0,
+  'min_exon_length|minexonlength=i' => 0,
+  'exonerate_path|exoneratepath=s' => 1,
+  'exonerate_threshold|exoneratethreshold=f' => 0,
+  'exonerate_jobs|exoneratejobs=i' => 0,
+  'exonerate_bytes_per_job|exoneratebytesperjob=f' => 0,
 );
 
-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'),
+  -LOGLEVEL     => $conf->param('loglevel'),
   -IS_COMPONENT => $conf->param('is_component'),
 );
 
 # initialise log
-$logger->init_log($conf->list_all_params);
-
-# check required parameters were set
-$conf->check_required_params(
-  qw(
-    dumppath
-    exonerate_path
-  )
-);
+$logger->init_log($conf->list_param_values);
 
 
 # instance variables
@@ -179,11 +141,15 @@ sub build_scores {
     -CONF         => $conf,
     -CACHE        => $cache
   );
-  #my $gsb = Bio::EnsEMBL::IdMapping::GeneScoreBuilder->new(
+  my $gsb = Bio::EnsEMBL::IdMapping::GeneScoreBuilder->new(
+    -LOGGER       => $logger,
+    -CONF         => $conf,
+    -CACHE        => $cache
+  );
 
   $exon_scores = $esb->score_exons;
-  $transcript_scores = $tsb->score_transcripts;
-  #$gene_scores = $gsb->score_genes;
+  $transcript_scores = $tsb->score_transcripts($exon_scores);
+  $gene_scores = $gsb->score_genes($transcript_scores);
 }
 
 
@@ -191,7 +157,7 @@ sub build_scores {
 # test memory consumption of cache after merging. used for debugging.
 #
 sub log_cache_stats {
-  $logger->log("\nCache memory usage:\n\n");
+  $logger->info("\nCache memory usage:\n\n");
 
   my $s;
   my %keys;
@@ -211,26 +177,26 @@ sub log_cache_stats {
   my $fmt = "%-50s%12.0f\n";
 
   foreach my $k (sort { $keys{$a} <=> $keys{$b} } keys %keys) {
-    $logger->log(sprintf($fmt, $k, $keys{$k}), 1);
+    $logger->info(sprintf($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);
+  $logger->info(sprintf($fmt, "total overhead", $s), 1);
+  $logger->info(sprintf($fmt, "data", ($ts-$s)), 1);
+  $logger->info(sprintf($fmt, "total", $ts)."\n", 1);
 
   # test
   my $i = 0;
   foreach my $eid (keys %{ $cache->get_by_name('exons_by_id', 'target') }) {
     last if ($i++ > 0);
     
-    $logger->log("\nData object memory usage:\n\n");
+    $logger->info("\nData object memory usage:\n\n");
     
     my $exon = $cache->get_by_key('exons_by_id', 'target', $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);
+    $logger->info(sprintf($fmt, "object", $s1), 1);
+    $logger->info(sprintf($fmt, "data", ($ts1-$s1)), 1);
+    $logger->info(sprintf($fmt, "total", $ts1)."\n", 1);
 
     print $exon->stable_id."\n";
     #warn Data::Dumper::Dumper($exon);

misc-scripts/id_mapping/run_all.pl

@@ -2,10 +2,11 @@
 
 =head1 NAME
 
+run_all.pl - wrapper script to run the stable ID mapping
 
 =head1 SYNOPSIS
 
-.pl [arguments]
+run_all.pl [arguments]
 
 Required arguments:
 
@@ -23,8 +24,8 @@ Optional arguments:
   --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)
 
-  -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)
@@ -53,135 +54,80 @@ 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;
-
+# parse configuration and commandline arguments
 my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-  -SERVERROOT => $SERVERROOT,
+  -SERVERROOT => "$Bin/../../..",
+  -DEFAULT_CONF => "$Bin/default.conf"
 );
 
