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Commit 61334766 authored by Magali Ruffier's avatar Magali Ruffier
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Merge branch 'master' of https://github.com/Ensembl/ensembl

parents 26de24c9 fd51dd09
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misc-scripts/assembly/exon_conservation_check.pl
+ 8
− 22
View file @ 61334766
......@@ -28,8 +28,6 @@ use lib "$Bin/../../../ensembl-analysis/modules";
require AssemblyMapper::Support;
use Bio::EnsEMBL::Utils::Exception qw( throw );
use Pod::Usage;
use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
use Bio::EnsEMBL::Utils::BiotypeMapper;
#Genebuilder utils
require Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptUtils;
......@@ -51,11 +49,9 @@ unless ($support->parse_arguments(@_)) {
}
$support->connect_dbs;
my $onto_db_adaptor = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
-DBNAME => $support->ref_dba->dbc->dbname,
-DBCONN => $support->ref_dba->dbc,
);
my $biotype_mapper = new Bio::EnsEMBL::Utils::BiotypeMapper($onto_db_adaptor);
my $biotype_manager =
Bio::EnsEMBL::Registry->get_DBAdaptor('multi', 'production')->get_biotype_manager();
$support->log_stamped("Beginning analysis.\n");
$support->log("EXON KEY : !! = Very bad (pc mismatch), %% = Somewhat bad (mismatch), ?? = No mapping, might be bad, && = eval error\n");
......@@ -149,18 +145,11 @@ sub exon {
# Determine severity of the problem
$difference = diff(\$old_seq, \$projected_seq);
my $group_list = $biotype_mapper->belongs_to_groups($parent_gene->biotype);
my $group_list = $biotype_manager->belongs_to_groups($parent_gene);
foreach my $group (@$group_list) {
if ($group eq 'protein_coding') {
$state = '!!';
last;
}
}
if (!$state) {
# Middle badness.
$state = '%%';
$state = '!!' and last if $group eq 'protein_coding'
}
$state = '%%' unless $state; # Middle badness
}
$location = sprintf('%d : %d', $projected_exon->start(), $projected_exon->end());
......@@ -220,13 +209,10 @@ sub transcript {
if ($projected_transcript) {
#Check if it was protein coding
my $group_list = $biotype_mapper->belongs_to_groups($projected_transcript->biotype);
my $group_list = $biotype_manager->belongs_to_groups($projected_transcript);
my $is_pc = 0;
foreach my $group (@$group_list) {
if ($group eq 'protein_coding') {
$is_pc = 1;
last;
}
$is_pc = 1 and last if $group eq 'protein_coding';
}
#Now check for protein sequence mis-match
......
modules/Bio/EnsEMBL/Utils/BiotypeMapper.pm deleted 100644 → 0
+ 0
− 375
View file @ 26de24c9
=head1 LICENSE
Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=pod
=head1 NAME
BiotypeMapper - Translates EnsEMBL biotypes into Sequence Ontology terms and back
=head1 AUTHOR
Kieron Taylor, 2011 - ktaylor@ebi.ac.uk
=head1 SYNOPSIS
use Bio::EnsEMBL::Utils::BiotypeMapper
my $ontology_adaptor = $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );
my $biotype_mapper = new BiotypeMapper($ontology_adaptor);
print $biotype_mapper->translate_feature_to_SO_term($feature);
my $list_of_biotypes = $biotype_mapper->biotypes_belonging_to_group('protein-coding');
=head1 DESCRIPTION
BiotypeMapper provides a series of nearest matches between EnsEMBL biotypes and
the Sequence Ontology (http://www.sequenceontology.org). In addition, biotypes
are members of groupings, such as "short non-coding". This allows one to
conveniently select all the biotypes of a certain kind.
SO Mappings are imperfect due to the inexact correspondance of biotypes to
several SO terms. The a best guess has been chosen in each case.
Reverse mappings from SO to biotype are vague, due to many-to-one relationships.
In this case a list of possible terms is given.
