├── .gitignore ├── .gitlab-ci.yml ├── .perlcriticrc ├── .perltidyrc ├── .travis.yml ├── CONTRIBUTING.md ├── DEPRECATED.md ├── LICENSE ├── NOTICE ├── PULL_REQUEST_TEMPLATE.md ├── README.md ├── cpanfile ├── docs ├── ConnectionFAQ.md ├── README.db_portability └── pipelines │ ├── fasta.html │ ├── fasta.textile │ ├── flatfile.html │ └── flatfile.textile ├── misc-scripts ├── CreateFile4CopyDBoverServer.pl ├── README.schema_patching ├── alt_alleles │ └── alt_alleles.pl ├── annual_copyright_updater.sh ├── assembly │ ├── AssemblyMapper │ │ └── BlastzAligner.pm │ ├── EXAMPLE.use_mapping.pl │ ├── README │ ├── align_by_clone_identity.pl │ ├── align_nonident_regions.pl │ ├── align_nonident_regions_wrapper.pl │ ├── blastz_matrix.txt │ ├── check_mapping.pl │ ├── cleanup_tmp_tables.sql │ ├── compare_assemblies.pl │ ├── conservation_statistics.pl │ ├── ensembl_assembly_to_chain.pl │ ├── exon_conservation_check.pl │ ├── find_overlaps.pl │ ├── fix_asm_overlaps.pl │ ├── fix_cmp_overlaps.pl │ ├── fix_overlaps.pl │ ├── load_alternative_assembly.pl │ ├── load_feature_mappings.ini.example │ ├── load_feature_mappings.pl │ ├── load_patch_fix_to_ref.pl │ ├── mapping_stats.pl │ ├── merge_cmp_gaps.pl │ ├── test_assembly_mapping.ini.example │ └── test_assembly_mapping.pl ├── assembly_patches │ └── README.TXT ├── canonical_transcripts │ ├── emit_canonical_encodings.pl │ ├── reason_changes.pl │ └── select_canonical_transcripts.pl ├── cloud │ ├── EnsCloud │ │ ├── Cmd.pm │ │ ├── Cmd │ │ │ └── Command │ │ │ │ ├── SpeciesToVolumes.pm │ │ │ │ └── list.pm │ │ ├── Describer.pm │ │ ├── Image.pm │ │ └── Image │ │ │ ├── VolumeBundle.pm │ │ │ └── VolumeBundle │ │ │ ├── Volume.pm │ │ │ └── Volume │ │ │ └── DatabaseDetails.pm │ └── ecloud ├── core_tutorial_test │ └── test_code_from_html.pl ├── db │ ├── cleanup_tmp_tables.pl │ ├── convert_tables_MyISAM_InnoDB.pl │ ├── cp_mysqldb │ ├── db-space.pl │ ├── dump_mysql.pl │ ├── fingerprint_db.pl │ ├── kill_process_by_db.pl │ ├── multidb_sql.pl │ ├── mv_mysqldb │ ├── remove_mysqldb.pl │ └── search_dbs.pl ├── doxygen_filter │ ├── EnsEMBL │ │ ├── Filter.pm │ │ └── PerlFilter.pm │ ├── customdoxygen.css │ ├── ensembldoxygenfilter.pl │ ├── header.html │ ├── layout.xml │ └── pod_styleguide.txt ├── email_blatter.sh ├── frameshift_transcript_attribs.pl ├── generate_stable_ids.pl ├── gifts_import │ └── populate_protein_feature.pl ├── id_mapping │ ├── README │ ├── default.conf │ ├── dump_by_seq_region.pl │ ├── dump_cache.pl │ ├── fake_stable_id_mapping.pl │ ├── id_mapping.pl │ ├── myRun.ksh │ ├── run.pl │ ├── synteny_rescore.pl │ └── utils │ │ ├── batch_id_history.pl │ │ ├── compare_results.pl │ │ ├── compare_scores.pl │ │ ├── dump_scores.pl │ │ ├── id_mapping_clean.sql │ │ ├── manage_id_mapping_tables.pl │ │ └── myManager.ksh ├── import │ ├── import_bed_simple_feature.pl │ ├── import_recombinant_hotspots.pl │ ├── karyotype_rank_assigner.pl │ └── sort_feature_table.pl ├── load_databases │ ├── load_database_from_ftp_site.pl │ └── load_multiple_databases.pl ├── meta_coord │ └── update_meta_coord.pl ├── meta_levels.pl ├── mouse_knockouts │ ├── IKMC_get_data.pl │ └── add_ikmc_as_simple_features.pl ├── ping_ensembl.pl ├── repeats │ ├── repeat-libraries.pl │ ├── repeat-types.pl │ ├── repeats.txt │ ├── shrink_trfs.pl │ └── vega_repeat_libraries.pl ├── schema_patcher.pl ├── stable_id_lookup │ ├── README │ ├── populate_stable_id_lookup.pl │ └── sql │ │ ├── indices.sql │ │ └── tables.sql ├── surgery │ ├── SchemaConverter.pm │ ├── SeqStoreConverter │ │ ├── AnophelesGambiae.pm │ │ ├── ApisMellifera.pm │ │ ├── BasicConverter.pm │ │ ├── CaenorhabditisBriggsae.pm │ │ ├── CaenorhabditisElegans.pm │ │ ├── CanisFamiliaris.pm │ │ ├── DanioRerio.pm │ │ ├── DrosophilaMelanogaster.pm │ │ ├── FuguRubripes.pm │ │ ├── GallusGallus.pm │ │ ├── HomoSapiens.pm │ │ ├── MusMusculus.pm │ │ ├── PanTroglodytes.pm │ │ ├── RattusNorvegicus.pm │ │ └── vega │ │ │ ├── CanisFamiliaris.pm │ │ │ ├── DanioRerio.pm │ │ │ ├── HomoSapiens.pm │ │ │ ├── MusMusculus.pm │ │ │ └── VBasicConverter.pm │ ├── convert_seqstore.pl │ ├── converter.input │ ├── create_fixsql.pl │ ├── dump_seq_in_region │ ├── fuller_test_genome_9_chr20.pl │ ├── push_align_features.pl │ ├── set_nonredundant_attribs.pl │ ├── shortintrons2frameshifts.pl │ └── table_column_munge ├── transfer_karyotype.pl ├── update_mapping_set.pl ├── web_stats.sh └── xref_mapping │ ├── Xref │ ├── DB.pm │ ├── Schema.pm │ ├── Schema │ │ ├── Result │ │ │ ├── AltAllele.pm │ │ │ ├── ChecksumXref.pm │ │ │ ├── CoordinateXref.pm │ │ │ ├── DependentSource.pm │ │ │ ├── DependentXref.pm │ │ │ ├── DisplayXrefPriority.pm │ │ │ ├── GeneDescPriority.pm │ │ │ ├── GeneDirectXref.pm │ │ │ ├── GeneStableId.pm │ │ │ ├── GeneTranscriptTranslation.pm │ │ │ ├── IdentityXref.pm │ │ │ ├── Mapping.pm │ │ │ ├── MappingJob.pm │ │ │ ├── Meta.pm │ │ │ ├── ObjectXref.pm │ │ │ ├── Pair.pm │ │ │ ├── PrimaryXref.pm │ │ │ ├── ProcessStatus.pm │ │ │ ├── Source.pm │ │ │ ├── SourceMappingMethod.pm │ │ │ ├── SourceUrl.pm │ │ │ ├── Species.pm │ │ │ ├── Synonym.pm │ │ │ ├── TranscriptDirectXref.pm │ │ │ ├── TranscriptStableId.pm │ │ │ ├── TranslationDirectXref.pm │ │ │ ├── TranslationStableId.pm │ │ │ └── Xref.pm │ │ └── ResultSet │ │ │ ├── DependentXref.pm │ │ │ ├── Synonym.pm │ │ │ └── Xref.pm │ └── Test │ │ └── TestDB.pm │ ├── XrefMapper │ ├── BasicMapper.pm │ ├── ChecksumMapper.pm │ ├── CoordinateMapper.pm │ ├── CoreInfo.pm │ ├── DirectXrefs.pm │ ├── DisplayXrefs.pm │ ├── LoadMapper.pm │ ├── Methods │ │ ├── ChecksumBasic.pm │ │ ├── ExonerateBasic.pm │ │ ├── ExonerateBest1.pm │ │ ├── ExonerateGappedBest1.pm │ │ ├── ExonerateGappedBest1_55_perc_id.pm │ │ ├── ExonerateGappedBest5.pm │ │ ├── ExonerateGappedBest5_55_perc_id.pm │ │ ├── ExonerateGappedBest5_subtran.pm │ │ ├── ExonerateGappedBest_100_perc_id.pm │ │ ├── ExonerateGappedBest_90_perc_id.pm │ │ ├── ExonerateUngappedBest1.pm │ │ ├── LocalExonerateGappedBest1.pm │ │ ├── MySQLChecksum.pm │ │ └── PBSExonerateGappedBest1.pm │ ├── OfficialNaming.pm │ ├── ProcessMappings.pm │ ├── ProcessPaired.pm │ ├── ProcessPrioritys.pm │ ├── RNACentralMapper.pm │ ├── SubmitMapper.pm │ ├── TestMappings.pm │ ├── UniParcMapper.pm │ ├── VBCoordinateMapper.pm │ ├── XrefLoader.pm │ ├── aedes_aegypti.pm │ ├── anopheles_gambiae.pm │ ├── culex_quinquefasciatus.pm │ ├── danio_rerio.pm │ ├── db.pm │ ├── drosophila.pm │ ├── eukaryota.pm │ ├── homo_sapiens.pm │ ├── ixodes_scapularis.pm │ ├── mus_musculus.pm │ ├── neurospora_crassa.pm │ ├── parasite.pm │ ├── rattus_norvegicus.pm │ ├── saccharomyces_cerevisiae.pm │ ├── sars_cov_2.pm │ ├── schizosaccharomyces_pombe.pm │ ├── sus_scrofa.pm │ └── wormbase.pm │ ├── XrefParser │ ├── ArrayExpressParser.pm │ ├── BaseParser.pm │ ├── CCDSParser.pm │ ├── ChecksumParser.pm │ ├── CodelinkParser.pm │ ├── CoordinateParser.pm │ ├── CoreXrefParser.pm │ ├── DBASSParser.pm │ ├── Database.pm │ ├── DirectParser.pm │ ├── EG_DBParser.pm │ ├── EntrezGeneParser.pm │ ├── FetchFiles.pm │ ├── FlybaseParser.pm │ ├── GramenePathwayParser.pm │ ├── HGNCParser.pm │ ├── HPAParser.pm │ ├── JGI_ProteinParser.pm │ ├── MGIParser.pm │ ├── MGI_CCDS_Parser.pm │ ├── MGI_Desc_Parser.pm │ ├── MIMParser.pm │ ├── Mim2GeneParser.pm │ ├── PGSCParser.pm │ ├── PHIbaseParser.pm │ ├── PhytozomeGmaxParser.pm │ ├── PomBaseParser.pm │ ├── RFAMParser.pm │ ├── RGDParser.pm │ ├── ReactomeParser.pm │ ├── RefSeqCoordinateParser.pm │ ├── RefSeqDatabaseParser.pm │ ├── RefSeqGPFFParser.pm │ ├── RefSeqParser.pm │ ├── SGDParser.pm │ ├── TAIRIDParser.pm │ ├── TAIROntologyParser.pm │ ├── UCSCParser.pm │ ├── UCSC_human_parser.pm │ ├── UCSC_mouse_parser.pm │ ├── UniProtDatabaseParser.pm │ ├── UniProtParser.pm │ ├── UniProtVarSplicParser.pm │ ├── VGNCParser.pm │ ├── WilsonAffyParser.pm │ ├── WormBaseCuratedSynonymsParser.pm │ ├── WormbaseCElegansBase.pm │ ├── WormbaseCElegansRefSeqGPFFParser.pm │ ├── WormbaseCElegansUniProtParser.pm │ ├── WormbaseDirectParser.pm │ ├── XenopusJamboreeParser.pm │ ├── ZFINDescParser.pm │ ├── ZFINParser.pm │ └── miRBaseParser.pm │ ├── sql │ └── table.sql │ ├── store_ccds_xrefs.pl │ ├── t │ ├── MultiTestDB.conf.default │ ├── dbass.t │ ├── entrezgene.t │ ├── hgnc.t │ ├── hpa.t │ ├── jgi_proteinparser.t │ ├── mgi.t │ ├── mgi_desc.t │ ├── mim2gene.t │ ├── omim.t │ ├── rgd.t │ ├── test-data │ │ ├── MGI_mini.rpt │ │ ├── MGIdesc_mini.rpt │ │ ├── dbass-badData-tooFewCols.txt │ │ ├── dbass-badHeader-tooFewCols.txt │ │ ├── dbass-badHeader-wrongName1.txt │ │ ├── dbass-badHeader-wrongName2.txt │ │ ├── dbass-badHeader-wrongName3.txt │ │ ├── dbass-mini3.txt │ │ ├── dbass-mini5.txt │ │ ├── entrez-gene_info │ │ ├── hgnc.tsv │ │ ├── hpa.txt │ │ ├── jgi_prot.fasta │ │ ├── mim2gene-badData-newEntryType.txt │ │ ├── mim2gene-badData-tooFewCols.txt │ │ ├── mim2gene-badData-tooManyCols.txt │ │ ├── mim2gene-badHeader-wrongName1.txt │ │ ├── mim2gene-badHeader-wrongName2.txt │ │ ├── mim2gene-badHeader-wrongName3.txt │ │ ├── mim2gene-badHeader-wrongName4.txt │ │ ├── mim2gene-badHeader-wrongName5.txt │ │ ├── mim2gene-badHeader-wrongName6.txt │ │ ├── mim2gene-mini.txt │ │ ├── omim-badTIfield.txt │ │ ├── omim-mini.txt │ │ ├── omim-truncated.txt │ │ ├── rgd.txt │ │ ├── ucsc.txt │ │ ├── vgnc.txt │ │ ├── xenopusjamboree.txt │ │ ├── xref_config.ini │ │ └── zfin_desc.txt │ ├── test-genome-DBs │ │ └── homo_sapiens │ │ │ ├── core │ │ │ ├── SQLite │ │ │ │ └── table.sql │ │ │ ├── alt_allele.txt │ │ │ ├── alt_allele_attrib.txt │ │ │ ├── alt_allele_group.txt │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── assembly_exception.txt │ │ │ ├── attrib_type.txt │ │ │ ├── biotype.txt │ │ │ ├── coord_system.txt │ │ │ ├── density_feature.txt │ │ │ ├── density_type.txt │ │ │ ├── ditag.txt │ │ │ ├── ditag_feature.txt │ │ │ ├── dna.txt │ │ │ ├── dna_align_feature.txt │ │ │ ├── exon.txt │ │ │ ├── exon_transcript.txt │ │ │ ├── external_db.txt │ │ │ ├── external_synonym.txt │ │ │ ├── gene.txt │ │ │ ├── gene_archive.txt │ │ │ ├── gene_attrib.txt │ │ │ ├── identity_xref.txt │ │ │ ├── interpro.txt │ │ │ ├── karyotype.txt │ │ │ ├── map.txt │ │ │ ├── mapping_session.txt │ │ │ ├── marker.txt │ │ │ ├── marker_feature.txt │ │ │ ├── marker_map_location.txt │ │ │ ├── marker_synonym.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── misc_attrib.txt │ │ │ ├── misc_feature.txt │ │ │ ├── misc_feature_misc_set.txt │ │ │ ├── misc_set.txt │ │ │ ├── object_xref.txt │ │ │ ├── ontology_xref.txt │ │ │ ├── operon.txt │ │ │ ├── operon_transcript.txt │ │ │ ├── operon_transcript_gene.txt │ │ │ ├── peptide_archive.txt │ │ │ ├── prediction_exon.txt │ │ │ ├── prediction_transcript.txt │ │ │ ├── protein_align_feature.txt │ │ │ ├── protein_feature.txt │ │ │ ├── repeat_consensus.txt │ │ │ ├── repeat_feature.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── seq_region_synonym.txt │ │ │ ├── simple_feature.txt │ │ │ ├── stable_id_event.txt │ │ │ ├── supporting_feature.txt │ │ │ ├── table.sql │ │ │ ├── transcript.txt │ │ │ ├── transcript_attrib.txt │ │ │ ├── transcript_supporting_feature.txt │ │ │ ├── translation.txt │ │ │ ├── unmapped_object.txt │ │ │ ├── unmapped_reason.txt │ │ │ └── xref.txt │ │ │ └── otherfeatures │ │ │ ├── alt_allele.txt │ │ │ ├── alt_allele_attrib.txt │ │ │ ├── alt_allele_group.txt │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── assembly_exception.txt │ │ │ ├── associated_group.txt │ │ │ ├── associated_xref.txt │ │ │ ├── attrib_type.txt │ │ │ ├── biotype.txt │ │ │ ├── coord_system.txt │ │ │ ├── data_file.txt │ │ │ ├── density_feature.txt │ │ │ ├── density_type.txt │ │ │ ├── dependent_xref.txt │ │ │ ├── ditag.txt │ │ │ ├── ditag_feature.txt │ │ │ ├── dna.txt │ │ │ ├── dna_align_feature.txt │ │ │ ├── dna_align_feature_attrib.txt │ │ │ ├── exon.txt │ │ │ ├── exon_transcript.txt │ │ │ ├── external_db.txt │ │ │ ├── external_synonym.txt │ │ │ ├── gene.txt │ │ │ ├── gene_archive.txt │ │ │ ├── gene_attrib.txt │ │ │ ├── genome_statistics.txt │ │ │ ├── identity_xref.txt │ │ │ ├── interpro.txt │ │ │ ├── intron_supporting_evidence.txt │ │ │ ├── karyotype.txt │ │ │ ├── map.txt │ │ │ ├── mapping_session.txt │ │ │ ├── mapping_set.txt │ │ │ ├── marker.txt │ │ │ ├── marker_feature.txt │ │ │ ├── marker_map_location.txt │ │ │ ├── marker_synonym.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── misc_attrib.txt │ │ │ ├── misc_feature.txt │ │ │ ├── misc_feature_misc_set.txt │ │ │ ├── misc_set.txt │ │ │ ├── object_xref.txt │ │ │ ├── ontology_xref.txt │ │ │ ├── operon.txt │ │ │ ├── operon_transcript.txt │ │ │ ├── operon_transcript_gene.txt │ │ │ ├── peptide_archive.txt │ │ │ ├── prediction_exon.txt │ │ │ ├── prediction_transcript.txt │ │ │ ├── protein_align_feature.txt │ │ │ ├── protein_feature.txt │ │ │ ├── repeat_consensus.txt │ │ │ ├── repeat_feature.