diff --git a/misc-scripts/id_mapping/dump_by_seq_region.pl b/misc-scripts/id_mapping/dump_by_seq_region.pl
index a434e9f2bcb9800b7096e909a8c555cbd5d98531..096a7faa36d70124dfed183601dd49719206c889 100755
--- a/misc-scripts/id_mapping/dump_by_seq_region.pl
+++ b/misc-scripts/id_mapping/dump_by_seq_region.pl
@@ -97,27 +97,6 @@ my $index = $conf->param('index');
my $logautobase = ($conf->param('logautobase') || 'dump_by_seq_region').
".$dbtype";
-# EG - need to determine species before opening the cache and log
-# determine which slice to process. To do so, read the file containing
-# the slices to be processed, and take the one at position $index. This
-# includes the species_id.
-my $logpath = $conf->param('logpath');
-my $filename = "$dbtype.dump_cache.slices.txt";
-open( my $fh, '<', "$logpath/$filename" )
- or throw("Unable to open $logpath/$filename for reading: $!");
-my @slice_names = <$fh>;
-my $slice_string = $slice_names[ $index - 1 ];
-chomp($slice_string);
-
-my ( $slice_name, $species_name, $species_id, $source_species_id ) =
- split( ',', $slice_string );
-
-close($fh);
-
-$conf->param('basedir',path_append($conf->param('basedir'), $species_id));
-$conf->param('species_id',$species_id);
-$conf->param('species_name',$species_name);
-
# get log filehandle and print heading and parameters to logfile
my $logger = new Bio::EnsEMBL::Utils::Logger(
-LOGFILE => $conf->param('logfile'),
@@ -139,6 +118,17 @@ my $cache = $cache_impl->new(
-CONF => $conf,
);
+# determine which slice to process. to do so, read the file containing the
+# slices to be processed, and take the one at position $index
+my $logpath = $conf->param('logpath');
+my $filename = "$dbtype.dump_cache.slices.txt";
+open(my $fh, '<', "$logpath/$filename") or
+ throw("Unable to open $logpath/$filename for reading: $!");
+my @slice_names = <$fh>;
+my $slice_name = $slice_names[$index-1];
+chomp($slice_name);
+close($fh);
+
# no build the cache for this slice
$cache->build_cache_by_slice($dbtype, $slice_name);
diff --git a/misc-scripts/id_mapping/dump_cache.pl b/misc-scripts/id_mapping/dump_cache.pl
index 6291687ff6b75ba6cad8f70c1a2ade827df641d7..8761134e5c5501bbabc548be675bcb684a57de1c 100755
--- a/misc-scripts/id_mapping/dump_cache.pl
+++ b/misc-scripts/id_mapping/dump_cache.pl
@@ -137,26 +137,18 @@ sub build_cache_auto {
my $cache_impl = 'Bio::EnsEMBL::IdMapping::Cache';
inject($cache_impl);
- # EG - populate cache for each species in turn
- $logger->debug("\nChecking number of toplevel seq_regions...\n");
- my $max = 0;
- my @species_ids = @{ get_species_ids("target") };
- foreach my $dbtype (qw(source target)) {
-
- # populate the cache for each species in turn
- for my $species (@species_ids) {
- $conf->param( 'species_id', $$species[1] );
- $conf->param( 'species_name', $$species[0] );
-
- my $cache = $cache_impl->new( -LOGGER => $logger,
- -CONF => $conf, );
+ my $cache = $cache_impl->new(
+ -LOGGER => $logger,
+ -CONF => $conf,
+ );
- my $num =
- scalar( @{ $cache->slice_names( $dbtype, @$species ) } );
+ $logger->debug("\nChecking number of toplevel seq_regions...\n");
+ my $max = 0;
- $max = $num if ( $num > $max );
- $logger->debug( "$dbtype: $num.\n", 1 );
- }
+ foreach my $dbtype (qw(source target)) {
+ my $num = scalar(@{ $cache->slice_names($dbtype) });
+ $max = $num if ($num > $max);
+ $logger->debug("$dbtype: $num.\n", 1);
}
my $threshold = $conf->param('build_cache_auto_threshold') || 100;
@@ -185,144 +177,99 @@ sub build_cache_by_seq_region {
system("mkdir -p $logpath") == 0 or
$logger->error("Can't create lsf log dir $logpath: $!\n");
-
- # EG get the list of species IDs for sources and targets
