From 5d0819811cca58d96f8366ab08d540d03ccf9d27 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Tue, 13 Jul 2010 09:21:47 +0000
Subject: [PATCH] Stable ID generators from Dan S. for Ensembl Genomes.
---
.../StableIdGenerator/EnsemblBacteria.pm | 144 ++++++++++++++++++
.../StableIdGenerator/EnsemblFungi.pm | 44 ++++++
.../StableIdGenerator/EnsemblProtists.pm | 41 +++++
3 files changed, 229 insertions(+)
create mode 100644 modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblBacteria.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblFungi.pm
create mode 100644 modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblProtists.pm
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblBacteria.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblBacteria.pm
new file mode 100644
index 0000000000..a46e9d6f45
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblBacteria.pm
@@ -0,0 +1,144 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2010 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblBacteria;
+use strict;
+use warnings;
+no warnings 'uninitialized';
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric);
+
+#
+# new generator for EnsemblBacteria
+# 1. generates EB style IDs
+# 2. updates base ID to allow for multi-species DBs to be correctly incremented
+#
+sub initial_stable_id {
+ my $self = shift;
+ my $type = shift;
+ my $base = $self->get_base();
+ # retrieve last good stable ID from hash
+ my $init_stable_id = $self->{stable_id_list}{$type};
+ if ( !$init_stable_id ) {
+ $self->logger->debug(
+ "Finding new init_stable_id as base for new $type stable IDs.\n");
+
+ # use stable ID from configuration if set
+ if ( $init_stable_id =
+ $self->conf->param("starting_${type}_stable_id") )
+ {
+ $self->logger->debug(
+"Using pre-configured $init_stable_id as base for new $type stable IDs.\n"
+ );
+ return $init_stable_id;
+ }
+ my $s_dba = $self->cache->get_DBAdaptor('source');
+ my $s_dbh = $s_dba->dbc->db_handle;
+
+ # look in the ${type}_stable_id table first
+ my $sql =
+qq(SELECT MAX(stable_id) FROM ${type}_stable_id where stable_id like '${base}%');
+ print $sql;
+ $init_stable_id = $self->fetch_value_from_db( $s_dbh, $sql );
+
+ # also look in gene_archive to make sure there are no larger Ids there
+ unless ( $type eq 'exon' ) {
+ $sql = qq(SELECT MAX(${type}_stable_id) FROM gene_archive);
+ my $archived_stable_id = $self->fetch_value_from_db( $s_dbh, $sql );
+ if ( $archived_stable_id
+ and $self->is_valid($archived_stable_id)
+ and ( $archived_stable_id gt $init_stable_id ) )
+ {
+ $init_stable_id = $archived_stable_id;
+ }
+ }
+ $self->{stable_id_list}{$type} = $init_stable_id;
+ } else {
+ $self->logger->debug(
+"Using preexisting initial $init_stable_id as base for new $type stable IDs.\n"
+ );
+ }
+ if ($init_stable_id) {
+
+ # since $init_stable_id now is the highest existing stable Id for this
+ # object type, we need to increment it to find the first one we want to use
+ # for new assignments
+ $init_stable_id = $self->increment_stable_id( $init_stable_id, $type );
+ $self->logger->debug(
+ "Using $init_stable_id as base for new $type stable IDs.\n");
+ } else {
+ $self->logger->warning(
+ "Can't find highest ${type}_stable_id in source db.\n");
+ my $pref =
+ $self->cache->get_DBAdaptor('target')->get_MetaContainer()
+ ->list_value_by_key('species.stable_id_prefix');
+ if ($pref) {
+ $init_stable_id =
+ $pref->[0] . substr( uc($type), 0, 1 ) . '00000000000';
+ $self->logger->debug(
+ "Using $init_stable_id as base for new $type stable IDs.\n");
+ }
+ }
+ return $init_stable_id;
+}
+
+sub increment_stable_id {
+ my $self = shift;
+ my $stable_id = shift;
+ my $type = shift;
+ unless ( $self->is_valid($stable_id) ) {
+ throw("Unknown or missing stable ID: $stable_id.");
+ }
+ my $base = $self->get_base();
+ $stable_id =~ /$base([A-Z]{1,4})(\d{11})/;
+ my $number = $2;
+ my $new_stable_id = $base . $1 . ( ++$number );
+ $self->{stable_id_list}{$type} = $new_stable_id;
+ return $new_stable_id;
+}
+
+=head2 is_valid
+
+ Arg[1] : String $stable_id - the stable Id to check
+ Example : unless ($generator->is_valid($stable_id)) {
+ die "Invalid stable Id: $stable_id.\n";
+ }
+ Description : Tests a stable Id to be valid (according to the Ensembl stable
+ Id format definition).
+ Return type : Boolean - TRUE if valid, FALSE otherwise
+ Exceptions : none
+ Caller : general
+ Status : At Risk
+ : under development
+
+=cut
+
+sub is_valid {
+ my ( $self, $stable_id ) = @_;
+
+ my $base = $self->get_base();
+
+ return ( $stable_id
+ and ( $stable_id =~ /$base([A-z]{1,4})(\d{11})/ ) );
+}
+
+sub get_base { return 'EB' }
+
+1;
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblFungi.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblFungi.pm
new file mode 100644
index 0000000000..d1cedea771
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblFungi.pm
@@ -0,0 +1,44 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2010 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblFungi;
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblBacteria);
+
+# new generator providing EF IDs
+
+sub is_valid {
+ my ( $self, $stable_id ) = @_;
+
+ my $base = $self->get_base();
+
+ return ( $stable_id and ( $stable_id =~ /$base([A-z]{1,4})(\d{11})/
+ or $stable_id =~ /SP.*/ ) );
+}
+
+
+sub get_base { return 'EF' }
+
+1;
+
diff --git a/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblProtists.pm b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblProtists.pm
new file mode 100644
index 0000000000..fe0e1265f3
--- /dev/null
+++ b/modules/Bio/EnsEMBL/IdMapping/StableIdGenerator/EnsemblProtists.pm
@@ -0,0 +1,41 @@
+=head1 LICENSE
+
+ Copyright (c) 1999-2010 The European Bioinformatics Institute and
+ Genome Research Limited. All rights reserved.
+
+ This software is distributed under a modified Apache license.
+ For license details, please see
+
+ http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+ Please email comments or questions to the public Ensembl
+ developers list at <ensembl-dev@ebi.ac.uk>.
+
+ Questions may also be sent to the Ensembl help desk at
+ <helpdesk@ensembl.org>.
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblProtists;
+use strict;
+use warnings;
+no warnings 'uninitialized';
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+use base qw(Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblBacteria);
+
+# new generator to create new protist IDs (and also deal with existing plasmodial IDs)
+
+sub is_valid {
+ my ( $self, $stable_id ) = @_;
+ my $base = $self->get_base();
+ return ( $stable_id and ( $stable_id =~ /$base([A-z]{1,4})(\d{11})/
+ or $stable_id =~ /PVX.*/
+ or $stable_id =~ /PKH.*/ ) );
+
+}
+
+sub get_base { return 'EPr' }
+
+1;
--
GitLab