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── seq_region_mapping.txt │ │ │ ├── seq_region_synonym.txt │ │ │ ├── simple_feature.txt │ │ │ ├── stable_id_event.txt │ │ │ ├── supporting_feature.txt │ │ │ ├── table.sql │ │ │ ├── transcript.txt │ │ │ ├── transcript_attrib.txt │ │ │ ├── transcript_intron_supporting_evidence.txt │ │ │ ├── transcript_supporting_feature.txt │ │ │ ├── translation.txt │ │ │ ├── translation_attrib.txt │ │ │ ├── unmapped_object.txt │ │ │ ├── unmapped_reason.txt │ │ │ └── xref.txt │ ├── testdb.conf.example │ ├── testdb.t │ ├── ucsc.t │ ├── vgnc.t │ ├── xenopus.t │ └── zfin_desc.t │ ├── xref_config.ini │ ├── xref_config2sql.pl │ ├── xref_mindmap │ ├── README │ ├── generate_xref_mindmap.pl │ ├── sql │ │ ├── tables.sql │ │ └── update.sql │ └── xref_mindmap.pdf │ └── xref_parser.pl ├── modules ├── Bio │ └── EnsEMBL │ │ ├── AltAlleleGroup.pm │ │ ├── Analysis.pm │ │ ├── Analysis │ │ ├── PairAlign.pm │ │ └── Programs.pm │ │ ├── ApiVersion.pm │ │ ├── ArchiveStableId.pm │ │ ├── AssemblyExceptionFeature.pm │ │ ├── AssemblyMapper.pm │ │ ├── Attribute.pm │ │ ├── BaseAlignFeature.pm │ │ ├── Biotype.pm │ │ ├── CDS.pm │ │ ├── ChainedAssemblyMapper.pm │ │ ├── CircularSlice.pm │ │ ├── CoordSystem.pm │ │ ├── DB │ │ └── ExternalFeatureFactoryI.pm │ │ ├── DBEntry.pm │ │ ├── DBLoader.pm │ │ ├── DBSQL │ │ ├── AltAlleleGroupAdaptor.pm │ │ ├── AnalysisAdaptor.pm │ │ ├── ArchiveStableIdAdaptor.pm │ │ ├── AssemblyExceptionFeatureAdaptor.pm │ │ ├── AssemblyMapperAdaptor.pm │ │ ├── AssemblySliceAdaptor.pm │ │ ├── AttributeAdaptor.pm │ │ ├── BaseAdaptor.pm │ │ ├── BaseAlignFeatureAdaptor.pm │ │ ├── BaseFeatureAdaptor.pm │ │ ├── BaseMetaContainer.pm │ │ ├── BaseSequenceAdaptor.pm │ │ ├── BiotypeAdaptor.pm │ │ ├── CoordSystemAdaptor.pm │ │ ├── DBAdaptor.pm │ │ ├── DBConnection.pm │ │ ├── DBEntryAdaptor.pm │ │ ├── DataFileAdaptor.pm │ │ ├── DensityFeatureAdaptor.pm │ │ ├── DensityTypeAdaptor.pm │ │ ├── DnaAlignFeatureAdaptor.pm │ │ ├── Driver.pm │ │ ├── Driver │ │ │ ├── Oracle.pm │ │ │ ├── Pg.pm │ │ │ ├── SQLite.pm │ │ │ ├── Sybase.pm │ │ │ ├── TestDummy.pm │ │ │ ├── mysql.pm │ │ │ └── odbc.pm │ │ ├── ExonAdaptor.pm │ │ ├── FastaSequenceAdaptor.pm │ │ ├── GeneAdaptor.pm │ │ ├── GenomeContainer.pm │ │ ├── IntronSupportingEvidenceAdaptor.pm │ │ ├── KaryotypeBandAdaptor.pm │ │ ├── MergedAdaptor.pm │ │ ├── MetaContainer.pm │ │ ├── MetaCoordContainer.pm │ │ ├── MiscFeatureAdaptor.pm │ │ ├── MiscSetAdaptor.pm │ │ ├── OntologyDBAdaptor.pm │ │ ├── OntologyTermAdaptor.pm │ │ ├── OperonAdaptor.pm │ │ ├── OperonTranscriptAdaptor.pm │ │ ├── PredictionExonAdaptor.pm │ │ ├── PredictionTranscriptAdaptor.pm │ │ ├── ProteinAlignFeatureAdaptor.pm │ │ ├── ProteinFeatureAdaptor.pm │ │ ├── ProxyDBConnection.pm │ │ ├── RNAProductAdaptor.pm │ │ ├── RepeatConsensusAdaptor.pm │ │ ├── RepeatFeatureAdaptor.pm │ │ ├── SeqRegionSynonymAdaptor.pm │ │ ├── SequenceAdaptor.pm │ │ ├── SimpleFeatureAdaptor.pm │ │ ├── SliceAdaptor.pm │ │ ├── StatementHandle.pm │ │ ├── Support │ │ │ ├── BaseCache.pm │ │ │ ├── FullIdCache.pm │ │ │ └── LruIdCache.pm │ │ ├── SupportingFeatureAdaptor.pm │ │ ├── TranscriptAdaptor.pm │ │ ├── TranscriptSupportingFeatureAdaptor.pm │ │ ├── TranslationAdaptor.pm │ │ └── UnmappedObjectAdaptor.pm │ │ ├── DataFile.pm │ │ ├── DensityFeature.pm │ │ ├── DensityFeatureSet.pm │ │ ├── DensityPlot │ │ ├── BinValue.pm │ │ └── BinValueSet.pm │ │ ├── DensityType.pm │ │ ├── DnaDnaAlignFeature.pm │ │ ├── DnaPepAlignFeature.pm │ │ ├── Exon.pm │ │ ├── ExonTranscript.pm │ │ ├── External │ │ └── ExternalFeatureAdaptor.pm │ │ ├── Feature.pm │ │ ├── FeaturePair.pm │ │ ├── Gene.pm │ │ ├── Genome.pm │ │ ├── IdMapping │ │ ├── Archiver.pm │ │ ├── BaseObject.pm │ │ ├── Cache.pm │ │ ├── Entry.pm │ │ ├── ExonScoreBuilder.pm │ │ ├── GeneScoreBuilder.pm │ │ ├── InternalIdMapper.pm │ │ ├── InternalIdMapper │ │ │ ├── BaseMapper.pm │ │ │ ├── EnsemblExonGeneric.pm │ │ │ ├── EnsemblGeneGeneric.pm │ │ │ └── EnsemblTranscriptGeneric.pm │ │ ├── MappingList.pm │ │ ├── ResultAnalyser.pm │ │ ├── ScoreBuilder.pm │ │ ├── ScoredMappingMatrix.pm │ │ ├── Serialisable.pm │ │ ├── StableIdGenerator │ │ │ ├── AedesAegypti.pm │ │ │ ├── AnophelesGambiae.pm │ │ │ ├── EnsemblGeneric.pm │ │ │ └── PristionchusPacificus.pm │ │ ├── StableIdMapper.pm │ │ ├── SyntenyFramework.pm │ │ ├── SyntenyRegion.pm │ │ ├── TinyExon.pm │ │ ├── TinyFeature.pm │ │ ├── TinyGene.pm │ │ ├── TinyTranscript.pm │ │ ├── TinyTranslation.pm │ │ └── TranscriptScoreBuilder.pm │ │ ├── IdentityXref.pm │ │ ├── Intron.pm │ │ ├── IntronSupportingEvidence.pm │ │ ├── KaryotypeBand.pm │ │ ├── LRGSlice.pm │ │ ├── MANE.pm │ │ ├── Map │ │ ├── DBSQL │ │ │ ├── DitagAdaptor.pm │ │ │ ├── DitagFeatureAdaptor.pm │ │ │ ├── MarkerAdaptor.pm │ │ │ └── MarkerFeatureAdaptor.pm │ │ ├── Ditag.pm │ │ ├── DitagFeature.pm │ │ ├── MapLocation.pm │ │ ├── Marker.pm │ │ ├── MarkerFeature.pm │ │ └── MarkerSynonym.pm │ │ ├── MappedSlice.pm │ │ ├── MappedSliceContainer.pm │ │ ├── Mapper.pm │ │ ├── Mapper │ │ ├── Coordinate.pm │ │ ├── Gap.pm │ │ ├── IndelCoordinate.pm │ │ ├── IndelPair.pm │ │ ├── Pair.pm │ │ ├── RangeRegistry.pm │ │ └── Unit.pm │ │ ├── MicroRNA.pm │ │ ├── MiscFeature.pm │ │ ├── MiscSet.pm │ │ ├── OntologyTerm.pm │ │ ├── OntologyXref.pm │ │ ├── Operon.pm │ │ ├── OperonTranscript.pm │ │ ├── PaddedSlice.pm │ │ ├── PepDnaAlignFeature.pm │ │ ├── PredictionExon.pm │ │ ├── PredictionTranscript.pm │ │ ├── ProjectionSegment.pm │ │ ├── ProteinFeature.pm │ │ ├── RNAProduct.pm │ │ ├── Registry.pm │ │ ├── RepeatConsensus.pm │ │ ├── RepeatFeature.pm │ │ ├── RepeatMaskedSlice.pm │ │ ├── SeqEdit.pm │ │ ├── SeqFeature.pm │ │ ├── SeqRegionSynonym.pm │ │ ├── SimpleFeature.pm │ │ ├── Slice.pm │ │ ├── StableIdEvent.pm │ │ ├── StableIdHistoryTree.pm │ │ ├── StopCodonReadthroughEdit.pm │ │ ├── Storable.pm │ │ ├── SubSlicedFeature.pm │ │ ├── TopLevelAssemblyMapper.pm │ │ ├── Transcript.pm │ │ ├── TranscriptFactory.pm │ │ ├── TranscriptMapper.pm │ │ ├── Translation.pm │ │ ├── UTR.pm │ │ ├── UnmappedObject.pm │ │ ├── Upstream.pm │ │ └── Utils │ │ ├── Argument.pm │ │ ├── AssemblyProjector.pm │ │ ├── BitString.pm │ │ ├── Cache.pm │ │ ├── CigarString.pm │ │ ├── CliHelper.pm │ │ ├── ConfParser.pm │ │ ├── ConfigRegistry.pm │ │ ├── ConversionSupport.pm │ │ ├── Converter.pm │ │ ├── Converter │ │ ├── bio_ens.pm │ │ ├── bio_ens_analysis.pm │ │ ├── bio_ens_exon.pm │ │ ├── bio_ens_featurePair.pm │ │ ├── bio_ens_gene.pm │ │ ├── bio_ens_hit.pm │ │ ├── bio_ens_hsp.pm │ │ ├── bio_ens_predictionExon.pm │ │ ├── bio_ens_predictionGene.pm │ │ ├── bio_ens_seqFeature.pm │ │ ├── bio_ens_transcript.pm │ │ ├── ens_bio.pm │ │ ├── ens_bio_featurePair.pm │ │ └── ens_bio_seqFeature.pm │ │ ├── EasyArgv.pm │ │ ├── Eprof.pm │ │ ├── EprofStack.pm │ │ ├── Exception.pm │ │ ├── IO.pm │ │ ├── Interval.pm │ │ ├── Iterator.pm │ │ ├── Logger.pm │ │ ├── Net.pm │ │ ├── PolyA.pm │ │ ├── Proxy.pm │ │ ├── RNAProductTypeMapper.pm │ │ ├── Scalar.pm │ │ ├── SchemaConversion.pm │ │ ├── ScriptUtils.pm │ │ ├── SeqDumper.pm │ │ ├── SeqRegionCache.pm │ │ ├── Sequence.pm │ │ ├── Slice.pm │ │ ├── SqlHelper.pm │ │ ├── TranscriptSelector.pm │ │ ├── Tree │ │ └── Interval │ │ │ ├── Immutable.pm │ │ │ ├── Immutable │ │ │ └── Node.pm │ │ │ ├── Mutable.pm │ │ │ └── Mutable │ │ │ ├── Node.pm │ │ │ └── PP.pm │ │ ├── URI.pm │ │ ├── VegaCuration │ │ ├── Gene.pm │ │ ├── Transcript.pm │ │ └── Translation.pm │ │ └── ensembl_init.example └── t │ ├── .cvsignore │ ├── MultiTestDB.conf.default │ ├── MultiTestDB.conf.example │ ├── MultiTestDB.t │ ├── README │ ├── altAlleleGroup.t │ ├── analysis.t │ ├── archiveStableId.t │ ├── argument.t │ ├── assemblyException.t │ ├── assemblyExceptionFeature.t │ ├── assemblyMapper.t │ ├── associated_xref.t │ ├── attribute.t │ ├── attributeAdaptor.t │ ├── baseAdaptor.t │ ├── baseAlignFeature.t │ ├── biotype.t │ ├── canonicalDBAdaptor.t │ ├── cds.t │ ├── chainedAssemblyMapper.t │ ├── circularSlice.t │ ├── cliHelper.t │ ├── compara.t │ ├── coordSystem.t │ ├── coordSystemAdaptor.t │ ├── dataFile.t │ ├── dbConnection.t │ ├── dbEntries.t │ ├── densityFeature.t │ ├── densityFeatureAdaptor.t │ ├── densityType.t │ ├── densityTypeAdaptor.t │ ├── dependencies.t │ ├── ditag.t │ ├── ditagAdaptor.t │ ├── ditagFeature.t │ ├── ditagFeatureAdaptor.t │ ├── dnaAlignFeatureAdaptor.t │ ├── dnaDnaAlignFeature.t │ ├── dnaPepAlignFeature.t │ ├── easyargv.t │ ├── exception.t │ ├── exon.t │ ├── exonTranscript.pm │ ├── externalFeatureAdaptor.t │ ├── fastaSequenceAdaptor.t │ ├── feature.t │ ├── featurePair.t │ ├── fullIdCaching.t │ ├── gene.t │ ├── geneview.t │ ├── genomeContainer.t │ ├── getNearestFeature.t │ ├── housekeeping_apache2.t │ ├── housekeeping_perlCritic.t │ ├── interval_tree_immutable.t │ ├── interval_tree_mutable.t │ ├── intron.t │ ├── intronSupportingEvidence.t │ ├── iterator.t │ ├── karyotypeBand.t │ ├── karyotypeBandAdaptor.t │ ├── lruIdCaching.t │ ├── mane.t │ ├── mapLocation.t │ ├── mappedSliceContainer.t │ ├── mapper.t │ ├── marker.t │ ├── markerAdaptor.t │ ├── markerFeature.t │ ├── markerFeatureAdaptor.t │ ├── markerSynonym.t │ ├── metaContainer.t │ ├── metaCoordContainer.t │ ├── miscFeature.t │ ├── miscFeatureAdaptor.t │ ├── miscSet.t │ ├── miscSetAdaptor.t │ ├── objectLoad.t │ ├── ontologyTerm.t │ ├── operon.t │ ├── operon_fetch.t │ ├── operon_transcript.t │ ├── paddedSlice.t │ ├── predictionTranscript.t │ ├── proteinAlignFeatureAdaptor.t │ ├── proteinFeature.t │ ├── proteinFeatureAdaptor.t │ ├── rangeRegistry.t │ ├── registry.t │ ├── registry_public_cores.t │ ├── regression_baseFeatureAdaptorMultiQuery.t │ ├── regression_featureAdaptorCache.t │ ├── regression_multiMappingContig.t │ ├── regression_transcriptProjectionAttributeDuplication.t │ ├── repeatConsensus.t │ ├── repeatConsensusAdaptor.t │ ├── repeatFeature.t │ ├── repeatFeatureAdaptor.t │ ├── repeatMaskedSlice.t │ ├── rnaProduct.t │ ├── schema.t │ ├── schemaPatches.t │ ├── seqDumper.t │ ├── seqEdit.t │ ├── sequenceAdaptor.t │ ├── simpleFeature.t │ ├── slice.t │ ├── sliceAdaptor.t │ ├── sliceVariation.t │ ├── sqlHelper.t │ ├── strainSlice.t │ ├── subSliceFeature.t │ ├── switchableAdaptors.t │ ├── test-genome-DBs │ ├── circ │ │ └── core │ │ │ ├── SQLite │ │ │ ├── table.sql │ │ │ ├── transcript.post │ │ │ └── transcript.pre │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── attrib_type.txt │ │ │ ├── coord_system.txt │ │ │ ├── dna.txt │ │ │ ├── exon.txt │ │ │ ├── exon_transcript.txt │ │ │ ├── external_db.txt │ │ │ ├── external_synonym.txt │ │ │ ├── gene.txt │ │ │ ├── gene_attrib.txt │ │ │ ├── identity_xref.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── object_xref.txt │ │ │ ├── ontology_xref.txt │ │ │ ├── protein_feature.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── simple_feature.txt │ │ │ ├── table.sql │ │ │ ├── transcript.txt │ │ │ ├── translation.txt │ │ │ ├── translation_attrib.txt │ │ │ └── xref.txt │ ├── homo_sapiens │ │ ├── core │ │ │ ├── SQLite │ │ │ │ └── table.sql │ │ │ ├── alt_allele.txt │ │ │ ├── alt_allele_attrib.txt │ │ │ ├── alt_allele_group.txt │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── assembly_exception.txt │ │ │ ├── attrib_type.txt │ │ │ ├── biotype.txt │ │ │ ├── coord_system.txt │ │ │ ├── density_feature.txt │ │ │ ├── density_type.txt │ │ │ ├── ditag.txt │ │ │ ├── ditag_feature.txt │ │ │ ├── dna.txt │ │ │ ├── dna_align_feature.txt │ │ │ ├── exon.txt │ │ │ ├── exon_transcript.txt │ │ │ ├── external_db.txt │ │ │ ├── external_synonym.txt │ │ │ ├── gene.txt │ │ │ ├── gene_archive.txt │ │ │ ├── gene_attrib.txt │ │ │ ├── identity_xref.txt │ │ │ ├── interpro.txt │ │ │ ├── karyotype.txt │ │ │ ├── map.txt │ │ │ ├── mapping_session.txt │ │ │ ├── marker.txt │ │ │ ├── marker_feature.txt │ │ │ ├── marker_map_location.txt │ │ │ ├── marker_synonym.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── misc_attrib.txt │ │ │ ├── misc_feature.txt │ │ │ ├── misc_feature_misc_set.txt │ │ │ ├── misc_set.txt │ │ │ ├── object_xref.txt │ │ │ ├── ontology_xref.txt │ │ │ ├── operon.txt │ │ │ ├── operon_transcript.txt │ │ │ ├── operon_transcript_gene.txt │ │ │ ├── peptide_archive.txt │ │ │ ├── prediction_exon.txt │ │ │ ├── prediction_transcript.txt │ │ │ ├── protein_align_feature.txt │ │ │ ├── protein_feature.txt │ │ │ ├── repeat_consensus.txt │ │ │ ├── repeat_feature.txt │ │ │ ├── rnaproduct.txt │ │ │ ├── rnaproduct_attrib.txt │ │ │ ├── rnaproduct_type.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── seq_region_synonym.txt │ │ │ ├── simple_feature.txt │ │ │ ├── stable_id_event.txt │ │ │ ├── supporting_feature.txt │ │ │ ├── table.sql │ │ │ ├── transcript.txt │ │ │ ├── transcript_attrib.txt │ │ │ ├── transcript_supporting_feature.txt │ │ │ ├── translation.txt │ │ │ ├── unmapped_object.txt │ │ │ ├── unmapped_reason.txt │ │ │ └── xref.txt │ │ ├── empty │ │ │ ├── SQLite │ │ │ │ └── table.sql │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── assembly_exception.txt │ │ │ ├── attrib_type.txt │ │ │ ├── coord_system.txt │ │ │ ├── dna.txt │ │ │ ├── external_db.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── seq_region_synonym.txt │ │ │ ├── table.sql │ │ │ └── unmapped_reason.txt │ │ ├── patch │ │ │ ├── SQLite │ │ │ │ └── table.sql │ │ │ ├── alt_allele.txt │ │ │ ├── alt_allele_attrib.txt │ │ │ ├── alt_allele_group.txt │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── assembly_exception.txt │ │ │ ├── attrib_type.txt │ │ │ ├── coord_system.txt │ │ │ ├── density_feature.txt │ │ │ ├── density_type.txt │ │ │ ├── dependent_xref.txt │ │ │ ├── ditag.txt │ │ │ ├── ditag_feature.txt │ │ │ ├── dna.txt │ │ │ ├── dna_align_feature.txt │ │ │ ├── exon.txt │ │ │ ├── exon_transcript.txt │ │ │ ├── external_db.txt │ │ │ ├── external_synonym.txt │ │ │ ├── gene.txt │ │ │ ├── gene_archive.txt │ │ │ ├── gene_attrib.txt │ │ │ ├── genome_statistics.txt │ │ │ ├── identity_xref.txt │ │ │ ├── interpro.txt │ │ │ ├── karyotype.txt │ │ │ ├── map.txt │ │ │ ├── mapping_session.txt │ │ │ ├── mapping_set.txt │ │ │ ├── marker.txt │ │ │ ├── marker_feature.txt │ │ │ ├── marker_map_location.txt │ │ │ ├── marker_synonym.