- my @source_species_ids = @{ get_species_ids("source") };
- my @species_ids = @{ get_species_ids("target") };
-
# load the cache implementation
my $cache_impl = 'Bio::EnsEMBL::IdMapping::Cache';
inject($cache_impl);
- # EG store the base directory onto which the species ID will be added
- my $basedir = $conf->param('basedir');
+ my $cache = $cache_impl->new(
+ -LOGGER => $logger,
+ -CONF => $conf,
+ );
# submit jobs to lsf
foreach my $dbtype (qw(source target)) {
- # EG iterate over individual species for source and target
+ $logger->info("\n".ucfirst($dbtype)." db...\n", 0, 'stamped');
# determine which slices need to be done
my $filename = "$dbtype.dump_cache.slices.txt";
- open( my $fh, '>', "$logpath/$filename" )
- or throw("Unable to open $logpath/$filename for writing: $!");
-
+ open(my $fh, '>', "$logpath/$filename") or
+ throw("Unable to open $logpath/$filename for writing: $!");
+
my $num_jobs = 0;
- for my $species (@species_ids) {
-
- # EG set config based on species ID in turn
- $conf->param( 'basedir', path_append( $basedir, $$species[1] ) );
- $conf->param( 'species_id', $$species[1] );
- $conf->param( 'species_name', $$species[0] );
-
- # EG load cache for current species ID
- my $cache = $cache_impl->new( -LOGGER => $logger,
- -CONF => $conf, );
- foreach my $slice_name (
- @{ $cache->slice_names( $dbtype, @$species ) } )
- {
- my $type = "$dbtype.$slice_name";
- my $src_species_id;
- for my $src_id (@source_species_ids) {
- if ( $$species[1] == $$src_id[1] ) {
- $src_species_id = $$src_id[1];
- last;
- }
- }
- $logger->info( "\n" . ucfirst($dbtype) . " db...\n",
- 0, 'stamped' );
-
- my $type = "$dbtype.$slice_name";
- unless ( $cache->cache_file_exists($type) ) {
- print $fh "$slice_name,$$species[0],$$species[1],"
- . $src_species_id . "\n";
- $num_jobs++;
- }
- }
- unless ($num_jobs) {
- $logger->info("All cache files for $dbtype exist.\n");
- next;
+ foreach my $slice_name (@{ $cache->slice_names($dbtype) }) {
+ my $type = "$dbtype.$slice_name";
+ unless ($cache->cache_file_exists($type)) {
+ print $fh "$slice_name\n";
+ $num_jobs++;
}
+ }
- } ## end for my $species (@species_ids)
close($fh);
- # EG reset original basedir
- $conf->param( 'basedir', $basedir );
+ unless ($num_jobs) {
+ $logger->info("All cache files for $dbtype exist.\n");
+ next;
+ }
# build lsf command
- my $lsf_name = 'dump_by_seq_region_' . time;
+ my $lsf_name = 'dump_by_seq_region_'.time;
my $concurrent = $conf->param('build_cache_concurrent_jobs') || 200;
- my $options =
- $conf->create_commandline_options(
- logauto => 1,
- logautobase => "dump_by_seq_region",
- interactive => 0,
- is_component => 1,
- dbtype => $dbtype,
- cache_impl => $cache_impl, );
-
- # EG invoke perl with correct path rather than relying on shebang
- my $cmd = 'perl dump_by_seq_region.pl '
- . qq{$options --index \$LSB_JOBINDEX};
-
- my $pipe =
- '|bsub '
- . $conf->param('lsf_opt_run')
- . qq{ -J '$lsf_name\[1-$num_jobs\]\%$concurrent' }
- . qq{-o $logpath/dump_by_seq_region.$dbtype.\%I.out }
- . qq{-e $logpath/dump_by_seq_region.$dbtype.\%I.err }
- . $conf->param('lsf_opt_dump_cache');
+ my $options = $conf->create_commandline_options(
+ logauto => 1,
+ logautobase => "dump_by_seq_region",
+ interactive => 0,
+ is_component => 1,
+ dbtype => $dbtype,
+ cache_impl => $cache_impl,
+ );
- # run lsf job array
- $logger->info("\nSubmitting $num_jobs jobs to lsf.\n");
+ my $cmd = qq{./dump_by_seq_region.pl $options --index \$LSB_JOBINDEX};
- if ( $num_jobs > 0 ) {
- $logger->debug("$cmd\n\n");
- $logger->debug("$pipe\n\n");
+ my $pipe = qq{|bsub -J$lsf_name\[1-$num_jobs\]\%$concurrent } .
