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DEPRECATED.md

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Ensembl Deprecated Methods

This file contains the list of methods deprecated in the Ensembl core API. A method is deprecated when it is not functional any more (schema/data change) or has been replaced by a better one. Backwards compatibility is provided whenever possible. When a method is deprecated, a deprecation warning is thrown whenever the method is used. The warning also contains instructions on replacing the deprecated method and when it will be removed. A year after deprecation (4 Ensembl releases), the method is removed from the API.

Removed in Ensembl Release 102

  • Bio::EnsEMBL::DBSQL::GenomeContainer::get_total_length()

Removed in Ensembl Release 100

  • Bio::EnsEMBL::DBFile::FileAdaptor::get_filehandle()
  • Bio::EnsEMBL::DBFile::FileAdaptor::open_file()
  • Bio::EnsEMBL::DBFile::FileAdaptor::validate_file_length()
  • Bio::EnsEMBL::DBFile::FileAdaptor::initialise_filehandle()
  • Bio::EnsEMBL::DBFile::CollectionAdaptor::initialise_filehandle()
  • Bio::EnsEMBL::DBFile::CollectionAdaptor::read_collection_blob()
  • Bio::EnsEMBL::Utils::Collector::new()
  • Bio::EnsEMBL::Utils::Collector::new_assembly()
  • Bio::EnsEMBL::Utils::Collector::max_data_type_size()
  • Bio::EnsEMBL::Utils::Collector::max_view_width()
  • Bio::EnsEMBL::Utils::Collector::bin_method()
  • Bio::EnsEMBL::Utils::Collector::bin_model()
  • Bio::EnsEMBL::Utils::Collector::window_sizes()
  • Bio::EnsEMBL::Utils::Collector::has_window_size()
  • Bio::EnsEMBL::Utils::Collector::pack_template()
  • Bio::EnsEMBL::Utils::Collector::packed_size()
  • Bio::EnsEMBL::Utils::Collector::bins_per_record()
  • Bio::EnsEMBL::Utils::Collector::current_packed_size()
  • Bio::EnsEMBL::Utils::Collector::score_cache()
  • Bio::EnsEMBL::Utils::Collector::collection_start()
  • Bio::EnsEMBL::Utils::Collector::collection_end()
  • Bio::EnsEMBL::Utils::Collector::collection_strand()
  • Bio::EnsEMBL::Utils::Collector::_get_Slice_chunks()
  • Bio::EnsEMBL::Utils::Collector::set_config()
  • Bio::EnsEMBL::Utils::Collector::store_window_bins_by_Slice()
  • Bio::EnsEMBL::Utils::Collector::_bin_features_by_Slice_window_sizes()
  • Bio::EnsEMBL::Utils::Collector::_calculate_count()
  • Bio::EnsEMBL::Utils::Collector::_calculate_average_score()
  • Bio::EnsEMBL::Utils::Collector::_post_process_average_score()
  • Bio::EnsEMBL::Utils::Collector::_calculate_max_magnitude()
  • Bio::EnsEMBL::Utils::Collector::_post_process_max_magnitude()
  • Bio::EnsEMBL::Utils::Collector::_calculate_RPKM()
  • Bio::EnsEMBL::Utils::Collector::_post_process_RPKM()
  • Bio::EnsEMBL::Utils::Collector::_set_up_RPKM()
  • Bio::EnsEMBL::Utils::Collector::_RPKM_factor()
  • Bio::EnsEMBL::Utils::Collector::get_diploid_genome_length_by_gender()

Removed in Ensembl Release 98

  • Bio::EnsEMBL::Utils::SequenceOntologyMapper::new()
  • Bio::EnsEMBL::Utils::SequenceOntologyMapper::to_accession()
  • Bio::EnsEMBL::Utils::SequenceOntologyMapper::to_name()
  • Bio::EnsEMBL::Utils::SequenceOntologyMapper::gene_biotype_to_name()
  • Bio::EnsEMBL::Utils::SequenceOntologyMapper::transcript_biotype_to_name()
  • Bio::EnsEMBL::Utils::SequenceOntologyMapper::_fetch_SO_name_by_accession()