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── misc_attrib.txt │ │ │ ├── misc_feature.txt │ │ │ ├── misc_feature_misc_set.txt │ │ │ ├── misc_set.txt │ │ │ ├── object_xref.txt │ │ │ ├── ontology_xref.txt │ │ │ ├── peptide_archive.txt │ │ │ ├── prediction_exon.txt │ │ │ ├── prediction_transcript.txt │ │ │ ├── protein_align_feature.txt │ │ │ ├── protein_feature.txt │ │ │ ├── repeat_consensus.txt │ │ │ ├── repeat_feature.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── seq_region_mapping.txt │ │ │ ├── seq_region_synonym.txt │ │ │ ├── simple_feature.txt │ │ │ ├── stable_id_event.txt │ │ │ ├── supporting_feature.txt │ │ │ ├── table.sql │ │ │ ├── transcript.txt │ │ │ ├── transcript_attrib.txt │ │ │ ├── transcript_supporting_feature.txt │ │ │ ├── translation.txt │ │ │ ├── translation_attrib.txt │ │ │ ├── unmapped_object.txt │ │ │ ├── unmapped_reason.txt │ │ │ └── xref.txt │ │ ├── variation │ │ │ ├── SQLite │ │ │ │ └── table.sql │ │ │ ├── allele.txt │ │ │ ├── allele_code.txt │ │ │ ├── associate_study.txt │ │ │ ├── attrib.txt │ │ │ ├── attrib_set.txt │ │ │ ├── attrib_type.txt │ │ │ ├── compressed_genotype_region.txt │ │ │ ├── compressed_genotype_var.txt │ │ │ ├── coord_system.txt │ │ │ ├── display_group.txt │ │ │ ├── failed_allele.txt │ │ │ ├── failed_description.txt │ │ │ ├── failed_structural_variation.txt │ │ │ ├── failed_variation.txt │ │ │ ├── genotype_code.txt │ │ │ ├── individual.txt │ │ │ ├── individual_synonym.txt │ │ │ ├── individual_type.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── motif_feature_variation.txt │ │ │ ├── phenotype.txt │ │ │ ├── phenotype_feature.txt │ │ │ ├── phenotype_feature_attrib.txt │ │ │ ├── population.txt │ │ │ ├── population_genotype.txt │ │ │ ├── population_structure.txt │ │ │ ├── population_synonym.txt │ │ │ ├── protein_function_predictions.txt │ │ │ ├── protein_function_predictions_attrib.txt │ │ │ ├── publication.txt │ │ │ ├── read_coverage.txt │ │ │ ├── regulatory_feature_variation.txt │ │ │ ├── sample.txt │ │ │ ├── sample_genotype_multiple_bp.txt │ │ │ ├── sample_population.txt │ │ │ ├── seq_region.txt │ │ │ ├── source.txt │ │ │ ├── structural_variation.txt │ │ │ ├── structural_variation_association.txt │ │ │ ├── structural_variation_feature.txt │ │ │ ├── structural_variation_sample.txt │ │ │ ├── study.txt │ │ │ ├── submitter_handle.txt │ │ │ ├── subsnp_handle.txt │ │ │ ├── table.sql │ │ │ ├── tagged_variation_feature.txt │ │ │ ├── tmp_sample_genotype_single_bp.txt │ │ │ ├── transcript_variation.txt │ │ │ ├── translation_md5.txt │ │ │ ├── variation.txt │ │ │ ├── variation_attrib.txt │ │ │ ├── variation_citation.txt │ │ │ ├── variation_feature.txt │ │ │ ├── variation_genename.txt │ │ │ ├── variation_hgvs.txt │ │ │ ├── variation_set.txt │ │ │ ├── variation_set_structural_variation.txt │ │ │ ├── variation_set_structure.txt │ │ │ ├── variation_set_variation.txt │ │ │ └── variation_synonym.txt │ │ └── xref │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ └── table.sql │ ├── mapping │ │ └── core │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── assembly.txt │ │ │ ├── attrib_type.txt │ │ │ ├── coord_system.txt │ │ │ ├── dna.txt │ │ │ ├── external_db.txt │ │ │ ├── meta.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ └── table.sql │ ├── multi │ │ └── compara │ │ │ ├── CAFE_gene_family.txt │ │ │ ├── CAFE_species_gene.txt │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── conservation_score.txt │ │ │ ├── constrained_element.txt │ │ │ ├── dnafrag.txt │ │ │ ├── dnafrag_region.txt │ │ │ ├── external_db.txt │ │ │ ├── family.txt │ │ │ ├── family_member.txt │ │ │ ├── gene_align.txt │ │ │ ├── gene_align_member.txt │ │ │ ├── gene_member.txt │ │ │ ├── gene_member_hom_stats.txt │ │ │ ├── gene_tree_node.txt │ │ │ ├── gene_tree_node_attr.txt │ │ │ ├── gene_tree_node_tag.txt │ │ │ ├── gene_tree_object_store.txt │ │ │ ├── gene_tree_root.txt │ │ │ ├── gene_tree_root_attr.txt │ │ │ ├── gene_tree_root_tag.txt │ │ │ ├── genome_db.txt │ │ │ ├── genomic_align.txt │ │ │ ├── genomic_align_block.txt │ │ │ ├── genomic_align_tree.txt │ │ │ ├── hmm_annot.txt │ │ │ ├── hmm_curated_annot.txt │ │ │ ├── hmm_profile.txt │ │ │ ├── homology.txt │ │ │ ├── homology_member.txt │ │ │ ├── mapping_session.txt │ │ │ ├── member_xref.txt │ │ │ ├── meta.txt │ │ │ ├── method_link.txt │ │ │ ├── method_link_species_set.txt │ │ │ ├── method_link_species_set_attr.txt │ │ │ ├── method_link_species_set_tag.txt │ │ │ ├── ncbi_taxa_name.txt │ │ │ ├── ncbi_taxa_node.txt │ │ │ ├── other_member_sequence.txt │ │ │ ├── peptide_align_feature.txt │ │ │ ├── seq_member.txt │ │ │ ├── sequence.txt │ │ │ ├── species_set.txt │ │ │ ├── species_set_header.txt │ │ │ ├── species_set_tag.txt │ │ │ ├── species_tree_node.txt │ │ │ ├── species_tree_node_attr.txt │ │ │ ├── species_tree_node_tag.txt │ │ │ ├── species_tree_root.txt │ │ │ ├── stable_id_history.txt │ │ │ ├── synteny_region.txt │ │ │ └── table.sql │ ├── mus_musculus │ │ ├── core │ │ │ ├── SQLite │ │ │ │ └── table.sql │ │ │ ├── assembly.txt │ │ │ ├── attrib_type.txt │ │ │ ├── coord_system.txt │ │ │ ├── dna.txt │ │ │ ├── external_db.txt │ │ │ ├── gene.txt │ │ │ ├── meta.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── table.sql │ │ │ └── unmapped_reason.txt │ │ └── variation │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── allele_code.txt │ │ │ ├── attrib.txt │ │ │ ├── attrib_set.txt │ │ │ ├── attrib_type.txt │ │ │ ├── compressed_genotype_region.txt │ │ │ ├── compressed_genotype_var.txt │ │ │ ├── failed_description.txt │ │ │ ├── genotype_code.txt │ │ │ ├── individual_type.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── read_coverage.txt │ │ │ ├── sample.txt │ │ │ ├── sample_genotype_multiple_bp.txt │ │ │ ├── seq_region.txt │ │ │ ├── source.txt │ │ │ ├── table.sql │ │ │ ├── tmp_sample_genotype_single_bp.txt │ │ │ ├── variation.txt │ │ │ └── variation_feature.txt │ ├── nameless │ │ └── core │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── external_db.txt │ │ │ ├── meta.txt │ │ │ └── table.sql │ ├── ontology │ │ └── ontology │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── alt_id.txt │ │ │ ├── aux_GO_Cross_product_review_map.txt │ │ │ ├── aux_GO_mf_needs_review_map.txt │ │ │ ├── aux_GO_virus_checked_map.txt │ │ │ ├── aux_SO_DBVAR_map.txt │ │ │ ├── aux_SO_SOFA_map.txt │ │ │ ├── aux_SO_biosapiens_map.txt │ │ │ ├── closure.txt │ │ │ ├── meta.txt │ │ │ ├── ontology.txt │ │ │ ├── relation.txt │ │ │ ├── relation_type.txt │ │ │ ├── subset.txt │ │ │ ├── table.sql │ │ │ └── term.txt │ ├── parus_major1 │ │ └── core │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── attrib_type.txt │ │ │ ├── biotype.txt │ │ │ ├── coord_system.txt │ │ │ ├── external_db.txt │ │ │ ├── meta.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── seq_region_synonym.txt │ │ │ ├── table.sql │ │ │ └── unmapped_reason.txt │ ├── polyploidy │ │ └── core │ │ │ ├── SQLite │ │ │ └── table.sql │ │ │ ├── analysis.txt │ │ │ ├── analysis_description.txt │ │ │ ├── assembly.txt │ │ │ ├── attrib_type.txt │ │ │ ├── coord_system.txt │ │ │ ├── density_type.txt │ │ │ ├── dna.txt │ │ │ ├── exon.txt │ │ │ ├── exon_transcript.txt │ │ │ ├── external_db.txt │ │ │ ├── external_synonym.txt │ │ │ ├── gene.txt │ │ │ ├── gene_attrib.txt │ │ │ ├── genome_statistics.txt │ │ │ ├── identity_xref.txt │ │ │ ├── interpro.txt │ │ │ ├── meta.txt │ │ │ ├── meta_coord.txt │ │ │ ├── misc_set.txt │ │ │ ├── protein_feature.txt │ │ │ ├── repeat_consensus.txt │ │ │ ├── repeat_feature.txt │ │ │ ├── seq_region.txt │ │ │ ├── seq_region_attrib.txt │ │ │ ├── table.sql │ │ │ ├── transcript.txt │ │ │ ├── translation.txt │ │ │ ├── translation_attrib.txt │ │ │ └── unmapped_reason.txt │ └── test_collection │ │ └── core │ │ ├── SQLite │ │ └── table.sql │ │ ├── external_db.txt │ │ ├── meta.txt │ │ └── table.sql │ ├── topLevelAssemblyMapper.t │ ├── transcript.t │ ├── transcriptSelector.t │ ├── transcriptSupportingFeatureAdaptor.t │ ├── translation.t │ ├── unmappedObject.t │ ├── unmappedObjectAdaptor.t │ ├── utilsIo.t │ ├── utilsNet.t │ ├── utilsScalar.t │ ├── utilsUri.t │ ├── utr.t │ ├── xref_parser.t │ └── xrefs.t ├── sql ├── README ├── foreign_keys.sql ├── patch_100_101_a.sql ├── patch_101_102_a.sql ├── patch_102_103_a.sql ├── patch_103_104_a.sql ├── patch_104_105_a.sql ├── patch_105_106_a.sql ├── patch_106_107_a.sql ├── patch_106_107_b.sql ├── patch_107_108_a.sql ├── patch_108_109_a.sql ├── patch_108_109_b.sql ├── patch_109_110_a.sql ├── patch_109_110_b.sql ├── patch_109_110_c.sql ├── patch_110_111_a.sql ├── patch_111_112_a.sql ├── patch_111_112_b.sql ├── patch_111_112_c.sql ├── patch_112_113_a.sql ├── patch_112_113_b.sql ├── patch_113_114_a.sql ├── patch_21_22.sql ├── patch_23_24.sql ├── patch_24_25.sql ├── patch_25_26.sql ├── patch_26_27.sql ├── patch_27_28.sql ├── patch_28_29.sql ├── patch_29_30.sql ├── patch_30_31.sql ├── patch_31_32.sql ├── patch_32_33.sql ├── patch_33_34.sql ├── patch_34_35.sql ├── patch_35_36.sql ├── patch_36_37.sql ├── patch_37_38.sql ├── patch_38_39_a.sql ├── patch_38_39_b.sql ├── patch_38_39_c.sql ├── patch_38_39_d.sql ├── patch_38_39_e.sql ├── patch_39_40_a.sql ├── patch_39_40_b.sql ├── patch_39_40_c.sql ├── patch_39_40_d.sql ├── patch_39_40_e.sql ├── patch_39_40_f.sql ├── patch_39_40_g.sql ├── patch_39_40_h.sql ├── patch_39_40_i.sql ├── patch_39_40_j.sql ├── patch_40_41_a.sql ├── patch_40_41_b.sql ├── patch_40_41_c.sql ├── patch_40_41_d.sql ├── patch_40_41_e.sql ├── patch_40_41_f.sql ├── patch_41_42_a.sql ├── patch_41_42_b.sql ├── patch_41_42_c.sql ├── patch_41_42_d.sql ├── patch_41_42_e.sql ├── patch_41_42_f.sql ├── patch_41_42_g.sql ├── patch_42_43_a.sql ├── patch_42_43_b.sql ├── patch_42_43_c.sql ├── patch_42_43_d.sql ├── patch_42_43_e.sql ├── patch_42_43_f.sql ├── patch_43_44_a.sql ├── patch_43_44_b.sql ├── patch_43_44_c.sql ├── patch_43_44_d.sql ├── patch_43_44_e.sql ├── patch_43_44_f.sql ├── patch_44_45_a.sql ├── patch_44_45_b.sql ├── patch_44_45_c.sql ├── patch_45_46_a.sql ├── patch_45_46_b.sql ├── patch_45_46_c.sql ├── patch_45_46_d.sql ├── patch_45_46_e.sql ├── patch_45_46_f.sql ├── patch_45_46_g.sql ├── patch_46_47_a.sql ├── patch_46_47_b.sql ├── patch_46_47_c.sql ├── patch_47_48_a.sql ├── patch_48_49_a.sql ├── patch_48_49_b.sql ├── patch_48_49_c.sql ├── patch_48_49_d.sql ├── patch_48_49_e.sql ├── patch_49_50_a.sql ├── patch_49_50_b.sql ├── patch_49_50_c.sql ├── patch_49_50_d.sql ├── patch_49_50_e.sql ├── patch_50_51_a.sql ├── patch_50_51_b.sql ├── patch_50_51_c.sql ├── patch_50_51_d.sql ├── patch_50_51_e.sql ├── patch_50_51_f.sql ├── patch_50_51_g.sql ├── patch_50_51_h.sql ├── patch_50_51_i.sql ├── patch_51_52_a.sql ├── patch_51_52_b.sql ├── patch_51_52_c.sql ├── patch_51_52_d.sql ├── patch_52_53_a.sql ├── patch_52_53_b.sql ├── patch_52_53_c.sql ├── patch_52_53_d.sql ├── patch_53_54_a.sql ├── patch_53_54_b.sql ├── patch_53_54_c.sql ├── patch_54_55_a.sql ├── patch_54_55_b.sql ├── patch_54_55_c.sql ├── patch_54_55_d.sql ├── patch_54_55_e.sql ├── patch_54_55_f.sql ├── patch_54_55_g.sql ├── patch_54_55_h.sql ├── patch_55_56_a.sql ├── patch_55_56_b.sql ├── patch_55_56_c.sql ├── patch_55_56_d.sql ├── patch_56_57_a.sql ├── patch_56_57_b.sql ├── patch_56_57_c.sql ├── patch_56_57_d.sql ├── patch_56_57_e.sql ├── patch_56_57_f.sql ├── patch_57_58_a.sql ├── patch_58_59_a.sql ├── patch_58_59_b.sql ├── patch_58_59_c.sql ├── patch_58_59_d.sql ├── patch_58_59_e.sql ├── patch_59_60_a.sql ├── patch_59_60_b.sql ├── patch_59_60_c.sql ├── patch_60_61_a.sql ├── patch_60_61_b.sql ├── patch_60_61_c.sql ├── patch_61_62_a.sql ├── patch_61_62_b.sql ├── patch_61_62_c.sql ├── patch_61_62_d.sql ├── patch_61_62_e.sql ├── patch_62_63_a.sql ├── patch_62_63_b.sql ├── patch_62_63_c.sql ├── patch_63_64_a.sql ├── patch_63_64_b.sql ├── patch_63_64_c.sql ├── patch_63_64_d.sql ├── patch_64_65_a.sql ├── patch_64_65_b.sql ├── patch_64_65_c.sql ├── patch_64_65_d.sql ├── patch_65_66_a.sql ├── patch_65_66_b.sql ├── patch_65_66_c.sql ├── patch_65_66_d.sql ├── patch_65_66_e.sql ├── patch_65_66_f.sql ├── patch_66_67_a.sql ├── patch_66_67_b.sql ├── patch_66_67_c.sql ├── patch_66_67_d.sql ├── patch_66_67_e.sql ├── patch_67_68_a.sql ├── patch_67_68_b.sql ├── patch_67_68_c.sql ├── patch_67_68_d.sql ├── patch_67_68_e.sql ├── patch_68_69_a.sql ├── patch_69_70_a.sql ├── patch_69_70_b.sql ├── patch_69_70_c.sql ├── patch_69_70_d.sql ├── patch_69_70_e.sql ├── patch_70_71_a.sql ├── patch_70_71_b.sql ├── patch_71_72_a.sql ├── patch_71_72_b.sql ├── patch_72_73_a.sql ├── patch_72_73_b.sql ├── patch_72_73_c.sql ├── patch_73_74_a.sql ├── patch_73_74_b.sql ├── patch_73_74_c.sql ├── patch_73_74_d.sql ├── patch_73_74_e.sql ├── patch_73_74_f.sql ├── patch_73_74_g.sql ├── patch_73_74_h.sql ├── patch_74_75_a.sql ├── patch_74_75_b.sql ├── patch_74_75_c.sql ├── patch_74_75_d.sql ├── patch_74_75_e.sql ├── patch_74_75_f.sql ├── patch_75_76_a.sql ├── patch_75_76_b.sql ├── patch_75_76_c.sql ├── patch_76_77_a.sql ├── patch_77_78_a.sql ├── patch_77_78_b.sql ├── patch_77_78_c.sql ├── patch_78_79_a.sql ├── patch_78_79_b.sql ├── patch_79_80_a.sql ├── patch_79_80_b.sql ├── patch_79_80_c.sql ├── patch_79_80_d.sql ├── patch_80_81_a.sql ├── patch_80_81_b.sql ├── patch_81_82_a.sql ├── patch_81_82_b.sql ├── patch_81_82_c.sql ├── patch_82_83_a.sql ├── patch_83_84_a.sql ├── patch_83_84_b.sql ├── patch_83_84_c.sql ├── patch_83_84_d.sql ├── patch_83_84_e.sql ├── patch_84_85_a.sql ├── patch_84_85_b.sql ├── patch_85_86_a.sql ├── patch_85_86_b.sql ├── patch_85_86_c.sql ├── patch_86_87_a.sql ├── patch_86_87_b.sql ├── patch_86_87_c.sql ├── patch_87_88_a.sql ├── patch_87_88_b.sql ├── patch_87_88_c.sql ├── patch_88_89_a.sql ├── patch_89_90_a.sql ├── patch_89_90_b.sql ├── patch_89_90_c.sql ├── patch_90_91_a.sql ├── patch_90_91_b.sql ├── patch_90_91_c.sql ├── patch_90_91_d.sql ├── patch_91_92_a.sql ├── patch_91_92_b.sql ├── patch_92_93_a.sql ├── patch_92_93_b.sql ├── patch_92_93_c.sql ├── patch_93_94_a.sql ├── patch_93_94_b.sql ├── patch_93_94_c.sql ├── patch_94_95_a.sql ├── patch_94_95_b.sql ├── patch_95_96_a.sql ├── patch_96_97_a.sql ├── patch_96_97_b.sql ├── patch_96_97_c.sql ├── patch_96_97_d.sql ├── patch_96_97_e.sql ├── patch_97_98_a.sql ├── patch_98_99_a.sql ├── patch_99_100_a.sql ├── patch_99_100_b.sql ├── patch_99_100_c.sql ├── populate_meta_coord.pl └── table.sql └── travisci ├── MultiTestDB.conf.gitlabci.mysql ├── MultiTestDB.conf.travisci.SQLite ├── MultiTestDB.conf.travisci.mysql ├── api_build_run_last_hour.py ├── harness.sh ├── testdb.conf.gitlabci.mysql ├── testdb.conf.travisci.SQLite ├── testdb.conf.travisci.mysql └── trigger-dependent-build.sh /.gitignore: -------------------------------------------------------------------------------- 1 | blib/ 2 | .build/ 3 | _build/ 4 | cover_db/ 5 | inc/ 6 | Build 7 | !Build/ 8 | Build.bat 9 | .last_cover_stats 10 | MANIFEST.bak 11 | META.yml 12 | MYMETA.yml 13 | nytprof.out 14 | pm_to_blib 15 | .DS_Store 16 | Thumbs.db 17 | *.swp 18 | *.swo 19 | *~ 20 | \#*\# 21 | /.emacs.desktop 22 | /.emacs.desktop.lock 23 | .elc 24 | auto-save-list 25 | tramp 26 | .