+ qq{-o $logpath/dump_by_seq_region.$dbtype.\%I.out } .
+ qq{-e $logpath/dump_by_seq_region.$dbtype.\%I.err } .
+ $conf->param('lsf_opt_dump_cache');
- local *BSUB;
- open BSUB, $pipe
- or $logger->error("Could not open open pipe to bsub: $!\n");
+ # run lsf job array
+ $logger->info("\nSubmitting $num_jobs jobs to lsf.\n");
+ $logger->debug("$cmd\n\n");
- print BSUB $cmd;
- $logger->error("Error submitting jobs: $!\n")
- unless ( $? == 0 );
- close BSUB;
+ local *BSUB;
+ open BSUB, $pipe or
+ $logger->error("Could not open open pipe to bsub: $!\n");
- # submit dependent job to monitor finishing of jobs
- $logger->info( "Waiting for jobs to finish...\n", 0, 'stamped' );
+ print BSUB $cmd;
+ $logger->error("Error submitting jobs: $!\n")
+ unless ($? == 0);
+ close BSUB;
- my $dependent_job =
- qq{bsub -K -w "ended($lsf_name)" }
- . $conf->param('lsf_opt_run_small')
- . qq{ -o $logpath/dump_cache.$dbtype.depend.out /bin/true};
+ # submit dependent job to monitor finishing of jobs
+ $logger->info("Waiting for jobs to finish...\n", 0, 'stamped');
- system($dependent_job) == 0
- or $logger->error("Error submitting dependent job: $!\n");
+ my $dependent_job = qq{bsub -K -w "ended($lsf_name)" -q small } .
+ qq{-o $logpath/dump_cache.$dbtype.depend.out /bin/true};
- $logger->info( "All jobs finished.\n", 0, 'stamped' );
+ system($dependent_job) == 0 or
+ $logger->error("Error submitting dependent job: $!\n");
- sleep(5);
- } ## end if ( $num_jobs > 0 )
+ $logger->info("All jobs finished.\n", 0, 'stamped');
# check for lsf errors
+ sleep(5);
my $err;
- foreach my $i ( 1 .. $num_jobs ) {
- if ( !-e "$logpath/dump_by_seq_region.$dbtype.$i.success" ) {
- $err++;
- }
+ foreach my $i (1..$num_jobs) {
+ $err++ unless (-e "$logpath/dump_by_seq_region.$dbtype.$i.success");
}
- if ( $err > 0 ) {
- $logger->error( "At least one of your jobs failed.\n"
- . "Please check the logfiles at $logpath for errors.\n" );
+ if ($err) {
+ $logger->error("At least one of your jobs failed.\nPlease check the logfiles at $logpath for errors.\n");
return 1;
}
- } ## end foreach my $dbtype (qw(source target))
+ }
return 0;
}
@@ -357,32 +304,3 @@ sub build_cache_all {
}
-# EG new method for getting species IDs
-sub get_species_ids {
-
- my ($prefix) = @_;
- my @speciesIds;
- my $dsn =
- "DBI:mysql:database="
- . $conf->param("${prefix}dbname")
- . ";host="
- . $conf->param("${prefix}host")
- . ";port="
- . $conf->param("${prefix}port");
-
- my $ensemblCoreDbh = DBI->connect( $dsn,
- $conf->param("${prefix}user"),
- $conf->param("${prefix}pass") )
- || die "Cannot connect to server: $DBI::errstr\n";
-
- my $query = "SELECT DISTINCT meta_value, species_id
- FROM meta WHERE meta_key = 'species.production_name'";
-
- my $psmt = $ensemblCoreDbh->prepare($query);
- $psmt->execute();
-
- while ( my (@results) = $psmt->fetchrow() ) {
- push @speciesIds, [ $results[0], $results[1] ];
- }
- return \@speciesIds;
-} ## end sub get_species_ids
diff --git a/misc-scripts/id_mapping/id_mapping.pl b/misc-scripts/id_mapping/id_mapping.pl
