diff --git a/misc-scripts/id_mapping/id_mapping.pl b/misc-scripts/id_mapping/id_mapping.pl
index 56aeade301e1b9d0b97db324cd4dc2c9218c1068..1aa084cb66f4670372640210217062ba55637d35 100755
--- a/misc-scripts/id_mapping/id_mapping.pl
+++ b/misc-scripts/id_mapping/id_mapping.pl
@@ -56,7 +56,8 @@ 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::Utils::Exception qw(throw);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append inject);
use Bio::EnsEMBL::IdMapping::Cache;
use Bio::EnsEMBL::IdMapping::ExonScoreBuilder;
use Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder;
@@ -77,26 +78,38 @@ my $conf = new Bio::EnsEMBL::Utils::ConfParser(
);
$conf->parse_options(
- 'mode=s' => 0,
- 'basedir|basedir=s' => 1,
- 'chromosomes|chr=s@' => 0,
- 'region=s' => 0,
- 'biotypes=s@' => 0,
- 'min_exon_length|minexonlength=i' => 0,
- 'exonerate_path|exoneratepath=s' => 1,
- 'exonerate_threshold|exoneratethreshold=f' => 0,
- 'exonerate_jobs|exoneratejobs=i' => 0,
+ 'mode=s' => 0,
+ 'basedir|basedir=s' => 1,
+ 'chromosomes|chr=s@' => 0,
+ 'region=s' => 0,
+ 'biotypes=s@' => 0,
+ 'min_exon_length|minexonlength=i' => 0,
+ 'exonerate_path|exoneratepath=s' => 1,
+ 'exonerate_threshold|exoneratethreshold=f' => 0,
+ 'exonerate_jobs|exoneratejobs=i' => 0,
'exonerate_bytes_per_job|exoneratebytesperjob=f' => 0,
- 'exonerate_extra_params|exonerateextraparams=s' => 0,
- 'plugin_internal_id_mappers_gene=s@' => 0,
- 'plugin_internal_id_mappers_transcript=s@' => 0,
- 'plugin_internal_id_mappers_exon=s@' => 0,
- 'mapping_types=s@' => 1,
- 'plugin_stable_id_generator=s' => 0,
- 'upload_events|uploadevents=s' => 0,
- 'upload_stable_ids|uploadstableids=s' => 0,
- 'upload_archive|uploadarchive=s' => 0,
-);
+ 'exonerate_extra_params|exonerateextraparams=s' => 0,
+ 'plugin_internal_id_mappers_gene=s@' => 0,
+ 'plugin_internal_id_mappers_transcript=s@' => 0,
+ 'plugin_internal_id_mappers_exon=s@' => 0,
+ 'mapping_types=s@' => 1,
+ 'plugin_stable_id_generator=s' => 0,
+ 'upload_events|uploadevents=s' => 0,
+ 'upload_stable_ids|uploadstableids=s' => 0,
+ 'upload_archive|uploadarchive=s' => 0,
+ # EG allow additional configs to be set on command line
+ 'sourcedbname=s' => 1,
+ 'sourcehost=s' => 1,
+ 'sourceuser=s' => 1,
+ 'sourcepass=s' => 1,
+ 'sourceport=i' => 1,
+ 'targetdbname=s' => 1,
+ 'targethost=s' => 1,
+ 'targetuser=s' => 1,
+ 'targetpass=s' => 1,
+ 'targetport=i' => 1,
+ 'species_id' => 0,
+ 'species_name' => 0 );
# set default logpath
unless ($conf->param('logpath')) {
@@ -131,35 +144,110 @@ my $transcript_mappings;
my $gene_mappings;
my $translation_mappings;
-# 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
-);
-
-
+# EG mapping code reworked to iterate over different species
# 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');
-# run in requested mode
-my $mode = $conf->param('mode') || 'normal';
-if ( $mode eq 'mapping' ) { $mode = 'normal' }
-my $run = "run_$mode";
-no strict 'refs';
-&$run;
+# EG create placeholder cache based on the first species to allow us to
+# create a stable ID generator to reuse for all species
+my $cache;
+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 $species (@species_ids)
# finish logfile
@@ -387,49 +475,73 @@ sub archive {
sub upload_mapping_session_and_events {
- if ($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');
- $logger->info("$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',
+ $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("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') and ! $conf->param('dry_run')) {
-
+ if ( $conf->is_true('upload_stable_ids')
+ && !$conf->param('dry_run') )
+ {
+
+ my $species_id = $conf->param('species_id');
+
$logger->info("Uploading stable ID tables...\n");
-
- 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);
+
+ 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 );
+ }
+
}
-
$logger->info("Done.\n\n");
-
+
} else {
$logger->info("Stable ID tables not uploaded.\n\n");
}
@@ -539,4 +651,61 @@ 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.db_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