\#* 27 | # Org-mode 28 | .org-id-locations 29 | *_archive 30 | a.out 31 | *.o 32 | *.obj 33 | *.class 34 | MultiTestDB.conf 35 | MultiTestDB.*.conf 36 | *.frozen.conf 37 | bioperl*.zip 38 | /modules/t/CLEAN.t 39 | /misc-scripts/xref_mapping/sql/populate_metadata.sql 40 | -------------------------------------------------------------------------------- /.perlcriticrc: -------------------------------------------------------------------------------- 1 | severity = 1 2 | color = 1 3 | color-severity-highest = red 4 | color-severity-high = magenta 5 | color-severity-medium = yellow 6 | 7 | [Subroutines::ProhibitExplicitReturnUndef] 8 | severity=4 9 | 10 | [CodeLayout::ProhibitHardTabs] 11 | allow_leading_tabs = 0 12 | 13 | [CodeLayout::RequireTidyCode] 14 | perltidyrc = .perltidyrc 15 | 16 | [Subroutines::ProhibitUnusedPrivateSubroutines] 17 | allow = _init_db _init_config _guess_config 18 | 19 | [Subroutines::ProhibitUnusedPrivateSubroutines] 20 | skip_when_using = Moose 21 | 22 | [Subroutines::ProhibitManyArgs] 23 | max_arguments = 7 24 | -------------------------------------------------------------------------------- /.perltidyrc: -------------------------------------------------------------------------------- 1 | # I/O control 2 | --standard-error-output 3 | 4 | # Basic Options 5 | --maximum-line-length=72 6 | --indent-columns=2 7 | 8 | # Code Indentation Control 9 | --line-up-parentheses 10 | 11 | # Whitespace Control 12 | --nospace-for-semicolon 13 | --nowant-left-space="* /" 14 | --nowant-right-space="* /" 15 | 16 | # Comment Controls 17 | --closing-side-comments 18 | --closing-side-comment-interval=25 19 | --closing-side-comment-else-flag=1 20 | 21 | # Line Break Control 22 | --nocuddled-else # for block readability 23 | --opening-token-right 24 | --vertical-tightness=2 25 | --vertical-tightness-closing=2 26 | -sot # --stack-opening-token 27 | -sct # --stack-closing-token 28 | --break-after-all-operators 29 | 30 | # Retaining or Ignoring Existing Line Breaks 31 | --ignore-old-breakpoints 32 | 33 | # Blank Line Control 34 | --no-blanks-before-comments 35 | -------------------------------------------------------------------------------- /misc-scripts/assembly/blastz_matrix.txt: -------------------------------------------------------------------------------- 1 | A C G T 2 | 100 -300 -150 -300 3 | -300 100 -300 -150 4 | -150 -300 100 -300 5 | -300 -150 -300 100 6 | 7 | -------------------------------------------------------------------------------- /misc-scripts/assembly/load_feature_mappings.ini.example: -------------------------------------------------------------------------------- 1 | dbname = mk8_bos_taurus_core_65_31 2 | host = ens-research 3 | port = 3306 4 | user = ensro 5 | assembly = UMD3.1 6 | altassembly = Btau_4.0 7 | altdbname = mk8_bos_taurus_core_63_4 8 | althost = ens-research 9 | altport = 3306 10 | vardbname = bos_taurus_variation_65_31 11 | varhost = ens-livemirror 12 | varport = 3306 13 | varaltdbname = bos_taurus_variation_63_4 14 | testdbname = mk8_test_assembly_mappings_chr1_6 15 | testuser = ensadmin 16 | testpass = WRITE_PASS 17 | logpath = /lustre/scratch103/ensembl/mk8/cow_mapping 18 | log_base_path = /lustre/scratch103/ensembl/mk8/cow_mapping 19 | chromosomes = 1,2,3,4,5,6 20 | features = genes,SNPs 21 | -------------------------------------------------------------------------------- /misc-scripts/assembly/test_assembly_mapping.ini.example: -------------------------------------------------------------------------------- 1 | dbname = mk8_test_assembly_mappings_chr1_6 2 | host = ens-research 3 | port = 3306 4 | user = ensadmin 5 | pass = WRITE_PASS 6 | logpath = /lustre/scratch103/ensembl/mk8/cow_mapping 7 | -------------------------------------------------------------------------------- /misc-scripts/assembly_patches/README.TXT: -------------------------------------------------------------------------------- 1 | #Get the sequence data. Should be able to down load fasta later but for now do it manually. 2 | 3 | mfetch -d embl -v fasta AC093223.3 AC145145.2 AC144587.2 AC142525.2 AC139494.2 AC118459.2 AC139500.2 AC108108.2 AC138827.3 AC146335.1 AC139463.2 AC138832.2 > seq.fasta 4 | 5 | 6 | Get the mappings 7 | 8 | In Genome workbench click on Patch Scaffolds and export agp. 9 | to get hap -> contig 10 | 11 | See file thjat was attached to get ref->hap mappings. 12 | 13 | 14 | NOW use.... 15 | ----------- 16 | 17 | wget https://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/PATCHES/patch_release_1/FASTA/alt.scaf.fa.gz 18 | gunzip alt.scaf.fa.gz 19 | 20 | wget https://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/PATCHES/patch_release_1/alt_scaffold_placement.txt 21 | 22 | wget https://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/PATCHES/patch_release_1/AGP/alt.scaf.agp.gz 23 | gunzip alt.scaf.agp.gz 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /misc-scripts/cloud/EnsCloud/Cmd.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | package EnsCloud::Cmd; 21 | use Moose; 22 | use MooseX::StrictConstructor; 23 | extends qw(MooseX::App::Cmd); 24 | __PACKAGE__->meta->make_immutable; 25 | 26 | 1; 27 | 28 | -------------------------------------------------------------------------------- /misc-scripts/cloud/ecloud: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | # See the NOTICE file distributed with this work for additional information 3 | # regarding copyright ownership. 4 | # 5 | # Licensed under the Apache License, Version 2.0 (the "License"); 6 | # you may not use this file except in compliance with the License. 7 | # You may obtain a copy of the License at 8 | # 9 | # http://www.apache.org/licenses/LICENSE-2.0 10 | # 11 | # Unless required by applicable law or agreed to in writing, software 12 | # distributed under the License is distributed on an "AS IS" BASIS, 13 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | # See the License for the specific language governing permissions and 15 | # limitations under the License. 16 | 17 | 18 | 19 | use EnsCloud::Cmd; 20 | 21 | EnsCloud::Cmd->run; 22 | 23 | 24 | 25 | -------------------------------------------------------------------------------- /misc-scripts/stable_id_lookup/sql/indices.sql: -------------------------------------------------------------------------------- 1 | #CREATE UNIQUE INDEX stable_id_lookup_idx USING BTREE ON stable_id_lookup(stable_id,db_type,object_type); 2 | CREATE INDEX stable_id_db_type USING BTREE ON stable_id_lookup(stable_id,db_type); 3 | CREATE INDEX stable_id_object_type USING BTREE ON stable_id_lookup(stable_id,object_type); 4 | -------------------------------------------------------------------------------- /misc-scripts/surgery/SeqStoreConverter/CanisFamiliaris.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | use strict; 21 | use warnings; 22 | 23 | use SeqStoreConverter::BasicConverter; 24 | 25 | package SeqStoreConverter::CanisFamiliaris; 26 | 27 | use vars qw(@ISA); 28 | 29 | @ISA = qw(SeqStoreConverter::BasicConverter); 30 | 31 | 1; 32 | -------------------------------------------------------------------------------- /misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | package SeqStoreConverter::vega::HomoSapiens; 21 | 22 | use strict; 23 | use warnings; 24 | 25 | use SeqStoreConverter::HomoSapiens; 26 | use SeqStoreConverter::vega::VBasicConverter; 27 | 28 | use vars qw(@ISA); 29 | 30 | @ISA = qw(SeqStoreConverter::HomoSapiens SeqStoreConverter::vega::VBasicConverter); 31 | 32 | 1; 33 | -------------------------------------------------------------------------------- /misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | package SeqStoreConverter::vega::MusMusculus; 21 | 22 | use strict; 23 | use warnings; 24 | 25 | use SeqStoreConverter::MusMusculus; 26 | use SeqStoreConverter::vega::VBasicConverter; 27 | 28 | use vars qw(@ISA); 29 | 30 | @ISA = qw(SeqStoreConverter::MusMusculus SeqStoreConverter::vega::VBasicConverter); 31 | 32 | 1; 33 | -------------------------------------------------------------------------------- /misc-scripts/surgery/converter.input: -------------------------------------------------------------------------------- 1 | HomoSapiens ecs3:3307 mouse_vega040719_raw pm2_mouse_vega040719 2 | #FuguRubripes ecs2f fugu_rubripes_core_18_2 mcvicker_new_fugu 3 | #CaenorhabditisElegans ecs2f caenorhabditis_elegans_core_18_102 mcvicker_new_elegans 4 | #CaenorhabditisBriggsae ecs2f caenorhabditis_briggsae_core_18_25 mcvicker_new_briggsae 5 | #RattusNorvegicus ecs2f rattus_norvegicus_core_18_3 mcvicker_new_rat 6 | #DrosophilaMelanogaster ecs2f drosophila_melanogaster_core_18_3a mcvicker_new_fly 7 | #MusMusculus ecs2f mus_musculus_core_18_30 mcvicker_new_mouse 8 | #DanioRerio ecs2f danio_rerio_core_18_2 mcvicker_new_zebrafish 9 | #AnophelesGambiae ecs2f anopheles_gambiae_core_18_2a mcvicker_new_mosquito 10 | -------------------------------------------------------------------------------- /misc-scripts/web_stats.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | # See the NOTICE file distributed with this work for additional information 3 | # regarding copyright ownership. 4 | # 5 | # Licensed under the Apache License, Version 2.0 (the "License"); 6 | # you may not use this file except in compliance with the License. 7 | # You may obtain a copy of the License at 8 | # 9 | # http://www.apache.org/licenses/LICENSE-2.0 10 | # 11 | # Unless required by applicable law or agreed to in writing, software 12 | # distributed under the License is distributed on an "AS IS" BASIS, 13 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 14 | # See the License for the specific language governing permissions and 15 | # limitations under the License. 16 | 17 | 18 | mysql -u ensro -h ecs3 -P 3307 -e 'SELECT week_beginning,hits,size,pi FROM summary WHERE YEAR(week_beginning) >= 2003 AND vhost_id = 3 ORDER BY week_beginning' ensembl_summary_stats 19 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/XrefMapper/LoadMapper.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | package XrefMapper::LoadMapper; 21 | use strict; 22 | 23 | use vars '@ISA'; 24 | @ISA = qw{ XrefMapper::BasicMapper }; 25 | 26 | use warnings; 27 | use XrefMapper::BasicMapper; 28 | 29 | use Cwd; 30 | use DBI; 31 | use File::Basename; 32 | use IPC::Open3; 33 | 34 | sub update_core { 35 | 36 | } 37 | 38 | 1; 39 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBest1.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | package XrefMapper::Methods::ExonerateBest1; 21 | 22 | use XrefMapper::Methods::ExonerateBasic; 23 | 24 | use vars '@ISA'; 25 | 26 | @ISA = qw{XrefMapper::Methods::ExonerateBasic}; 27 | 28 | 29 | 30 | sub options { 31 | 32 | return ('--bestn', '1'); 33 | 34 | } 35 | 36 | 37 | 1; 38 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/XrefParser/UCSC_human_parser.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | # This module replicates the generic UCSC parser for human-specific data 21 | # This prevents cross-mapping between species by treating each species as a separate source 22 | 23 | package XrefParser::UCSC_human_parser; 24 | 25 | use strict; 26 | use warnings; 27 | 28 | use parent qw( XrefParser::UCSCParser ); 29 | 30 | 31 | 1; 32 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/XrefParser/UCSC_mouse_parser.pm: -------------------------------------------------------------------------------- 1 | =head1 LICENSE 2 | 3 | See the NOTICE file distributed with this work for additional information 4 | regarding copyright ownership. 5 | 6 | Licensed under the Apache License, Version 2.0 (the "License"); 7 | you may not use this file except in compliance with the License. 