index 9ae9df1565d648202b7cf807dff771bb2fc6fc41..56aeade301e1b9d0b97db324cd4dc2c9218c1068 100755
--- a/misc-scripts/id_mapping/id_mapping.pl
+++ b/misc-scripts/id_mapping/id_mapping.pl
@@ -56,8 +56,7 @@ no warnings 'uninitialized';
use FindBin qw($Bin);
use Bio::EnsEMBL::Utils::ConfParser;
use Bio::EnsEMBL::Utils::Logger;
-use Bio::EnsEMBL::Utils::Exception qw(throw);
-use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append inject);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
use Bio::EnsEMBL::IdMapping::Cache;
use Bio::EnsEMBL::IdMapping::ExonScoreBuilder;
use Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder;
@@ -78,38 +77,26 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
);
$conf->parse_options(
- 'mode=s' => 0,
- 'basedir|basedir=s' => 1,
- 'chromosomes|chr=s@' => 0,
- 'region=s' => 0,
- 'biotypes=s@' => 0,
- 'min_exon_length|minexonlength=i' => 0,
- 'exonerate_path|exoneratepath=s' => 1,
- 'exonerate_threshold|exoneratethreshold=f' => 0,
- 'exonerate_jobs|exoneratejobs=i' => 0,
+ 'mode=s' => 0,
+ 'basedir|basedir=s' => 1,
+ 'chromosomes|chr=s@' => 0,
+ 'region=s' => 0,
+ 'biotypes=s@' => 0,
+ 'min_exon_length|minexonlength=i' => 0,
+ 'exonerate_path|exoneratepath=s' => 1,
+ 'exonerate_threshold|exoneratethreshold=f' => 0,
+ 'exonerate_jobs|exoneratejobs=i' => 0,
'exonerate_bytes_per_job|exoneratebytesperjob=f' => 0,
- 'exonerate_extra_params|exonerateextraparams=s' => 0,
- 'plugin_internal_id_mappers_gene=s@' => 0,
- 'plugin_internal_id_mappers_transcript=s@' => 0,
- 'plugin_internal_id_mappers_exon=s@' => 0,
- 'mapping_types=s@' => 1,
- 'plugin_stable_id_generator=s' => 0,
- 'upload_events|uploadevents=s' => 0,
- 'upload_stable_ids|uploadstableids=s' => 0,
- 'upload_archive|uploadarchive=s' => 0,
- # EG allow additional configs to be set on command line
- 'sourcedbname=s' => 1,
- 'sourcehost=s' => 1,
- 'sourceuser=s' => 1,
- 'sourcepass=s' => 0,
- 'sourceport=i' => 1,
- 'targetdbname=s' => 1,
- 'targethost=s' => 1,
- 'targetuser=s' => 1,
- 'targetpass=s' => 0,
- 'targetport=i' => 1,
- 'species_id' => 0,
- 'species_name' => 0 );
+ 'exonerate_extra_params|exonerateextraparams=s' => 0,
+ 'plugin_internal_id_mappers_gene=s@' => 0,
+ 'plugin_internal_id_mappers_transcript=s@' => 0,
+ 'plugin_internal_id_mappers_exon=s@' => 0,
+ 'mapping_types=s@' => 1,
+ 'plugin_stable_id_generator=s' => 0,
+ 'upload_events|uploadevents=s' => 0,
+ 'upload_stable_ids|uploadstableids=s' => 0,
+ 'upload_archive|uploadarchive=s' => 0,
+);
# set default logpath
unless ($conf->param('logpath')) {
@@ -144,109 +131,35 @@ my $transcript_mappings;
my $gene_mappings;
my $translation_mappings;
-# EG mapping code reworked to iterate over different species
+# loading cache from file
+my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
+ -LOGGER => $logger,
+ -CONF => $conf,
+ -LOAD_INSTANCE => 1,
+);
+
+
+# get a stable ID mapper
+my $stable_id_mapper = Bio::EnsEMBL::IdMapping::StableIdMapper->new(
+ -LOGGER => $logger,
+ -CONF => $conf,
+ -CACHE => $cache
+);
+
+
# find out which entities we want to map
my %mapping_types = ();
-foreach my $type ( $conf->param('mapping_types') ) {