Removed in Ensembl Release 95

  • Bio::EnsEMBL::AlignStrainSlice::alignFeature()
  • Bio::EnsEMBL::AlignStrainSlice::get_all_Slices()
  • Bio::EnsEMBL::AlignStrainSlice::length()
  • Bio::EnsEMBL::AlignStrainSlice::mapper()
  • Bio::EnsEMBL::AlignStrainSlice::new()
  • Bio::EnsEMBL::AlignStrainSlice::Slice()
  • Bio::EnsEMBL::AlignStrainSlice::strains()
  • Bio::EnsEMBL::AlignStrainSlice::_get_indels()
  • Bio::EnsEMBL::IndividualSlice::add_AlleleFeature()
  • Bio::EnsEMBL::IndividualSlice::alleleFeatures()
  • Bio::EnsEMBL::IndividualSlice::get_all_differences_IndividualSlice()
  • Bio::EnsEMBL::IndividualSlice::get_all_differences_Slice()
  • Bio::EnsEMBL::IndividualSlice::get_all_Exons()
  • Bio::EnsEMBL::IndividualSlice::get_all_Genes()
  • Bio::EnsEMBL::IndividualSlice::get_all_Transcripts()
  • Bio::EnsEMBL::IndividualSlice::individual_name()
  • Bio::EnsEMBL::IndividualSlice::map_to_Individual()
  • Bio::EnsEMBL::IndividualSlice::mapper()
  • Bio::EnsEMBL::IndividualSlice::new()
  • Bio::EnsEMBL::IndividualSlice::seq()
  • Bio::EnsEMBL::IndividualSlice::sub_Slice()
  • Bio::EnsEMBL::IndividualSlice::subseq()
  • Bio::EnsEMBL::IndividualSlice::_convert_difference()
  • Bio::EnsEMBL::IndividualSliceFactory::adaptor()
  • Bio::EnsEMBL::IndividualSliceFactory::get_all_IndividualSlice()
  • Bio::EnsEMBL::IndividualSliceFactory::new()
  • Bio::EnsEMBL::IndividualSliceFactory::_rearrange_Individuals_Alleles()
  • Bio::EnsEMBL::Slice::calculate_pi()
  • Bio::EnsEMBL::Slice::calculate_theta()
  • Bio::EnsEMBL::Slice::get_all_IndividualSlice()
  • Bio::EnsEMBL::Slice::get_by_Individual()
  • Bio::EnsEMBL::Slice::get_by_strain()
  • Bio::EnsEMBL::Slice::_calculate_a

Removed in Ensembl Release 91

  • Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data()
  • Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data()

Removed in Ensembl Release 90

  • Bio::EnsEMBL::Gene::is_known()
  • Bio::EnsEMBL::Gene::status()
  • Bio::EnsEMBL::Transcript::is_known()
  • Bio::EnsEMBL::Transcript::status()

Removed in Ensembl Release 88

  • Bio::EnsEMBL::Slice::get_all_VariationFeatures_with_phenotype()
  • Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures()
  • Bio::EnsEMBL::Slice::get_all_somatic_StructuralVariationFeatures()
  • Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures_by_size_range()
  • Bio::EnsEMBL::Slice::get_all_somatic_StructuralVariationFeatures_by_size_range()
  • Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures_by_Study()
  • Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures_by_source()
  • Bio::EnsEMBL::Slice::get_all_somatic_StructuralVariationFeatures_by_source()
  • Bio::EnsEMBL::Slice::get_all_VariationFeatures_by_VariationSet()
  • Bio::EnsEMBL::Slice::get_all_StructuralVariationFeatures_by_VariationSet()
  • Bio::EnsEMBL::Slice::get_all_PhenotypeFeatures()
  • Bio::EnsEMBL::Slice::get_all_CopyNumberVariantProbeFeatures()
  • Bio::EnsEMBL::Slice::get_all_genotyped_VariationFeatures()
  • Bio::EnsEMBL::StrainSlice::remove_indels()
  • Bio::EnsEMBL::StrainSlice::get_original_seq_region_position()
  • Bio::EnsEMBL::StrainSlice::get_all_VariationFeatures()
  • Bio::EnsEMBL::StrainSlice::mapper()
  • Bio::EnsEMBL::StrainSlice::subseq()
  • Bio::EnsEMBL::StrainSlice::ref_subseq()
  • Bio::EnsEMBL::StrainSlice::sub_Slice()
  • Bio::EnsEMBL::StrainSlice::_convert_difference()
  • Bio::EnsEMBL::StrainSlice::get_all_differences_StrainSlice()
  • Bio::EnsEMBL::StrainSlice::get_all_AlleleFeatures_Slice()
  • Bio::EnsEMBL::StrainSlice::get_all_AlleleFeature()
  • Bio::EnsEMBL::StrainSlice::_add_coverage_information()
  • Bio::EnsEMBL::StrainSlice::expanded_length()
  • Bio::EnsEMBL::StrainSlice::seq()
  • Bio::EnsEMBL::StrainSlice::display_Slice_name()
  • Bio::EnsEMBL::StrainSlice::sample()
  • Bio::EnsEMBL::StrainSlice::strain_name()
  • Bio::EnsEMBL::StrainSlice::_filter_af_by_coverage()
  • Bio::EnsEMBL::StrainSlice::new()
  • Bio::EnsEMBL::DBSQL::StrainSliceAdaptor::new()
  • Bio::EnsEMBL::DBSQL::StrainSliceAdaptor::fetch_by_name()