8 | You may obtain a copy of the License at 9 | 10 | http://www.apache.org/licenses/LICENSE-2.0 11 | 12 | Unless required by applicable law or agreed to in writing, software 13 | distributed under the License is distributed on an "AS IS" BASIS, 14 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 15 | See the License for the specific language governing permissions and 16 | limitations under the License. 17 | 18 | =cut 19 | 20 | # This module replicates the generic UCSC parser for mouse-specific data 21 | # This prevents cross-mapping between species by treating each species as a separate source 22 | 23 | package XrefParser::UCSC_mouse_parser; 24 | 25 | use strict; 26 | use warnings; 27 | 28 | use parent qw( XrefParser::UCSCParser ); 29 | 30 | 31 | 1; 32 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/MultiTestDB.conf.default: -------------------------------------------------------------------------------- 1 | # This provides a default set of configurations which is merged with your 2 | # provided MultiTestDB.conf. 3 | # 4 | # You should provide a MultiTestDB.conf which defines the databases 5 | 6 | { 7 | 'databases' => { 8 | 'homo_sapiens' => { 9 | 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 10 | 'otherfeatures' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 11 | }, 12 | }, 13 | } 14 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/hpa.txt: -------------------------------------------------------------------------------- 1 | Antibody,antibody_id,ensembl_peptide_id,link 2 | CAB000001,1,ENSP00000363822,http://www.proteinatlas.org/ENSG00000169083-AR 3 | CAB000001,1,ENSP00000379358,http://www.proteinatlas.org/ENSG00000169083-AR 4 | CAB000001,1,ENSP00000379359,http://www.proteinatlas.org/ENSG00000169083-AR 5 | CAB000001,1,ENSP00000421155,http://www.proteinatlas.org/ENSG00000169083-AR 6 | CAB000001,1,ENSP00000479013,http://www.proteinatlas.org/ENSG00000169083-AR 7 | CAB000001,1,ENSP00000482407,http://www.proteinatlas.org/ENSG00000169083-AR 8 | CAB000001,1,ENSP00000484033,http://www.proteinatlas.org/ENSG00000169083-AR 9 | CAB000002,2,ENSP00000224784,http://www.proteinatlas.org/ENSG00000107796-ACTA2 10 | CAB000002,2,ENSP00000396730,http://www.proteinatlas.org/ENSG00000107796-ACTA2 11 | CAB000002,2,ENSP00000398239,http://www.proteinatlas.org/ENSG00000107796-ACTA2 12 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badData-newEntryType.txt: -------------------------------------------------------------------------------- 1 | # MIM Number MIM Entry Type (see FAQ 1.3 at https://omim.org/help/faq) Entrez Gene ID (NCBI) Approved Gene Symbol (HGNC) Ensembl Gene ID (Ensembl) 2 | 142830 frobnicator 3106 HLA-B ENSG00000234745 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badData-tooFewCols.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID type Source MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - 3 | 100070 - - C1853365 - 4 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badData-tooManyCols.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID type Source MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - ExtraCol 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badHeader-wrongName1.txt: -------------------------------------------------------------------------------- 1 | #MIMO GeneID type Source MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badHeader-wrongName2.txt: -------------------------------------------------------------------------------- 1 | #MIM number Gene type Source MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badHeader-wrongName3.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID typo Source MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - 3 | 100070 - phenotype - C1853365 - 4 | 100100 1131 phenotype GeneMap C0033770 question 5 | 100200 - phenotype - C4551519 - 6 | 100300 57514 phenotype GeneMap C4551482 - 7 | 100600 - phenotype - C0000889 - 8 | 100640 216 gene - - - 9 | 100650 217 gene - - - 10 | 100660 218 gene - - - 11 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badHeader-wrongName4.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID type eSourc MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - 3 | 100070 - phenotype - C1853365 - 4 | 100100 1131 phenotype GeneMap C0033770 question 5 | 100200 - phenotype - C4551519 - 6 | 100300 57514 phenotype GeneMap C4551482 - 7 | 100600 - phenotype - C0000889 - 8 | 100640 216 gene - - - 9 | 100650 217 gene - - - 10 | 100660 218 gene - - - 11 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badHeader-wrongName5.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID type Source MedGenGUI Comment 2 | 100050 - phenotype - C3149220 - 3 | 100660 218 gene - - - 4 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-badHeader-wrongName6.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID type Source MedGenCUI FooBar 2 | 100050 - phenotype - C3149220 - 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/mim2gene-mini.txt: -------------------------------------------------------------------------------- 1 | #MIM number GeneID type Source MedGenCUI Comment 2 | 100050 - phenotype - C3149220 - 3 | 100070 - phenotype - C1853365 - 4 | 100100 1131 phenotype GeneMap C0033770 question 5 | 100200 - phenotype - C4551519 - 6 | 100300 57514 phenotype GeneMap C4551482 - 7 | 100600 - phenotype - C0000889 - 8 | 100640 216 gene - - - 9 | 100650 217 gene - - - 10 | 100660 218 gene - - - 11 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/omim-badTIfield.txt: -------------------------------------------------------------------------------- 1 | *RECORD* 2 | *FIELD* NO 3 | 100050 4 | *FIELD* TI 5 | AARSKOG SYNDROME, AUTOSOMAL DOMINANT 6 | *FIELD* TX 7 | 8 | DESCRIPTION 9 | 10 | Aarskog syndrome is characterized by short stature and facial, limb, 11 | and genital anomalies. One form of the disorder is X-linked (see 12 | 305400), but there is also evidence for autosomal dominant and 13 | autosomal recessive (227330) inheritance (summary by Grier et al., 14 | 1983). 15 | 16 | *THEEND* 17 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/omim-truncated.txt: -------------------------------------------------------------------------------- 1 | *RECORD* 2 | *FIELD* NO 3 | 100050 4 | *FIELD* TI 5 | 100050 AAR -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/ucsc.txt: -------------------------------------------------------------------------------- 1 | ENST00000619216.1 chr1 - 17368 17436 17368 17368 1 17368, 17436, uc031tla.1 2 | ENST00000473358.1 chr1 + 29553 31097 29553 29553 3 29553,30563,30975, 30039,30667,31097, uc057aty.1 3 | ENST00000469289.1 chr1 + 30266 31109 30266 30266 2 30266,30975, 30667,31109, uc057atz.1 4 | ENST00000607096.1 chr1 + 30365 30503 30365 30365 1 30365, 30503, uc031tlb.1 5 | ENST00000417324.1 chr1 - 34553 36081 34553 34553 3 34553,35276,35720, 35174,35481,36081, uc001aak.4 6 | ENST00000461467.1 chr1 - 35244 36073 35244 35244 2 35244,35720, 35481,36073, uc057aua.1 7 | ENST00000641515.2 chr1 + 65418 71585 65564 70008 3 65418,65519,69036, 65433,65573,71585, A0A2U3U0J3 uc001aal.2 8 | ENST00000335137.4 chr1 + 69054 70108 69090 70008 1 69054, 70108, Q8NH21 uc285fxb.1 9 | ENST00000466430.5 chr1 - 89294 120932 89294 89294 4 89294,92090,112699,120774, 91629,92240,112804,120932, uc057aub.1 10 | ENST00000495576.1 chr1 - 89550 91105 89550 89550 2 89550,90286, 90050,91105, uc057auc.1 11 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/xenopusjamboree.txt: -------------------------------------------------------------------------------- 1 | XB-GENE-478054 trnt1 tRNA nucleotidyl transferase, CCA-adding, 1 ENSXETG00000025091 2 | XB-GENE-478064 foxh1.2 forkhead box H1, gene 2 ENSXETG00000005286 3 | XB-GENE-478074 nr5a2 nuclear receptor subfamily 5 group A member 2 ENSXETG00000000314 4 | XB-GENE-478084 tbx1 T-box 1 ENSXETG00000006304 5 | XB-GENE-478094 nr1d1 nuclear receptor subfamily 1 group D member 1 ENSXETG00000024397 6 | XB-GENE-478104 nucb1 nucleobindin 1 ENSXETG00000021229 7 | XB-GENE-478113 nsa2 NSA2, ribosome biogenesis homolog ENSXETG00000005077 8 | XB-GENE-478121 csnk1a1 casein kinase 1 alpha 1 ENSXETG00000020861 9 | XB-GENE-478131 hoxc6 homeobox C6 ENSXETG00000023479 10 | XB-GENE-478141 hba1 hemoglobin subunit alpha 1 ENSXETG00000025664 11 | XB-GENE-940866 rtp3c receptor (chemosensory) transporter protein 3 gene C [provisional] ENSXETG00000019753 12 | XB-GENE-981482 or1e2l conserved hypothetical olfactory receptor, 8 of 17 ENSXETG00000026609 13 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-data/zfin_desc.txt: -------------------------------------------------------------------------------- 1 | ZDB-GENE-030131-3003 HNF1 homeobox Bb hnf1bb 21 ZDB-REFCROSS-990707-1 2 | ZDB-GENE-030131-1077 hepatocyte nuclear factor 4, alpha hnf4a 23 ZDB-REFCROSS-000320-1 3 | ZDB-GENE-040718-488 WD repeat domain, phosphoinositide interacting 2 wipi2 0 4 | ZDB-GENE-070117-2473 wirbel wir 0 5 | ZDB-GENE-000710-5 WITHDRAWN:cripto WITHDRAWN:cripto 0 6 | ZDB-GENE-030516-5 WITHDRAWN:sb:cb476 WITHDRAWN:sb:cb476 0 7 | ZDB-GENE-030131-8698 WITHDRAWN:wu:fa94g04 WITHDRAWN:wu:fa94g04 0 8 | ZDB-GENE-070117-2162 lawrence welk wlk 0 9 | ZDB-GENE-040426-2161 wntless Wnt ligand secretion mediator wls 2 ZDB-REFCROSS-000320-1 10 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/alt_allele.txt: -------------------------------------------------------------------------------- 1 | 1 1 18256 2 | 2 1 18257 3 | 3 1 18258 4 | 4 1 18259 5 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/alt_allele_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 IS_REPRESENTATIVE 2 | 4 HAS_CODING_POTENTIAL 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/alt_allele_group.txt: -------------------------------------------------------------------------------- 1 | 1 2 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/assembly_exception.txt: -------------------------------------------------------------------------------- 1 | 1 469294 10000000 10500000 PAR 469283 30300000 30800000 1 2 | 2 469351 30500000 30599999 HAP 469283 30500000 30699999 1 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/biotype.txt: -------------------------------------------------------------------------------- 1 | 64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217 2 | 65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234 3 | 87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263 4 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 chromosome NCBI33 1 default_version 2 | 2 1 supercontig \N 2 default_version 3 | 3 1 clone \N 3 default_version 4 | 4 1 contig \N 4 default_version,sequence_level 5 | 6 1 chunk \N 5 default_version 6 | 7 1 alt_chrom \N 6 default_version 7 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/density_feature.txt: -------------------------------------------------------------------------------- 1 | 1 1 469283 1 100 50.30 2 | 2 1 469283 101 200 68.80 3 | 3 1 469283 201 300 32.00 4 | 4 1 469283 301 400 90.90 5 | 5 1 469283 401 500 88.80 6 | 6 1 469283 501 600 12.00 7 | 7 2 469283 1 100 50.30 8 | 8 2 469283 101 200 68.80 9 | 9 2 469283 201 300 32.00 10 | 10 2 469283 301 400 90.90 11 | 11 2 469283 401 500 88.80 12 | 12 2 469283 501 600 12.00 13 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/density_type.txt: -------------------------------------------------------------------------------- 1 | 1 1292 100 0 sum 2 | 2 1293 100 0 ratio 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/external_synonym.txt: -------------------------------------------------------------------------------- 1 | 315 syn1 2 | 315 syn2 3 | 994 syn3 4 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/gene_archive.txt: -------------------------------------------------------------------------------- 1 | G2 1 T2 1 P2 1 1 1 2 | G3 1 T4 1 P4 1 2 1 3 | G3 1 T5 1 P5 1 3 1 4 | G4 1 T1 1 P1 1 4 2 5 | G2 2 T2 2 P2 1 1 2 6 | G2 2 T3 1 P3 1 5 2 7 | G3 2 T4 2 P4 2 6 2 8 | G3 2 T5 1 P5 1 3 2 9 | G1 1 T6 1 P6 1 7 3 10 | G2 3 T2 3 P2 2 8 3 11 | G3 3 T3 2 P3 2 9 3 12 | G3 3 T8 1 P8 1 10 3 13 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/gene_attrib.txt: -------------------------------------------------------------------------------- 1 | 18256 10 This is a note on gene 18256 2 | 18259 10 Another note on gene 18259 3 | 18256 20 ENSG_PARENT_GENE 4 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/interpro.txt: -------------------------------------------------------------------------------- 1 | IPR000001 PF000001 2 | IPR000010 PF000019 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/karyotype.txt: -------------------------------------------------------------------------------- 1 | 1 469283 30200000 32600000 q11.21 gneg 2 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/map.txt: -------------------------------------------------------------------------------- 1 | 1 genethon 2 | 2 marshfield 3 | 3 decode 4 | 4 gm99gb4 5 | 5 gm99g3 6 | 6 tng 7 | 7 wiyac 8 | 8 wirh 9 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/mapping_session.txt: -------------------------------------------------------------------------------- 1 | 1 release_1 release_2 1 2 assembly_1 assembly_2 2002-04-01 00:00:00 2 | 2 release_2 release_3 2 3 assembly_2 assembly_3 2002-12-24 00:00:00 3 | 3 release_3 release_4 3 4 assembly_3 assembly_4 2003-03-03 00:00:00 4 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt: -------------------------------------------------------------------------------- 1 | assembly_exception 1 500001 2 | density_feature 1 100 3 | exon 1 5179 4 | gene 1 79572 5 | karyotype 1 2400001 6 | marker_feature 4 363 7 | misc_feature 1 26257626 8 | qtl_feature 1 736330 9 | repeat_feature 4 1851 10 | simple_feature 4 2900 11 | transcript 1 79572 12 | dna_align_feature 4 4366 13 | protein_align_feature 4 1983 14 | prediction_transcript 4 78040 15 | prediction_exon 4 1984 16 | affy_feature 1 25 17 | regulatory_feature 1 121 18 | regulatory_search_region 1 121 19 | operon 1 106713 20 | operon_transcript 1 106713 21 | ditag_feature 1 19 22 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/misc_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 7 NT_011333 2 | 2 7 NT_011362 3 | 3 7 NT_011387 4 | 4 7 NT_025215 5 | 5 7 NT_028392 6 | 6 7 NT_030871 7 | 7 7 NT_035608 8 | 1 1 NT_SYN1 9 | 1 1 NT_SYN2 10 | 2 6 AL000001 11 | 2 6 AL000002 12 | 5 10 This is a note type annotation 13 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/misc_feature.txt: -------------------------------------------------------------------------------- 1 | 1 469283 61140848 62842997 1 2 | 2 469283 34675572 59657811 1 3 | 3 469283 50001 26307626 1 4 | 4 469283 29307627 29541965 1 5 | 5 469283 29591966 34655571 1 6 | 6 469283 59707812 60855021 1 7 | 7 469283 60955022 60990847 1 8 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/misc_feature_misc_set.txt: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 1 3 | 3 1 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/misc_set.txt: -------------------------------------------------------------------------------- 1 | 1 ntctgs NT contigs 70000000 2 | 2 tilepath Tilepath 15000000 3 | 4 cloneset 1Mb cloneset 6000000 4 | 8 gap Gaps 50000000 5 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/ontology_xref.txt: -------------------------------------------------------------------------------- 1 | 22988 IC \N 2 | 22988 IEA \N 3 | 22988 IC 152200 4 | 22989 IEA \N 5 | 22990 IC \N 6 | 22991 IEA \N 7 | 22992 IC \N 8 | 22993 IEA \N 9 | 22994 IC \N 10 | 41176 IEA \N 11 | 41177 IDA \N 12 | 41178 IEA \N 13 | 41179 IC \N 14 | 41180 IEA \N 15 | 41181 IEA \N 16 | 41182 IDA \N 17 | 41183 IC \N 18 | 83268 IEA \N 19 | 83269 IEA \N 20 | 83270 IDA \N 21 | 149843 IDA \N 22 | 151219 IDA \N 23 | 151220 IC \N 24 | 151221 IDA \N 25 | 151222 IC \N 26 | 151223 IEA \N 27 | 151224 IC \N 28 | 179294 IDA \N 29 | 179295 IEA \N 30 | 179296 IC \N 31 | 191222 IEA \N 32 | 191223 IC \N 33 | 191224 IC \N 34 | 191225 IC \N 35 | 191226 IDA \N 36 | 191227 IDA \N 37 | 191244 IEA \N 38 | 191245 IDA \N 39 | 191246 IC \N 40 | 229064 IDA \N 41 | 229065 IC \N 42 | 229077 IDA \N 43 | 229078 IC \N 44 | 238791 IC \N 45 | 238792 IDA \N 46 | 238793 IDA \N 47 | 238794 IC \N 48 | 238795 IDA \N 49 | 238796 IEA \N 50 | 238797 IDA \N 51 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/operon.txt: -------------------------------------------------------------------------------- 1 | 1 469283 30371004 30477716 1 16152-16153-4840 1 16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09 2 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/operon_transcript.txt: -------------------------------------------------------------------------------- 1 | 1 469283 30371004 30477716 1 1 T16152-16153-4840 1 T16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09 2 | 2 469283 30371004 30408041 1 1 T16152-16153 1 T16152-16153 1 2011-06-30 16:03:09 2011-06-30 16:03:09 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/operon_transcript_gene.txt: -------------------------------------------------------------------------------- 1 | 1 18259 2 | 1 18260 3 | 1 18261 4 | 2 18259 5 | 2 18260 6 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/peptide_archive.txt: -------------------------------------------------------------------------------- 1 | 1 9EC495A0515C5F375E59D148B6B02E3B PTWOVERSIONONE* 2 | 2 0FFD225A9A55DC380DC8B51AC14BE9AD PFOURVERSIONONE* 3 | 3 7A30C57C00E144FF4D3D3980519EC2DE PFIVEVERSIONONE* 4 | 4 596353EEF1CEC434652AD93FCC09B1D8 PONEVERSIONONE* 5 | 5 87DF805495C5EA826430FDDB9FCD00D6 PTHREEVERSIONONE* 6 | 6 1F95AAD49088C3CB66FD575E1AC66D2E PFOURVERSIONTWO* 7 | 7 5A25371E4A3960CAE76199C5FA764453 PSIXVERSIONONE* 8 | 8 05581EEC770C844D0A2B95DB65DB6923 PTWOVERSIONTWO* 9 | 9 F271E71E8F174C839142A486D3102E7E PTHREEVERSIONTWO* 10 | 10 722553799FF48CE68B51AC168A606A5E PEIGHTVERSIONONE* 11 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 469341 13 4 2 | 469339 13 4 3 | 469336 13 4 4 | 469335 13 4 5 | 469343 13 4 6 | 469333 13 4 7 | 469340 13 4 8 | 469342 13 4 9 | 469338 13 4 10 | 469332 13 4 11 | 469334 13 4 12 | 469337 13 4 13 | 469283 14 1 14 | 965899 17 2 15 | 965888 17 2 16 | 469351 18 1 17 | 469283 19 20 18 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/seq_region_synonym.txt: -------------------------------------------------------------------------------- 1 | 1 469283 alt_20 \N 2 | 2 469283 anoth_20 4200 3 | 3 469293 chrx 11000 4 | 4 469272 chr10 11000 5 | 5 469271 chr1 11000 6 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt: -------------------------------------------------------------------------------- 1 | 21716 21 ENSG_PARENT_TRANSCRIPT 2 | 21716 468 CCDS13194.1 3 | 21717 468 CCDS13197.1 4 | 21718 468 CCDS13195.1 5 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt: -------------------------------------------------------------------------------- 1 | 21742 dna_align_feature 1449321 2 | 21742 dna_align_feature 11290104 3 | 21742 protein_align_feature 813252 4 | 21742 protein_align_feature 813424 5 | 21742 protein_align_feature 813184 -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt: -------------------------------------------------------------------------------- 1 | 1 xref 9 4100 X1234 1 70.5 60.2 21716 Translation \N 2 | 2 xref 9 4100 X5678 1 75 50.1 21717 Transcript \N 3 | 3 cDNA 1290 4200 cDNA12 2 80 40 21718 Translation \N 4 | 4 cDNA 1290 4200 cDNA34 2 60.5 30.9 21719 Transcript \N 5 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/core/unmapped_reason.txt: -------------------------------------------------------------------------------- 1 | 1 exonerate failed to match in xref system exonerate match was below the thresholds of 90% 2 | 2 failed to map failed to map the cDNA viw exonerate using the cutoff of 95% 3 | -------------------------------------------------------------------------------- /misc-scripts/xref_mapping/t/test-genome-DBs/homo_sapiens/otherfeatures/alt_allele.txt: 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-------------------------------------------------------------------------------- 1 | MultiTestDB.conf 2 | CLEAN.t 3 | *.MultiTestDB.frozen.conf 4 | -------------------------------------------------------------------------------- /modules/t/MultiTestDB.conf.example: -------------------------------------------------------------------------------- 1 | { 2 | 'port' => '3306', 3 | 'driver' => 'mysql', 4 | 'user' => 'ensadmin', 5 | 'pass' => 'XXX', 6 | 'host' => 'ens-research', 7 | 8 | # add a line with the dbname and module 9 | # You can specify this databases hash in your own MultiTestDB.conf.default file 10 | # 'databases' => { 11 | # 'homo_sapiens' => { 12 | # 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 13 | # 'empty' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 14 | # }, 15 | # 'circ' => { 16 | # 'core' => 'Bio::EnsEMBL::DBSQL::DBAdaptor', 17 | # } 18 | # }, 19 | 20 | # uncomment to use preloaded databases (useful when doing lots of 21 | # testing) 22 | # 'preloaded' => 23 | # { 'homo_sapiens' => { 'core' => 'mcvicker_new_schema' } } 24 | } 25 | -------------------------------------------------------------------------------- /modules/t/easyargv.t: -------------------------------------------------------------------------------- 1 | # See the NOTICE file distributed with this work for additional information 2 | # regarding copyright ownership. 3 | # 4 | # Licensed under the Apache License, Version 2.0 (the "License"); 5 | # you may not use this file except in compliance with the License. 6 | # You may obtain a copy of the License at 7 | # 8 | # http://www.apache.org/licenses/LICENSE-2.0 9 | # 10 | # Unless required by applicable law or agreed to in writing, software 11 | # distributed under the License is distributed on an "AS IS" BASIS, 12 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | # See the License for the specific language governing permissions and 14 | # limitations under the License. 15 | 16 | use strict; 17 | 18 | use Test::More; 19 | use Test::Warnings; 20 | 21 | use Bio::EnsEMBL::Utils::EasyArgv; 22 | ok(1); 23 | 24 | my @argv = @ARGV; 25 | 26 | done_testing(); 27 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/SQLite/transcript.post: -------------------------------------------------------------------------------- 1 | CREATE UNIQUE INDEX canonical_translation_idx ON transcript (canonical_translation_id); 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/SQLite/transcript.pre: -------------------------------------------------------------------------------- 1 | DROP INDEX canonical_translation_idx; 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/assembly.txt: -------------------------------------------------------------------------------- 1 | 3 2 1 235425 1 235425 1 2 | 7 8 1 349599 1 349599 1 3 | 11 12 1 5495278 1 5495278 1 4 | 4 13 1 224872 1 224872 1 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 plasmid GCA_000292705.1 2 default_version 2 | 2 1 contig 4 default_version,sequence_level 3 | 3 1 chromosome GCA_000292705.1 1 default_version 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/external_synonym.txt: -------------------------------------------------------------------------------- 1 | 90628 BTF1_18475 2 | 89175 BTF1_27355 3 | 89805 BTF1_27545 4 | 89825 BTF1_27550 5 | 90154 BTF1_27650 6 | 90174 BTF1_27655 7 | 90195 BTF1_27660 8 | 91277 BTF1_28005 9 | 89952 BTF1_31107 10 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/meta_coord.txt: -------------------------------------------------------------------------------- 1 | exon 1 3018 2 | gene 1 3018 3 | simple_feature 1 687 4 | transcript 1 3018 5 | exon 3 3582 6 | gene 3 3582 7 | simple_feature 3 817 8 | transcript 3 3582 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/seq_region.txt: -------------------------------------------------------------------------------- 1 | 2 CP003765.1 2 235425 2 | 3 p02 1 235425 3 | 4 p03 1 224872 4 | 7 p01 1 349599 5 | 8 CP003764.1 2 349599 6 | 11 Chromosome 3 5495278 7 | 12 CP003763.1 2 5495278 8 | 13 CP003766.1 2 224872 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 2 316 1 2 | 3 6 1 3 | 3 11 11 4 | 3 367 2 5 | 3 316 1 6 | 3 376 2012-08-23 7 | 3 377 2012-08-23 8 | 4 6 1 9 | 4 11 11 10 | 4 367 3 11 | 4 316 1 12 | 4 376 2012-08-23 13 | 4 377 2012-08-23 14 | 7 6 1 15 | 7 11 11 16 | 7 367 1 17 | 7 316 1 18 | 7 376 2012-08-23 19 | 7 377 2012-08-23 20 | 8 316 1 21 | 11 6 1 22 | 11 11 11 23 | 11 367 7 24 | 11 316 1 25 | 11 376 2012-08-23 26 | 11 377 2012-08-23 27 | 12 316 1 28 | 13 316 1 29 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/circ/core/simple_feature.txt: -------------------------------------------------------------------------------- 1 | 33 3 157870 158193 -1 potential protein location (hypothetical protein BTF1_31232 [Bacillus thuringiensis HD-789]) that overlaps RNA (tRNA-S); potential protein location (hypothetical protein BTF1_31232 [Bacillus thuringiensis HD-789]) that overlaps RNA (tRNA-W); potential ... 