=cut
package Bio::EnsEMBL::Utils::BiotypeMapper;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Utils::Cache;
my %gene_so_mapping = (
'protein_coding' => 'SO:0001217', # protein_coding_gene
'pseudogene' => 'SO:0000336', # pseudogene
'processed_transcript' => 'SO:0001503', # processed_transcript
'lincRNA' => 'SO:0001641', # lincRNA_gene
'polymorphic_pseudogene'=> 'SO:0000336', # pseudogene
'Mt_tRNA' => 'SO:0000088', # mt_gene
'IG_D_gene' => 'SO:0000510', # D_gene
'snoRNA' => 'SO:0001267', #snoRNA_gene
'misc_RNA' => 'SO:0000356', #RNA
'miRNA' => 'SO:0001265', #miRNA_gene
'rRNA' => 'SO:0001637', #rRNA_gene
'snRNA' => 'SO:0001268', #snRNA_gene
'snRNA_pseudogene' => 'SO:0000336', # pseudogene
'tRNA_pseudogene' => 'SO:0000778', # pseudogenic_tRNA
'rRNA_pseudogene' => 'SO:0000777', # pseudogenic_rRNA
'TR_J_gene' => 'SO:0000470', # J_gene
'TR_V_gene' => 'SO:0000466', # V_gene
'TR_C_gene' => 'SO:0000478', # C_gene
'ncRNA' => 'SO:0001263', # ncRNA_gene
'tRNA' => 'SO:0001272', # tRNA_gene
'retrotransposed' => 'SO:0000569', # retrotransposed
## heavily abbreviated
);
my %transcript_so_mapping = (
'processed_transcript' => 'SO:0001503', # processed_transcript
'nonsense_mediated_decay' => 'SO:0001621', # NMD_transcript_variant
'retained_intron' => 'SO:0000681', # aberrant_processed_transcript
'transcribed_unprocessed_pseudogene'=> 'SO:0000516', # pseudogenic_transcript
'processed_pseudogene' => 'SO:0000043', # processed_pseudogene
'unprocessed_pseudogene' => 'SO:0000336', # pseudogene
'unitary_pseudogene' => 'SO:0000336',
'pseudogene' => 'SO:0000336', # pseudogene
'transcribed_processed_pseudogene' => 'SO:0000043',
'retrotransposed' => 'SO:0000569', #retrotransposed
'ncrna_host' => 'SO:0000483',
'polymorphic_pseudogene' => 'SO:0000336',
'lincRNA' => 'SO:0001463',
'ncrna_host' => 'SO:0000483',
'3prime_overlapping_ncrna' => 'SO:0000483',
'TR_V_gene' => 'SO:0000466',
'TR_V_pseudogene' => 'SO:0000336',
'TR_J_gene' => 'SO:0000470',
'IG_C_gene' => 'SO:0000478',
'IG_C_pseudogene' => 'SO:0000336',
'TR_C_gene' => 'SO:0000478',
'IG_J_pseudogene' => 'SO:0000336',
'miRNA' => 'SO:0000276', #miRNA
'miRNA_pseudogene' => 'SO:0000336',
'disrupted_domain' => 'SO:0000681', # aberrant_processed_transcript
'rRNA' => 'SO:0000252', #rRNA
'rRNA_pseudogene' => 'SO:0000777',
'scRNA_pseudogene' => 'SO:0000336',
'snoRNA' => 'SO:0000275', # snoRNA
'snoRNA_pseudogene' => 'SO:0000336',
'snRNA' => 'SO:0000274', # snRNA
'snRNA_pseudogene' => 'SO:0000336',
);
my %feature_so_mapping = (
'Bio::EnsEMBL::Feature' => 'SO:0000001', # region
'Bio::EnsEMBL::Gene' => 'SO:0000704', # gene
'Bio::EnsEMBL::Transcript' => 'SO:0000673', # transcript
'Bio::EnsEMBL::Exon' => 'SO:0000147', # exon
'Bio::EnsEMBL::Slice' => 'SO:0000001', # region
'Bio::EnsEMBL::SimpleFeature' => 'SO:0001411', # biological_region
'Bio::EnsEMBL::MiscFeature' => 'SO:0001411', # biological_region
'Bio::EnsEMBL::RepeatFeature' => 'SO:0000657', # repeat region
'Bio::EnsEMBL::Variation::VariationFeature' => 'SO:0001060', # sequence variant
'Bio::EnsEMBL::Variation::StructuralVariationFeature' => 'SO:0001537', # structural variant
'Bio::EnsEMBL::Compara::ConstrainedElement' => 'SO:0001009', #DNA_constraint_sequence ????