Removed in Ensembl Release 87

  • Bio::EnsEMBL::AssemblyMapper::in_assembly()
  • Bio::EnsEMBL::AssemblyMapper::map_coordinates_to_assembly()
  • Bio::EnsEMBL::AssemblyMapper::fast_to_assembly()
  • Bio::EnsEMBL::AssemblyMapper::map_coordinates_to_rawcontig()
  • Bio::EnsEMBL::AssemblyMapper::list_contig_ids()
  • Bio::EnsEMBL::ChainedAssemblyMapper::in_assembly()
  • Bio::EnsEMBL::ChainedAssemblyMapper::map_coordinates_to_assembly()
  • Bio::EnsEMBL::ChainedAssemblyMapper::fast_to_assembly()
  • Bio::EnsEMBL::ChainedAssemblyMapper::map_coordinates_to_rawcontig()
  • Bio::EnsEMBL::ChainedAssemblyMapper::list_contig_ids()
  • Bio::EnsEMBL::DBEntry::get_synonyms()
  • Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor::register_region()
  • Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor::register_contig()
  • Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor::fetch_by_type()
  • Bio::EnsEMBL::DBSQL::KaryotypeBandAdaptor::fetch_by_chr_band()
  • Bio::EnsEMBL::DBSQL::TranslationAdaptor::fetch_all_by_DBEntry()
  • Bio::EnsEMBL::DBSQL::TranslationAdaptor::get_stable_entry_info()
  • Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_all_Groups()
  • Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_all_Groups_by_type()
  • Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_Group_by_id()
  • Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_Group_by_Gene_dbID()
  • Bio::EnsEMBL::DBSQL::AnalysisAdaptor::feature_classes()
  • Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_RawContig_and_pid()
  • Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_constraint()
  • Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig()
  • Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_RawContig_and_score()
  • Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::remove_by_RawContig()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::db_handle()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::port()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::driver()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::password()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::username()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::host()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::reconnect_when_lost()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::disconnect_when_inactive()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::dbname()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::prepare()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::list_supported_assemblies()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::assembly_type()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::db()
  • Bio::EnsEMBL::DBSQL::DBConnection::group()
  • Bio::EnsEMBL::DBSQL::DBConnection::species()
  • Bio::EnsEMBL::DBSQL::DBEntryAdaptor::geneids_by_extids()
  • Bio::EnsEMBL::DBSQL::DBEntryAdaptor::translationids_by_extids()
  • Bio::EnsEMBL::DBSQL::DBEntryAdaptor::transcriptids_by_extids()
  • Bio::EnsEMBL::DBSQL::DataFileAdaptor::DataFile_to_extension()
  • Bio::EnsEMBL::DBSQL::ExonAdaptor::get_stable_entry_info()
  • Bio::EnsEMBL::DBSQL::ExonAdaptor::fetch_all_by_gene_id()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_nearest_Gene_by_Feature()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_by_maximum_DBLink()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::get_display_xref()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::get_description()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_all_by_DBEntry()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::get_stable_entry_info()
  • Bio::EnsEMBL::DBSQL::GeneAdaptor::fetch_by_Peptide_id()
  • Bio::EnsEMBL::DBSQL::MetaContainer::get_Species()
  • Bio::EnsEMBL::DBSQL::MetaContainer::get_default_assembly()
  • Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::fetch_by_translation_id()
  • Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor::fetch_all_by_feature_and_dbID()
  • Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::fetch_by_class_seq()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_mapfrag()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_chr_start_end()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_contig_name()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_clone_accession()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_supercontig_name()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::list_overlapping_supercontigs()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_chr_name()
  • Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_display_xref()
  • Bio::EnsEMBL::DBSQL::TranscriptAdaptor::get_stable_entry_info()
  • Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_DBEntry()
  • Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_assembly_location()
  • Bio::EnsEMBL::DBSQL::SequenceAdaptor::fetch_by_RawContig_start_end_strand()
  • Bio::EnsEMBL::Exon::temporary_id()
  • Bio::EnsEMBL::Exon::created()
  • Bio::EnsEMBL::Exon::modified()
  • Bio::EnsEMBL::Exon::type()
  • Bio::EnsEMBL::FeaturePair::feature1()
  • Bio::EnsEMBL::FeaturePair::feature2()
  • Bio::EnsEMBL::FeaturePair::set_featurepair_fields()
  • Bio::EnsEMBL::FeaturePair::gffstring()
  • Bio::EnsEMBL::FeaturePair::hphase()
  • Bio::EnsEMBL::FeaturePair::hend_phase()
  • Bio::EnsEMBL::Feature::contig()
  • Bio::EnsEMBL::Feature::id()
  • Bio::EnsEMBL::Gene::add_DBLink()
  • Bio::EnsEMBL::Gene::temporary_id()
  • Bio::EnsEMBL::Gene::chr_name()
  • Bio::EnsEMBL::Gene::type()
  • Bio::EnsEMBL::Gene::confidence()
  • Bio::EnsEMBL::IdentityXref::query_identity()
  • Bio::EnsEMBL::IdentityXref::target_identity()
  • Bio::EnsEMBL::IdentityXref::translation_start()
  • Bio::EnsEMBL::IdentityXref::translation_end()
  • Bio::EnsEMBL::IdentityXref::query_start()
  • Bio::EnsEMBL::IdentityXref::query_end()
  • Bio::EnsEMBL::KaryotypeBand::chr_name()
  • Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor::fetch_all_by_RawContig_and_priority()
  • Bio::EnsEMBL::Map::DitagFeature::fetch_ditag()
  • Bio::EnsEMBL::Map::MapLocation::chromosome()
  • Bio::EnsEMBL::OperonTranscript::add_gene()
  • Bio::EnsEMBL::PredictionTranscript::get_exon_count()
  • Bio::EnsEMBL::PredictionTranscript::get_cdna()
  • Bio::EnsEMBL::Registry::load_registry_with_web_adaptors()
  • Bio::EnsEMBL::Root::throw()
  • Bio::EnsEMBL::Root::warn()
  • Bio::EnsEMBL::Root::verbose()
  • Bio::EnsEMBL::Root::stack_trace_dump()
  • Bio::EnsEMBL::Root::stack_trace()
  • Bio::EnsEMBL::Slice::get_all_SNPs()
  • Bio::EnsEMBL::Slice::get_all_genotyped_SNPs()
  • Bio::EnsEMBL::Slice::get_all_supercontig_Slices()
  • Bio::EnsEMBL::Slice::get_Chromosome()
  • Bio::EnsEMBL::Slice::chr_name()
  • Bio::EnsEMBL::Slice::chr_start()
  • Bio::EnsEMBL::Slice::chr_end()
  • Bio::EnsEMBL::Slice::assembly_type()
  • Bio::EnsEMBL::Slice::dbID()
  • Bio::EnsEMBL::Slice::get_all_MapFrags()
  • Bio::EnsEMBL::Slice::has_MapSet()
  • Bio::EnsEMBL::StrainSlice::get_all_differences_Slice()
  • Bio::EnsEMBL::Transcript::created()
  • Bio::EnsEMBL::Transcript::modified()
  • Bio::EnsEMBL::Transcript::temporary_id()
  • Bio::EnsEMBL::Transcript::type()
  • Bio::EnsEMBL::Transcript::confidence()
  • Bio::EnsEMBL::Translation::temporary_id()
  • Bio::EnsEMBL::Utils::ConversionSupport::user_confirm()