37 \N 2 | 34 4 212311 212529 1 COG1132 ABC-type multidrug transport system, ATPase and permease components; putative deletion pseudogene 38 \N 3 | 35 4 6267 6953 1 potential frameshift: common BLAST hit: gi|161598601|ref|YP_001573816.1| IS element transposase 37 \N 4 | 36 11 5336890 5337706 1 potential frameshift: common BLAST hit: gi|218895386|ref|YP_002443797.1| proline dehydrogenase 37 \N 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.txt: -------------------------------------------------------------------------------- 1 | 1 1 18256 2 | 2 1 18257 3 | 3 1 18258 4 | 4 1 18259 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/alt_allele_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 IS_REPRESENTATIVE 2 | 4 HAS_CODING_POTENTIAL 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/alt_allele_group.txt: -------------------------------------------------------------------------------- 1 | 1 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.txt: -------------------------------------------------------------------------------- 1 | 1 469294 10000000 10500000 PAR 469283 30300000 30800000 1 2 | 2 469351 30500000 30599999 HAP 469283 30500000 30699999 1 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/biotype.txt: -------------------------------------------------------------------------------- 1 | 64 protein_coding gene core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0001217 protein_coding_gene 2 | 65 protein_coding transcript core,otherfeatures,rnaseq,vega,presite \N \N coding SO:0000234 mRNA 3 | 87 tRNA gene core,otherfeatures,presite 76 \N snoncoding SO:0001263 ncRNA_gene 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 chromosome NCBI33 1 default_version 2 | 2 1 supercontig \N 2 default_version 3 | 3 1 clone \N 3 default_version 4 | 4 1 contig \N 4 default_version,sequence_level 5 | 6 1 chunk \N 5 default_version 6 | 7 1 alt_chrom \N 6 default_version 7 | 8 1 chromosome NCBI32 7 \N 8 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt: -------------------------------------------------------------------------------- 1 | 1 1 469283 1 100 50.30 2 | 2 1 469283 101 200 68.80 3 | 3 1 469283 201 300 32.00 4 | 4 1 469283 301 400 90.90 5 | 5 1 469283 401 500 88.80 6 | 6 1 469283 501 600 12.00 7 | 7 2 469283 1 100 50.30 8 | 8 2 469283 101 200 68.80 9 | 9 2 469283 201 300 32.00 10 | 10 2 469283 301 400 90.90 11 | 11 2 469283 401 500 88.80 12 | 12 2 469283 501 600 12.00 13 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/density_type.txt: -------------------------------------------------------------------------------- 1 | 1 1292 100 0 sum 2 | 2 1293 100 0 ratio 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/external_synonym.txt: -------------------------------------------------------------------------------- 1 | 315 syn1 2 | 315 syn2 3 | 994 syn3 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/gene_archive.txt: -------------------------------------------------------------------------------- 1 | G2 1 T2 1 P2 1 1 1 2 | G3 1 T4 1 P4 1 2 1 3 | G3 1 T5 1 P5 1 3 1 4 | G4 1 T1 1 P1 1 4 2 5 | G2 2 T2 2 P2 1 1 2 6 | G2 2 T3 1 P3 1 5 2 7 | G3 2 T4 2 P4 2 6 2 8 | G3 2 T5 1 P5 1 3 2 9 | G1 1 T6 1 P6 1 7 3 10 | G2 3 T2 3 P2 2 8 3 11 | G3 3 T3 2 P3 2 9 3 12 | G3 3 T8 1 P8 1 10 3 13 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/gene_attrib.txt: -------------------------------------------------------------------------------- 1 | 18256 10 This is a note on gene 18256 2 | 18259 10 Another note on gene 18259 3 | 18256 20 ENSG_PARENT_GENE 4 | 140608 1 USP9Y 5 | 70674 1 AC009947.3 6 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/interpro.txt: -------------------------------------------------------------------------------- 1 | IPR000001 PF000001 2 | IPR000010 PF000019 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/karyotype.txt: -------------------------------------------------------------------------------- 1 | 1 469283 30200000 32600000 q11.21 gneg 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/map.txt: -------------------------------------------------------------------------------- 1 | 1 genethon 2 | 2 marshfield 3 | 3 decode 4 | 4 gm99gb4 5 | 5 gm99g3 6 | 6 tng 7 | 7 wiyac 8 | 8 wirh 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/mapping_session.txt: -------------------------------------------------------------------------------- 1 | 1 release_1 release_2 1 2 assembly_1 assembly_2 2002-04-01 00:00:00 2 | 2 release_2 release_3 2 3 assembly_2 assembly_3 2002-12-24 00:00:00 3 | 3 release_3 release_4 3 4 assembly_3 assembly_4 2003-03-03 00:00:00 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt: -------------------------------------------------------------------------------- 1 | assembly_exception 1 500001 2 | density_feature 1 100 3 | exon 1 5179 4 | gene 1 79572 5 | karyotype 1 2400001 6 | marker_feature 4 363 7 | misc_feature 1 26257626 8 | qtl_feature 1 736330 9 | repeat_feature 4 1851 10 | simple_feature 4 2900 11 | transcript 1 79572 12 | dna_align_feature 4 4366 13 | protein_align_feature 4 1983 14 | prediction_transcript 4 78040 15 | prediction_exon 4 1984 16 | affy_feature 1 25 17 | regulatory_feature 1 121 18 | regulatory_search_region 1 121 19 | operon 1 106713 20 | operon_transcript 1 106713 21 | ditag_feature 1 19 22 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/misc_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 7 NT_011333 2 | 2 7 NT_011362 3 | 3 7 NT_011387 4 | 4 7 NT_025215 5 | 5 7 NT_028392 6 | 6 7 NT_030871 7 | 7 7 NT_035608 8 | 1 1 NT_SYN1 9 | 1 1 NT_SYN2 10 | 2 6 AL000001 11 | 2 6 AL000002 12 | 5 10 This is a note type annotation 13 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/misc_feature.txt: -------------------------------------------------------------------------------- 1 | 1 469283 61140848 62842997 1 2 | 2 469283 34675572 59657811 1 3 | 3 469283 50001 26307626 1 4 | 4 469283 29307627 29541965 1 5 | 5 469283 29591966 34655571 1 6 | 6 469283 59707812 60855021 1 7 | 7 469283 60955022 60990847 1 8 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/misc_feature_misc_set.txt: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 1 3 | 3 1 4 | 4 2 5 | 5 2 6 | 6 2 7 | 7 2 8 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/misc_set.txt: -------------------------------------------------------------------------------- 1 | 1 ntctgs NT contigs 70000000 2 | 2 tilepath Tilepath 15000000 3 | 4 cloneset 1Mb cloneset 6000000 4 | 8 gap Gaps 50000000 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/ontology_xref.txt: -------------------------------------------------------------------------------- 1 | 22988 IC \N 2 | 22988 IEA \N 3 | 22988 IC 152200 4 | 22989 IEA \N 5 | 22990 IC \N 6 | 22991 IEA \N 7 | 22992 IC \N 8 | 22993 IEA \N 9 | 22994 IC \N 10 | 41176 IEA \N 11 | 41177 IDA \N 12 | 41178 IEA \N 13 | 41179 IC \N 14 | 41180 IEA \N 15 | 41181 IEA \N 16 | 41182 IDA \N 17 | 41183 IC \N 18 | 83268 IEA \N 19 | 83269 IEA \N 20 | 83270 IDA \N 21 | 149843 IDA \N 22 | 151219 IDA \N 23 | 151220 IC \N 24 | 151221 IDA \N 25 | 151222 IC \N 26 | 151223 IEA \N 27 | 151224 IC \N 28 | 179294 IDA \N 29 | 179295 IEA \N 30 | 179296 IC \N 31 | 191222 IEA \N 32 | 191223 IC \N 33 | 191224 IC \N 34 | 191225 IC \N 35 | 191226 IDA \N 36 | 191227 IDA \N 37 | 191244 IEA \N 38 | 191245 IDA \N 39 | 191246 IC \N 40 | 229064 IDA \N 41 | 229065 IC \N 42 | 229077 IDA \N 43 | 229078 IC \N 44 | 238791 IC \N 45 | 238792 IDA \N 46 | 238793 IDA \N 47 | 238794 IC \N 48 | 238795 IDA \N 49 | 238796 IEA \N 50 | 238797 IDA \N 51 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/operon.txt: -------------------------------------------------------------------------------- 1 | 1 469283 30371004 30477716 1 16152-16153-4840 1 16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/operon_transcript.txt: -------------------------------------------------------------------------------- 1 | 1 469283 30371004 30477716 1 1 T16152-16153-4840 1 T16152-16153-4840 1 2011-06-30 16:03:09 2011-06-30 16:03:09 2 | 2 469283 30371004 30408041 1 1 T16152-16153 1 T16152-16153 1 2011-06-30 16:03:09 2011-06-30 16:03:09 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/operon_transcript_gene.txt: -------------------------------------------------------------------------------- 1 | 1 18259 2 | 1 18260 3 | 1 18261 4 | 2 18259 5 | 2 18260 6 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/peptide_archive.txt: -------------------------------------------------------------------------------- 1 | 1 9EC495A0515C5F375E59D148B6B02E3B PTWOVERSIONONE* 2 | 2 0FFD225A9A55DC380DC8B51AC14BE9AD PFOURVERSIONONE* 3 | 3 7A30C57C00E144FF4D3D3980519EC2DE PFIVEVERSIONONE* 4 | 4 596353EEF1CEC434652AD93FCC09B1D8 PONEVERSIONONE* 5 | 5 87DF805495C5EA826430FDDB9FCD00D6 PTHREEVERSIONONE* 6 | 6 1F95AAD49088C3CB66FD575E1AC66D2E PFOURVERSIONTWO* 7 | 7 5A25371E4A3960CAE76199C5FA764453 PSIXVERSIONONE* 8 | 8 05581EEC770C844D0A2B95DB65DB6923 PTWOVERSIONTWO* 9 | 9 F271E71E8F174C839142A486D3102E7E PTHREEVERSIONTWO* 10 | 10 722553799FF48CE68B51AC168A606A5E PEIGHTVERSIONONE* 11 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/rnaproduct.txt: -------------------------------------------------------------------------------- 1 | 1 2 21717 46 162035 67 162035 ENSS00000000001 1 2018-05-14 12:00:00 2018-05-14 12:00:00 2 | 2 2 21717 7 \N 28 \N ENSS00000000002 1 2018-05-21 17:00:00 2018-05-21 17:00:00 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/rnaproduct_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 10 Placeholder 2 | 1 22 3 3 | 2 10 Placeholder 4 | 2 22 5 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/rnaproduct_type.txt: -------------------------------------------------------------------------------- 1 | 1 generic generic Generic mature RNA 2 | 2 miRNA microRNA Mature microRNA strand 3 | 3 circRNA Circular RNA \N 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 469341 13 4 2 | 469339 13 4 3 | 469336 13 4 4 | 469335 13 4 5 | 469343 13 4 6 | 469333 13 4 7 | 469340 13 4 8 | 469342 13 4 9 | 469338 13 4 10 | 469332 13 4 11 | 469334 13 4 12 | 469337 13 4 13 | 469283 14 1 14 | 965899 17 2 15 | 965888 17 2 16 | 469351 18 1 17 | 469283 19 20 18 | 469294 19 24 19 | 469294 14 1 20 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/seq_region_synonym.txt: -------------------------------------------------------------------------------- 1 | 1 469283 alt_20 \N 2 | 2 469283 anoth_20 4200 3 | 3 469293 chrx 11000 4 | 4 369272 chr10 11000 5 | 5 469272 chr10 11000 6 | 6 469271 chr1 11000 7 | 7 1069283 anoth_20 4200 8 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/transcript_attrib.txt: -------------------------------------------------------------------------------- 1 | 21716 21 ENSG_PARENT_TRANSCRIPT 2 | 21738 24 principal1 3 | 21719 535 NM_030815.3 4 | 21726 417 GENCODE basic 5 | 21726 576 GENCODE primary 6 | 548627 1 AC002531.1-005 7 | 548627 124 1 8 | 548627 126 1 9 | 548627 428 tsl3 10 | 272999 1 AC009947.3-001 11 | 272999 428 tslNA 12 | 272999 554 1 -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt: -------------------------------------------------------------------------------- 1 | 21742 dna_align_feature 1449321 2 | 21742 dna_align_feature 11290104 3 | 21742 protein_align_feature 813252 4 | 21742 protein_align_feature 813424 5 | 21742 protein_align_feature 813184 -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt: -------------------------------------------------------------------------------- 1 | 1 xref 9 4100 X1234 1 70.5 60.2 21716 Translation \N 2 | 2 xref 9 4100 X5678 1 75 50.1 21717 Transcript \N 3 | 3 cDNA 1290 4200 cDNA12 2 80 40 21718 Translation \N 4 | 4 cDNA 1290 4200 cDNA34 2 60.5 30.9 21719 Transcript \N 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/core/unmapped_reason.txt: -------------------------------------------------------------------------------- 1 | 1 exonerate failed to match in xref system exonerate match was below the thresholds of 90% 2 | 2 failed to map failed to map the cDNA viw exonerate using the cutoff of 95% 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/analysis_description.txt: -------------------------------------------------------------------------------- 1 | 1282 Genes were annotated by the Ensembl automatic analysis pipeline using either a GeneWise model from a human/vertebrate protein, a set of aligned human cDNAs followed by GenomeWise for ORF prediction or from Genscan exons supported by protein, cDNA and EST evidence. GeneWise models are further combined with available aligned cDNAs to annotate UTRs. ensembl transcript 1 web data 1 0 \N 2 | 1503 new description new label 0 0 \N 3 | 1504 updated description N 0 0 \N 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/assembly_exception.txt: -------------------------------------------------------------------------------- 1 | 1 469294 10000000 10500000 PAR 469283 30300000 30800000 1 2 | 2 469351 30500000 30599999 HAP 469283 30500000 30699999 1 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/attrib_type.txt: -------------------------------------------------------------------------------- 1 | 1 synonym Alternate names for clone Synonyms 2 | 2 FISHmap FISH information FISH map 3 | 3 organisation Organisation sequencing clone 4 | 4 state Current state of clone 5 | 5 BACend_flag BAC end flags 6 | 6 embl_acc EMBL accession number 7 | 7 superctg Super contig id. 8 | 8 seq_len Accession length 9 | 9 fp_size FP size 10 | 10 note Note 11 | 11 positioned_by Positioned by 12 | 12 bac_acc BAC end accession 13 | 13 htg_phase HTG Phase High Throughput Genome Phase 14 | 14 toplevel Top Level Top Level Non-Redundant Sequence Region 15 | 15 _rna_edit RNA editing \N 16 | 16 _selenocysteine Selenocysteine \N 17 | 17 codon_table Codon Table Alternate codon table 18 | 18 non_ref Non Reference Non Reference Sequence Region 19 | 554 is_canonical Is Canonical Flag to state that a feature is a canonical one. 20 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 chromosome NCBI33 1 default_version 2 | 2 1 supercontig \N 2 default_version 3 | 3 1 clone \N 3 default_version 4 | 4 1 contig \N 4 default_version,sequence_level 5 | 6 1 chunk \N 5 default_version 6 | 7 1 alt_chrom \N 6 default_version 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/meta_coord.txt: -------------------------------------------------------------------------------- 1 | assembly_exception 1 500001 2 | density_feature 1 6000000 3 | dna_align_feature 4 4366 4 | exon 1 5179 5 | gene 1 79572 6 | karyotype 1 2400001 7 | marker_feature 4 363 8 | misc_feature 1 26257626 9 | prediction_exon 4 1984 10 | prediction_transcript 4 78040 11 | protein_align_feature 4 1983 12 | qtl_feature 1 736330 13 | repeat_feature 4 1851 14 | simple_feature 4 2900 15 | transcript 1 79572 16 | dna_align_feature 1 2082 17 | protein_align_feature 1 1914 18 | prediction_transcript 1 202 19 | prediction_exon 1 101 20 | affy_feature 1 25 21 | regulatory_feature 1 121 22 | regulatory_search_region 1 121 23 | operon 1 106713 24 | operon_transcript 1 106713 25 