'Bio::EnsEMBL::Funcgen::RegulatoryFeature' => 'SO:0005836', # regulatory_region
);
my %grouping_of_biotypes = (
# Genebuilder/Havana categorisation
'protein_coding' => [qw( protein_coding polymorphic_pseudogene )],
'pseudogene' => [qw( pseudogene retrotransposed snRNA_pseudogene tRNA_pseudogene
miRNA_pseudogene Mt_tRNA_pseudogene rRNA_pseudogene
scRNA_pseudogene misc_RNA_pseudogene snoRNA_pseudogene
processed_pseudogene
)],
'long_noncoding' => [qw( 3prime_overlapping_ncrna antisense lincRNA ncrna_host non_coding
processed_transcript sense_intronic sense_overlapping
)],
'short_noncoding'=> [qw( miRNA misc_RNA Mt_tRNA
rRNA snoRNA snRNA
)],
# practical Ensembl core categories for fasta dumping
# protein coding/pseudogene
'cdna' => [qw( protein_coding polymorphic_pseudogene IG_V_gene TR_V_gene
IG_J_gene TR_J_gene IG_D_gene IG_C_gene TR_C_gene pseudogene
retrotransposed IG_V_pseudogene TR_V_pseudogene
IG_J_pseudogene IG_C_pseudogene processed_transcript
antisense ambiguous_orf transcribed_processed_pseudogene
disrupted_domain processed_pseudogene
)],
# protein coding transcript
# protein coding
'peptide_producing' => [qw( protein_coding polymorphic_pseudogene IG_V_gene TR_V_gene
IG_J_gene TR_J_gene IG_D_gene IG_C_gene TR_C_gene IG_LV_gene
nonsense_mediated_decay
)],
# short/long noncoding
'ncrna' => [qw( ncRNA miRNA miRNA_pseudogene misc_RNA misc_RNA_pseudogene Mt_tRNA
Mt_tRNA_pseudogene Mt_rRNA rRNA rRNA_pseudogene scRNA_pseudogene
snoRNA snoRNA_pseudogene snRNA snRNA_pseudogene tRNA_pseudogene
3prime_overlapping_ncrna lincRNA ncrna_host non_coding
sense_intronic sense_overlapping tRNA
)],
);
=head2 new
Constructor
Arg [1] : OntologyAdaptor from the EnsEMBL registry
Returntype : Bio::EnsEMBL::BiotypeMapper
=cut
sub new {
my $class = shift;
my $self = {
ontology_adaptor => shift,
};
tie my %cache, 'Bio::EnsEMBL::Utils::Cache', 100;
$self->{cache} = \%cache;
bless $self, $class;
return $self;
}
=head2 translate_feature_to_SO_term
Arg [0] : Bio::EnsEMBL::Feature, subclass or related Storable
Description: Translates a Feature type into an SO term. If the Feature is a
Gene or Transcript, then a further refinement of the type is made
via Biotype
Returntype : String
=cut
sub translate_feature_to_SO_term {
my $self = shift;
my $feature = shift;
my $so_accession;
my $so_name;
my $ref = ref($feature);
if ($feature->isa('Bio::EnsEMBL::Gene') && exists $gene_so_mapping{$feature->biotype}) {
$so_accession = $gene_so_mapping{$feature->biotype};
}
elsif ($feature->isa('Bio::EnsEMBL::Transcript') && exists $transcript_so_mapping{$feature->biotype}) {
$so_accession = $transcript_so_mapping{$feature->biotype};
}
elsif ($feature->isa('Bio::EnsEMBL::Variation::BaseVariationFeature')) {
$so_name = $feature->class_SO_term();
}
if (! $so_accession && ! $so_name && exists $feature_so_mapping{$ref}) {
$so_accession = $feature_so_mapping{$ref};
}
else {
if($feature->can('SO_term')) {
$so_accession = $feature->SO_term();
}
}
if ($so_accession) {
$so_name = $self->fetch_SO_name_by_accession($so_accession);
}
throw ("Ontology mapping not found for ".ref($feature)) unless $so_name;
return $so_name;
}
=head2 fetch_SO_name_by_accession
Arg [0] : Sequence Ontology accession
Description: Returns the name linked to the given accession. These are
internally cached for speed.