+foreach my $type ($conf->param('mapping_types')) {
$mapping_types{$type} = 1;
}
-# EG get list of species
-my @species_ids = @{ get_species_ids( "target", $conf ) };
-my $basedir = $conf->param('basedir');
-# EG create placeholder cache based on the first species to allow us to
-# create a stable ID generator to reuse for all species
-my $stable_id_mapper;
-my $s = $species_ids[0];
-$conf->param( 'basedir', path_append( $basedir, $$s[1] ) );
-$conf->param( 'species_id', $$s[1] );
-$conf->param( 'species_name', $$s[0] );
-
-# loading cache from file
-my $cache = Bio::EnsEMBL::IdMapping::Cache->new(
- -LOGGER => $logger,
- -CONF => $conf,
- -LOAD_INSTANCE => 1,
- -SPECIES_ID => $$s[1], # EG
- -SPECIES_NAME => $$s[0] # EG
-);
-
-my $type_count_sql = { gene => 'select count(*) '
- . 'from gene_stable_id '
- . 'join gene using (gene_id) '
- . 'join seq_region using (seq_region_id) '
- . 'join coord_system using (coord_system_id) '
- . 'where species_id=?',
- transcript => 'select count(*) '
- . 'from transcript_stable_id '
- . 'join transcript using (transcript_id) '
- . 'join seq_region using (seq_region_id) '
- . 'join coord_system using (coord_system_id) '
- . 'where species_id=?',
- exon => 'select count(*) '
- . 'from exon_stable_id '
- . 'join exon using (exon_id) '
- . 'join seq_region using (seq_region_id) '
- . 'join coord_system using (coord_system_id) '
- . 'where species_id=?',
- translation => 'select count(*) '
- . 'from translation_stable_id '
- . 'join translation using (translation_id) '
- . 'join transcript using (transcript_id) '
- . 'join seq_region using (seq_region_id) '
- . 'join coord_system using (coord_system_id) '
- . 'where species_id=?' };
-
-# eg get the stable id generator and inject the cache into it
-my $stable_id_generator = $conf->param('plugin_stable_id_generator')
- || 'Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric';
-inject($stable_id_generator);
-
-# create a new stableidgenerator object
-my $generator_instance =
- $stable_id_generator->new( -logger => $logger,
- -conf => $conf,
- -cache => $cache );
-
-# EG iterate over species
-for my $species (@species_ids) {
- # EG create a new cache for the current species
- print( "Handling species " . $$species[0] . "/" . $$species[1],
- "\n" );
-
- $conf->param( 'basedir', path_append( $basedir, $$species[1] ) );
- $conf->param( 'species_id', $$species[1] );
- $conf->param( 'species_name', $$species[0] );
-
- $cache =
- Bio::EnsEMBL::IdMapping::Cache->new( -LOGGER => $logger,
- -CONF => $conf,
- -LOAD_INSTANCE => 1 );
-
- # get a stable ID mapper
- $stable_id_mapper =
- Bio::EnsEMBL::IdMapping::StableIdMapper->new( -LOGGER => $logger,
- -CONF => $conf,
- -CACHE => $cache );
-
- # EG replace the genny cache with the species specific one
- $generator_instance->cache($cache);
- $stable_id_mapper->stable_id_generator($generator_instance);
-
- ##? # find out which entities we want to map
- ##? my %mapping_types = ();
- ##? foreach my $type ( $conf->param('mapping_types') ) {
- ##? $mapping_types{$type} = 1;
- ##? }
-
- # run in requested mode