-# parse options
-$conf->param('default_conf', './default.conf');
-$conf->parse_common_options(@_);
-$conf->parse_extra_options(qw(
-  sourcehost|source_host=s
-  sourceport|source_port=n
-  sourceuser|source_user=s
-  sourcepass|source_pass=s
-  sourcedbname|source_dbname=s
-  targethost|target_host=s
-  targetport|target_port=n
-  targetuser|target_user=s
-  targetpass|target_pass=s
-  targetdbname|target_dbname=s
-  mode=s
-  dumppath|dump_path=s
-  cachefile|cache_file=s
-  chromosomes|chr=s@
-  region=s
-  biotypes=s@
-  min_exon_length|minexonlength=i
-  exonerate_path|exoneratepath=s
-  exonerate_threshold|exoneratethreshold=i
-  exonerate_jobs|exoneratejobs=i
-  exonerate_bytes_per_job|exoneratebytesperjob=i
-));
-$conf->allowed_params(
-  $conf->get_common_params,
-  qw(
-    sourcehost sourceport sourceuser sourcepass sourcedbname
-    targethost targetport targetuser targetpass targetdbname
-    mode
-    dumppath cachefile
-    chromosomes region biotypes
-    min_exon_length
-    exonerate_path exonerate_threshold exonerate_jobs exonerate_byte_per_job
-  )
+$conf->parse_options(
+  'sourcehost|source_host=s' => 1,
+  'sourceport|source_port=n' => 1,
+  'sourceuser|source_user=s' => 1,
+  'sourcepass|source_pass=s' => 0,
+  'sourcedbname|source_dbname=s' => 1,
+  'targethost|target_host=s' => 1,
+  'targetport|target_port=n' => 1,
+  'targetuser|target_user=s' => 1,
+  'targetpass|target_pass=s' => 0,
+  'targetdbname|target_dbname=s' => 1,
+  'mode=s' => 0,
+  'dumppath|dump_path=s' => 1,
+  'chromosomes|chr=s@' => 0,
+  'region=s' => 0,
+  'biotypes=s@' => 0,
+  'min_exon_length|minexonlength=i' => 0,
+  'exonerate_path|exoneratepath=s' => 1,
+  'exonerate_threshold|exoneratethreshold=f' => 0,
+  'exonerate_jobs|exoneratejobs=i' => 0,
+  'exonerate_bytes_per_job|exoneratebytesperjob=f' => 0,
 );
 
-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'),
+  -LOGLEVEL     => $conf->param('loglevel'),
 );
 
 # initialise log
-$logger->init_log($conf->list_all_params);
-
-# check required parameters were set
-$conf->check_required_params(
-  qw(
-    sourcehost sourceport sourceuser sourcedbname
-    targethost targetport targetuser targetdbname
-    dumppath
-  )
-);
+$logger->init_log($conf->list_param_values);
 
-# define options for the components
+# this script is only a wrapper and will run one or more components.
+# define options for the components here.
 my %options;
 
 $options{'dump_cache'} = $conf->create_commandline_options(
-    -ALLOWED_PARAMS => 1,
-    -REPLACE => {
-        interactive => 0,
-        is_component => 1,
-    },
-    -EXCLUDE => [qw(mode min_exon_length exonerate_path exonerate_threshold
-                    exonerate_jobs exonerate_byte_per_job)]
+  interactive => 0,
+  is_component => 1,
 );
 
 $options{'id_mapping'} = $conf->create_commandline_options(
-    -ALLOWED_PARAMS => 1,
-    -REPLACE => {
-        interactive => 0,
-        is_component => 1,
-    },
-    -EXCLUDE => [qw(
-        sourcehost sourceport sourceuser sourcepass sourcedbname
-        targethost targetport targetuser targetpass targetdbname
-    )]
+  interactive => 0,
+  is_component => 1,
 );
 
-# dump cache files (this is done for all modes)
-&run_component('dump_cache.pl', $options{'dump_cache'}, 'building cache');
-
 # run components, depending on mode
 my $mode = $conf->param('mode') || 'normal';
 my $sub = "run_$mode";
 no strict 'refs';
 &$sub;
 
-
 # finish logfile
 $logger->finish_log;
 
-
 ### END main ###
 
 
 sub run_normal {
+  
+  # dump cache files (this is done for all modes)
+  &run_component('dump_cache.pl', $options{'dump_cache'}, 'building cache');
+
   # ID mapping
   &run_component('id_mapping.pl', $options{'id_mapping'}, 'Id mapping');
 
@@ -193,6 +139,7 @@ sub run_normal {
 
   # QC
   #&run_component('qc.pl', $options{'qc'}, 'QC');
+
 }
 
 
@@ -201,11 +148,11 @@ sub run_component {
   my $options = shift;
   my $logtext = shift || $cmd;
 
-  $logger->log_stamped("----- $logtext -----\n");
-  
+  $logger->info("----- $logtext -----\n", 0, 'stamped');
+
   system("./$cmd $options") == 0
-    or $logger->log_error("Error running $cmd. Please see the respective logfile for more information.\n");
+    or $logger->error("Error running $cmd. Please see the respective logfile for more information.\n");
   
-  $logger->log_stamped("----- done with $logtext -----\n\n");
+  $logger->info("----- done with $logtext -----\n\n", 0, 'stamped');
 }