Returntype : The name of the given accession.
=cut
sub fetch_SO_name_by_accession {
my ($self, $so_accession) = @_;
my $so_name = $self->{cache}->{$so_accession};
if(!$so_name) {
my $so_term = $self->{'ontology_adaptor'}->fetch_by_accession($so_accession);
$so_name = $so_term->name();
$self->{cache}->{$so_accession} = $so_name;
}
return $so_name;
}
=head2 translate_SO_to_biotype
Arg [0] : Sequence Ontology term, either in name or URI format
Description: Returns the closest corresponding Ensembl biotypes to a given SO term
Returntype : Listref Array of Strings containing possible biotypes
=cut
sub translate_SO_to_biotype {
my $self = shift;
my $translate_me = shift;
my @so_names;
# look up text in ontology database
if ($translate_me !~ /^SO:/) {
my $so_terms = $self->{'ontology_adaptor'}->fetch_all_by_name($translate_me);
@so_names = [];
foreach my $term (@{$so_terms}) {
push @so_names,$term->accession();
}
} else {
push @so_names,$translate_me;
}
# convert list of accessions into biotypes
my @biotypes;
foreach my $accession (@so_names) {
foreach my $key (keys %gene_so_mapping) {
if ($gene_so_mapping{$key} eq $accession) {
push @biotypes,$key;
}
}
foreach my $key (keys %transcript_so_mapping) {
if ($transcript_so_mapping{$key} eq $accession) {
push @biotypes,$key;
}
}
foreach my $key (keys %feature_so_mapping) {
if ($feature_so_mapping{$key} eq $accession) {
push @biotypes,$key;
}
}
}
return \@biotypes;
}
=head2 belongs_to_groups
Arg [0] : Biotype (string)
Description: Returns the group names that include the given biotype
Returntype : Listref of strings
=cut
sub belongs_to_groups {
my $self = shift;
my $member = shift;
my @belongs_to;
foreach my $group (keys %grouping_of_biotypes) {
my $lc_group = lc($group);
foreach my $biotype ( @{ $grouping_of_biotypes{$group} }) {
if ($biotype eq $member) {
push(@belongs_to, $lc_group);
}
}
}
return \@belongs_to;
}
=head2 group_members
Arg [0] : Biotype group name (string)
Description: Returns a list of biotypes that belong in the group.
Returntype : Listref of strings
=cut
sub group_members {
my $self = shift;
my $group = lc(shift);
if (exists($grouping_of_biotypes{$group})) {
my @biotypes = @{ $grouping_of_biotypes{$group} };
return \@biotypes;
}
else {
throw ("$group is not a valid group name for biotypes");
}
}
=head2 member_of_group
Arg [0] : Biotype (string)
Arg [1] : Group to check (string)
Description: Returns true if a biotype is present in a group
Returntype : Boolean
=cut
sub member_of_group {
my $self = shift;
my $biotype = shift;
my $query_group = lc(shift);
my @groups = @{ $self->belongs_to_groups($biotype) };
while (my $group = shift @groups) {
my $lc_group = lc($group);
if ($lc_group eq $query_group) {
return 1;
}
}
return 0;
}
1;
modules/Bio/EnsEMBL/Utils/IO/GFFSerializer.pm
+ 1
− 1
View file @ 61334766
......@@ -77,7 +77,7 @@ sub new {
};
bless $self, $class;
if ( ! check_ref($self->{'ontology_adaptor'}, "Bio::EnsEMBL::DBSQL::OntologyTermAdaptor" )) {
throw("GFF format requires an instance of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor to function. See also Bio::EnsEMBL::Utils::BiotypeMapper");
throw("GFF format requires an instance of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor to function.");
}
$self->{'mapper'} = Bio::EnsEMBL::Utils::SequenceOntologyMapper->new($self->{'ontology_adaptor'});
......
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