- my $mode = $conf->param('mode') || 'normal';
- if ( $mode eq 'mapping' ) { $mode = 'normal' }
- my $run = "run_$mode";
- no strict 'refs';
- &$run;
-} ## end for my $species (@species_ids)
+# run in requested mode
+my $mode = $conf->param('mode') || 'normal';
+if ( $mode eq 'mapping' ) { $mode = 'normal' }
+my $run = "run_$mode";
+no strict 'refs';
+&$run;
# finish logfile
@@ -474,73 +387,49 @@ sub archive {
sub upload_mapping_session_and_events {
- if ( $conf->is_true('upload_events') and !$conf->param('dry_run') ) {
-
- $logger->info(
- "Uploading mapping_session and stable_id_event tables...\n");
+ if ($conf->is_true('upload_events') and ! $conf->param('dry_run')) {
+
+ $logger->info("Uploading mapping_session and stable_id_event tables...\n");
my $i = 0;
my $j = 0;
-
- $logger->info( "mapping_session...\n", 1 );
-
- $i +=
- $stable_id_mapper->upload_file_into_table( 'target',
- 'mapping_session', 'mapping_session.txt',
- $conf->param('species_id') > 1 ? 1 : 0 );
-
- $logger->info( "$i\n", 1 );
-
- $logger->info( "stable_id_event...\n", 1 );
-
- $j += $stable_id_mapper->upload_file_into_table( 'target',
- 'stable_id_event', 'stable_id_event_existing.txt' );
- $j += $stable_id_mapper->upload_file_into_table( 'target',
- 'stable_id_event', 'stable_id_event_new.txt', 1 );
- $j += $stable_id_mapper->upload_file_into_table( 'target',
- 'stable_id_event', 'stable_id_event_similarity.txt', 1 );
- $logger->info( "$j\n", 1 );
-
+
+ $logger->info("mapping_session...\n", 1);
+ $i += $stable_id_mapper->upload_file_into_table('target', 'mapping_session',
+ 'mapping_session.txt');
+ $logger->info("$i\n", 1);
+
+ $logger->info("stable_id_event...\n", 1);
+ $j += $stable_id_mapper->upload_file_into_table('target', 'stable_id_event',
+ 'stable_id_event_existing.txt');
+ $j += $stable_id_mapper->upload_file_into_table('target', 'stable_id_event',
+ 'stable_id_event_new.txt', 1);
+ $j += $stable_id_mapper->upload_file_into_table('target', 'stable_id_event',
+ 'stable_id_event_similarity.txt', 1);
+ $logger->info("$j\n", 1);
+
$logger->info("Done.\n\n");
-
+
} else {
- $logger->info(
- "Stable ID event and mapping session tables not uploaded.\n\n");
+ $logger->info("Stable ID event and mapping session tables not uploaded.\n\n");
}
-} ## end sub upload_mapping_session_and_events
+}
sub upload_stable_ids {
- if ( $conf->is_true('upload_stable_ids')
- && !$conf->param('dry_run') )
- {
-
- my $species_id = $conf->param('species_id');
-
+ if ($conf->is_true('upload_stable_ids') and ! $conf->param('dry_run')) {
+
$logger->info("Uploading stable ID tables...\n");
-
- foreach my $t ( $conf->param('mapping_types') ) {
- $logger->info( "${t}_stable_id...\n", 1 );
-
- # EG check if empty for species
- my $cnt = get_stable_id_count( $t, 'target', $species_id );
- if ( $cnt > 0 ) {
- $logger->warning( "Existing stable IDs found "
- . "for $t for species ID $species_id "
- . "- not uploading",
- 1 );
- $logger->info( "Data not uploaded!\n", 1 );
- } else {
-
- my $i = $stable_id_mapper->upload_file_into_table( 'target',
- "${t}_stable_id", "${t}_stable_id.txt", 1 );