Removed in Ensembl Release 84

  • Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::_fetch_by_attrib()
  • Bio::EnsEMBL::DBSQL::CoordSystemAdaptor::_fetch_all_by_attrib()
  • Bio::EnsEMBL::DBSQL::DBAdaptor::source()
  • Bio::EnsEMBL::DBSQL::SliceAdaptor::fetch_by_band()
  • Bio::EnsEMBL::DBSQL::MetaContainer::get_short_name()
  • Bio::EnsEMBL::DBSQL::MetaContainer::get_max_assembly_contig()
  • Bio::EnsEMBL::DBEntry::ensembl_object_type()
  • Bio::EnsEMBL::DBEntry::ensembl_id()
  • Bio::EnsEMBL::Exon::_get_stable_entry_info()
  • Bio::EnsEMBL::FeaturePair::validate()
  • Bio::EnsEMBL::FeaturePair::validate_prot_feature()
  • Bio::EnsEMBL::PredictionTranscript::set_exon_count()
  • Bio::EnsEMBL::Root::_rearrange()
  • Bio::EnsEMBL::SeqFeatureI::analysis()
  • Bio::EnsEMBL::SeqFeatureI::validate()
  • Bio::EnsEMBL::SeqFeatureI::id()
  • Bio::EnsEMBL::SeqFeatureI::percent_id()
  • Bio::EnsEMBL::SeqFeatureI::e_value()
  • Bio::EnsEMBL::SeqFeatureI::phase()
  • Bio::EnsEMBL::SeqFeatureI::end_phase()
  • Bio::EnsEMBL::SeqFeatureI::location()
  • Bio::EnsEMBL::Slice::get_all_SNPs_transcripts()
  • Bio::EnsEMBL::Slice::get_all_AffyFeatures()
  • Bio::EnsEMBL::Slice::get_all_OligoFeatures()
  • Bio::EnsEMBL::Slice::get_all_OligoFeatures_by_type()
  • Bio::EnsEMBL::Slice::get_tiling_path()
  • Bio::EnsEMBL::Transcript::sort()
  • Bio::EnsEMBL::Transcript::_translation_id()