-
- $logger->info( "$i\n", 1 );
- }
-
+
+ foreach my $t ($conf->param('mapping_types')) {
+ $logger->info("${t}_stable_id...\n", 1);
+ my $i = $stable_id_mapper->upload_file_into_table('target',
+ "${t}_stable_id", "${t}_stable_id.txt");
+ $logger->info("$i\n", 1);
}
+
$logger->info("Done.\n\n");
-
+
} else {
$logger->info("Stable ID tables not uploaded.\n\n");
}
@@ -650,61 +539,4 @@ sub log_cache_stats {
}
}
-sub get_stable_id_count {
- my ( $type, $dbtype, $species_id ) = @_;
-
- # EG new subroutine for finding if stable ID table has entries for
- # this species already
-
- my $dba = $cache->get_DBAdaptor($dbtype);
- my $dbh = $dba->dbc->db_handle;
-
- # check table is empty
- my $sql = $type_count_sql->{$type};
-
- if ( !defined($sql) ) {
- throw("Cannot count stable ids of type $type");
- }
-
- my $sth = $dbh->prepare($sql);
- $sth->execute($species_id);
-
- my ($c) = $sth->fetchrow_array;
- $sth->finish;
-
- return $c;
-}
-
-sub get_species_ids {
- my ( $prefix, $conf ) = @_;
-
- # EG additional subroutine for determining which species IDs are
- # present
-
- my @speciesIds;
-
- my $dsn =
- "DBI:mysql:database="
- . $conf->param("${prefix}dbname")
- . ";host="
- . $conf->param("${prefix}host")
- . ";port="
- . $conf->param("${prefix}port");
-
- my $ensemblCoreDbh = DBI->connect( $dsn,
- $conf->param("${prefix}user"),
- $conf->param("${prefix}pass") )
- || die "Cannot connect to server: $DBI::errstr\n";
-
- my $query = "SELECT DISTINCT meta_value, species_id
- FROM meta WHERE meta_key = 'species.production_name'";
-
- my $psmt = $ensemblCoreDbh->prepare($query);
- $psmt->execute();
-
- while ( my (@results) = $psmt->fetchrow() ) {
- push @speciesIds, [ $results[0], $results[1] ];
- }
- return \@speciesIds;
-} ## end sub get_species_ids
diff --git a/misc-scripts/id_mapping/myRun.ksh b/misc-scripts/id_mapping/myRun.ksh
index 7f864c7d0ef0ab110a36bbec749912a6aac00578..8a6e152b7dc0790444bc14e27f72a6941755620c 100755
--- a/misc-scripts/id_mapping/myRun.ksh
+++ b/misc-scripts/id_mapping/myRun.ksh
@@ -52,6 +52,6 @@ if [[ ${conf#/} == ${conf} ]]; then
exit
fi
-./run.pl --lsf --conf=${conf} --mode=${mode} --logauto
+./run.pl --lsf --conf=${conf} --logauto --mode=${mode}
# $Id$
diff --git a/misc-scripts/id_mapping/synteny_rescore.pl b/misc-scripts/id_mapping/synteny_rescore.pl
index f13b6efed57c9c3514f2840de093a6e0d90a07f5..0a0344d1cb88bc76b78875940f1c9b4e24e24f2e 100755
--- a/misc-scripts/id_mapping/synteny_rescore.pl
+++ b/misc-scripts/id_mapping/synteny_rescore.pl
@@ -67,23 +67,12 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
-DEFAULT_CONF => "$Bin/default.conf"
);
-$conf->parse_options( 'basedir|basedir=s' => 1,
- 'index|i=n' => 1,
- 'chromosomes|chr=s@' => 0,
- 'region=s' => 0,
- 'species_id=i' => 1,
- 'species_name=s' => 1,
- 'sourcedbname=s' => 1,
- 'sourcehost=s' => 1,
- 'sourceuser=s' => 1,
- 'sourcepass=s' => 0,
- 'sourceport=i' => 1,
- 'targetdbname=s' => 1,
- 'targethost=s' => 1,
- 'targetuser=s' => 1,
- 'targetpass=s' => 0,
- 'targetport=i' => 1 );
-
+$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');