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 469341 13 4 2 | 469339 13 4 3 | 469336 13 4 4 | 469335 13 4 5 | 469343 13 4 6 | 469333 13 4 7 | 469340 13 4 8 | 469342 13 4 9 | 469338 13 4 10 | 469332 13 4 11 | 469334 13 4 12 | 469337 13 4 13 | 469283 14 1 14 | 965899 17 2 15 | 965888 17 2 16 | 469351 18 1 17 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/seq_region_synonym.txt: -------------------------------------------------------------------------------- 1 | 1 469283 alt_20 \N 2 | 2 469283 anoth_20 4200 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/empty/unmapped_reason.txt: -------------------------------------------------------------------------------- 1 | 1 exonerate failed to match in xref system exonerate match was below the thresholds of 90% 2 | 2 failed to map failed to map the cDNA viw exonerate using the cutoff of 95% 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/alt_allele.txt: -------------------------------------------------------------------------------- 1 | 1 4679 633682 2 | 2 4679 633696 3 | 3 4790 633688 4 | 4 4790 633702 5 | 5 4795 633683 6 | 6 4795 633697 7 | 7 4998 633686 8 | 8 4998 633700 9 | 9 5212 633689 10 | 10 5212 633703 11 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/alt_allele_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 IS_REPRESENTATIVE 2 | 3 IS_REPRESENTATIVE 3 | 5 IS_REPRESENTATIVE 4 | 7 IS_REPRESENTATIVE 5 | 9 IS_REPRESENTATIVE 6 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/alt_allele_group.txt: -------------------------------------------------------------------------------- 1 | 4679 2 | 4790 3 | 4795 4 | 4998 5 | 5212 6 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/assembly_exception.txt: -------------------------------------------------------------------------------- 1 | 154 1000759268 112323682 112586593 PATCH_FIX 27515 112323682 112586593 1 2 | 1 27507 10001 2649520 PAR 27516 60001 2699520 1 3 | 2 27507 59034050 59373566 PAR 27516 154931044 155270560 1 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 contig \N 4 default_version,sequence_level 2 | 2 1 chromosome GRCh37 1 default_version 3 | 3 1 supercontig GRCh37 2 default_version 4 | 4 1 clone \N 3 default_version 5 | 27 1 chromosome NCBI36 5 6 | 101 1 chromosome NCBI35 6 7 | 1001 1 chromosome NCBI34 7 8 | 1003 1 lrg \N 8 default_version 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/density_feature.txt: -------------------------------------------------------------------------------- 1 | 16758821 106 27516 1 1035137 3 2 | 16758820 106 27515 111795178 112935944 4 3 | 16758822 107 27515 111795178 112935944 1 4 | 16758807 98 27515 111795178 112935944 8.20553 5 | 16758808 98 27516 1 1035137 25.5257 6 | 16758825 109 27516 1 1035137 1 7 | 16758824 108 27516 1 1035137 1 8 | 16758823 108 27515 111795178 112935944 4 9 | 16758812 99 27515 111795178 112935944 39.6 10 | 16758813 99 27516 1 1035137 51.6 11 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/density_type.txt: -------------------------------------------------------------------------------- 1 | 107 8441 0 150 sum 2 | 106 8442 0 150 sum 3 | 98 8443 0 150 ratio 4 | 99 8444 0 150 ratio 5 | 109 8445 0 150 sum 6 | 108 8446 0 150 sum 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/ditag.txt: -------------------------------------------------------------------------------- 1 | 241886 U_71322 SHC013 1 GGCCTGCCTGCCCGCTCCCGAAAAACCCAGAAAAAG 2 | 1161749 U_142006 SHC019 1 AAGCATATACAATTATGTTGTATATTTTAGAATC 3 | 697898 U_287123 SHC016 1 ATTACAGGATTTTGATCAAATCTTCCCCTTCTATCC 4 | 1366611 U_221680 SHC019 1 TGCCATTACATGTGAGATGTGCTGTGTTTAAAAATGA 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/ditag_feature.txt: -------------------------------------------------------------------------------- 1 | 1221441 241886 1 27515 614299 614315 -1 41 19 35 1 17M R 2 | 1221442 241886 1 27515 615532 615548 -1 41 2 18 1 17M L 3 | 1221443 1161749 1 27515 7594781 7594796 -1 42 18 33 1 16M R 4 | 1221444 1161749 1 27515 7884188 7884203 -1 42 1 16 1 16M L 5 | 1221445 697898 1 27515 9042706 9042723 1 42 1 18 1 18M L 6 | 1221446 697898 1 27515 9045216 9045233 1 42 19 36 1 18M R 7 | 1221447 1366611 3 27515 9078184 9078201 1 42 20 37 1 18M R 8 | 1221448 1366611 3 27515 9154857 9154875 1 42 1 19 1 19M L 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/genome_statistics.txt: -------------------------------------------------------------------------------- 1 | 67 pseudogene_cnt 1 1 67 2015-01-21 16:08:37 2 | 36 SNPCount 5724063 1 10 2013-11-28 09:52:41 3 | 33 total_length 967294 1 394 2015-01-21 16:08:37 4 | 41 noncoding_cnt 6 1 353 2015-01-21 16:08:37 5 | 68 alt_transcript 7 1 404 2015-01-21 16:08:37 6 | 30 ref_length 326385627 1 393 2015-01-21 16:08:37 7 | 69 noncoding_acnt_s 1 1 400 2015-01-21 16:08:37 8 | 60 transcript 6 1 402 2015-01-21 16:08:37 9 | 70 PredictionTranscript 18 1 392 2015-01-21 16:08:40 10 | 61 noncoding_cnt_l 5 1 398 2015-01-21 16:08:37 11 | 62 coding_acnt 4 1 369 2015-01-21 16:08:37 12 | 58 pseudogene_acnt 0 1 370 2015-01-21 16:08:37 13 | 47 noncoding_acnt 5 1 368 2015-01-21 16:08:37 14 | 65 coding_cnt 7 1 64 2015-01-21 16:08:37 15 | 66 noncoding_acnt_l 4 1 399 2015-01-21 16:08:37 16 | 63 noncoding_cnt_s 1 1 397 2015-01-21 16:08:37 17 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/interpro.txt: -------------------------------------------------------------------------------- 1 | IPR027628 TIGR04346 2 | IPR027629 TIGR04168 3 | IPR027631 TIGR04105 4 | IPR027632 TIGR03893 5 | IPR027633 TIGR04055 6 | IPR027634 TIGR04053 7 | IPR027635 TIGR03898 8 | IPR027636 TIGR04035 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/map.txt: -------------------------------------------------------------------------------- 1 | 1 deCODE 2 | 2 GM99-G3 3 | 3 GM99-GB4 4 | 4 Genethon 5 | 5 Marshfield 6 | 6 NCBI_RH 7 | 7 NHGRI-7 8 | 8 SHGC-G3 9 | 9 TNG 10 | 10 WI-RH 11 | 11 WI-YAC 12 | 12 WUSTL-X 13 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/mapping_set.txt: -------------------------------------------------------------------------------- 1 | 1 72_37 71_37 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/marker_synonym.txt: -------------------------------------------------------------------------------- 1 | 27381 11 UniSTS D6S1133E 2 | 31115 26 UniSTS RH79598 3 | 34501 15 UniSTS WI-18524 4 | 36536 6 UniSTS SHGC-84449 5 | 94998 10 UniSTS RH18133 6 | 174694 4 UniSTS RH102853 7 | 181343 12 UniSTS A005A32 8 | 212839 1 UniSTS RH123445 9 | 214499 21 UniSTS SGC38229 10 | 230168 8 UniSTS D6S1259 11 | 235351 23 UniSTS RH92961 12 | 305573 14 UniSTS WI-12186 13 | 336756 24 UniSTS SHGC-84081 14 | 340278 25 UniSTS SHGC-82095 15 | 348628 5 UniSTS SHGC-79592 16 | 369354 19 UniSTS D6S416 17 | 373103 13 UniSTS G20221 18 | 394698 2 UniSTS AL022440 19 | 410886 20 UniSTS WI-11550 20 | 424885 7 UniSTS RH102944 21 | 425058 9 UniSTS A006N46 22 | 452823 18 UniSTS D6S416 23 | 476401 17 UniSTS D6S416 24 | 493205 3 UniSTS WISP3_7927 25 | 689527 22 UniSTS RH45937 26 | 716770 16 UniSTS D6S998 27 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/meta_coord.txt: -------------------------------------------------------------------------------- 1 | gene 1003 26740 2 | exon 1003 491 3 | dna_align_feature 2 146695 4 | protein_align_feature 2 40171 5 | transcript 1003 26740 6 | gene 2 146179 7 | exon 2 4472 8 | transcript 2 145955 9 | repeat_feature 2 50000 10 | simple_feature 2 17502 11 | misc_feature 2 216723 12 | prediction_transcript 2 154711 13 | prediction_exon 2 870 14 | assembly_exception 2 262912 15 | karyotype 2 10000000 16 | splicing_event 1003 19814 17 | splicing_event 2 110378 18 | density_feature 2 1140767 19 | marker_feature 2 470 20 | ditag_feature 2 19 21 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/misc_feature.txt: -------------------------------------------------------------------------------- 1 | 92975 27515 112324681 112379141 1 2 | 92976 27515 112378167 112378947 1 3 | 92977 27515 112442364 112616253 1 4 | 92978 27515 112567078 112709945 1 5 | 92979 27515 112379142 112567919 1 6 | 92980 27515 112567078 112709945 1 7 | 92981 27515 112323682 112380141 1 8 | 92982 27515 112380142 112568919 1 9 | 92983 27515 112568920 112586593 1 10 | 92984 27516 120001 154821 1 11 | 92985 27516 289643 376205 1 12 | 92986 27516 344529 561251 1 13 | 92987 27516 60001 94821 1 14 | 92988 27516 144822 182592 1 15 | 92989 27516 182593 217464 -1 16 | 92990 27516 217465 231384 1 17 | 92991 27516 281385 312288 -1 18 | 92992 27516 312289 345528 1 19 | 92993 27516 345529 562251 1 20 | 92994 27516 60001 94821 1 21 | 92995 27516 144822 182592 1 22 | 92996 27516 182593 217464 -1 23 | 92997 27516 217465 231384 1 24 | 92998 27516 281385 312288 -1 25 | 92999 27516 312289 345528 1 26 | 93000 27516 345529 562251 1 27 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/misc_feature_misc_set.txt: -------------------------------------------------------------------------------- 1 | 92975 4 2 | 92976 4 3 | 92977 5 4 | 92978 5 5 | 92979 6 6 | 92980 6 7 | 92981 3 8 | 92982 3 9 | 92983 3 10 | 92984 2 11 | 92985 2 12 | 92986 6 13 | 92987 3 14 | 92988 3 15 | 92989 3 16 | 92990 3 17 | 92991 3 18 | 92992 3 19 | 92993 3 20 | 92994 3 21 | 92995 3 22 | 92996 3 23 | 92997 3 24 | 92998 3 25 | 92999 3 26 | 93000 3 27 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/seq_region.txt: -------------------------------------------------------------------------------- 1 | 22328 AL449423.14 1 101155 2 | 22566 AL512299.20 1 58460 3 | 23120 AL590106.7 1 17774 4 | 24555 AL732314.18 1 218723 5 | 24823 AL954664.18 1 30904 6 | 24829 AL954722.18 1 37771 7 | 26177 BX000476.5 1 33340 8 | 26178 BX000483.7 1 15918 9 | 26443 BX537334.4 1 36872 10 | 26483 BX640545.2 1 34821 11 | 27454 Z99289.1 1 190778 12 | 27515 6 2 171115067 13 | 27516 X 2 155270560 14 | 27605 HSCHRX_CTG1 3 34821 15 | 27609 HSCHR6_CTG5 3 75224524 16 | 27641 HSCHRX_CTG2 3 86563 17 | 27688 HSCHRX_CTG3 3 766173 18 | 1000759268 HG1304_PATCH 2 171115067 19 | 1000759269 HG1304_PATCH 3 262912 20 | 1000759337 Z99289.2 1 190778 21 | 1001161223 LRG_11 1003 33740 22 | 27507 Y 2 59373566 23 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 27515 10 3428761 2 | 27515 367 6 3 | 27515 6 1 4 | 27515 353 1028 5 | 1000759268 388 4 6 | 27516 367 23 7 | 27516 6 1 8 | 27516 10 2295302 9 | 27516 353 735 10 | 27515 64 4 11 | 1000759268 16 1 12 | 1000759268 312 2012-04-27 12:12:07 13 | 1000759268 6 1 14 | 27515 353 5 15 | 1000759268 368 1028 16 | 1001161223 314 1 17 | 1001161223 16 1 18 | 1001161223 6 1 19 | 1000759268 399 4 20 | 27515 390 4 21 | 27515 389 1 22 | 1000759268 387 1 23 | 27516 390 1 24 | 27516 67 1 25 | 1000759268 369 4 26 | 1000759268 368 5 27 | 27515 397 1 28 | 27515 398 4 29 | 27516 353 1 30 | 27516 398 1 31 | 27516 64 3 32 | 1000759268 400 1 33 | 1001161223 145 28690 28690 T 34 | 1001161223 145 28791 28792 AT 35 | 1001161223 145 28821 28823 GTA 36 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/seq_region_mapping.txt: -------------------------------------------------------------------------------- 1 | 1000859602 1001161223 1 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/patch/seq_region_synonym.txt: -------------------------------------------------------------------------------- 1 | 6 27515 CM000668.1 700 2 | 23 27516 CM000685.1 700 3 | 176 1000759269 JH636056.1 700 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql: -------------------------------------------------------------------------------- 1 | BEGIN TRANSACTION; 2 | 3 | COMMIT; 4 | 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6770005270575 1 \N 10 | 6770001148328 677 172177 \N 1048 6770004847974 1 \N 11 | 6770001148329 677 172177 \N 333 6770004847974 1 \N 12 | 6770001148330 677 172177 \N 383 6770004847974 1 \N 13 | 6770001148331 677 172177 \N 795 6770004847974 1 \N 14 | 6770001148332 677 172177 \N 437 6770004847974 1 \N 15 | 6770001148333 677 172177 \N 1176 6770004847974 1 \N 16 | 6770001148334 677 172177 \N 796 6770004847974 1 \N 17 | 6770001148335 677 172177 \N 884 6770004847974 1 \N 18 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/multi/compara/genomic_align_tree.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Ensembl/ensembl/1117691dd6357010e09e583d09ad2b4399b07337/modules/t/test-genome-DBs/multi/compara/genomic_align_tree.txt -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/multi/compara/hmm_annot.txt: 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ProteinTree.protein_tree_node Protein-trees 2 | 201 ENSEMBL_ORTHOLOGUES Homology.homology Orthologues 3 | 202 ENSEMBL_PARALOGUES Homology.homology Paralogues 4 | 402 NC_TREES NCTree.nc_tree_node ncRNA-trees 5 | 101 SYNTENY SyntenyRegion.synteny Synteny 6 | 16 LASTZ_NET GenomicAlignBlock.pairwise_alignment LastZ 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/multi/compara/method_link_species_set_attr.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Ensembl/ensembl/1117691dd6357010e09e583d09ad2b4399b07337/modules/t/test-genome-DBs/multi/compara/method_link_species_set_attr.txt -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/multi/compara/method_link_species_set_tag.txt: -------------------------------------------------------------------------------- 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16 | 51486 10080 17 | 51487 10080 18 | 51488 10080 19 | 51489 10080 20 | 51490 10080 21 | 51491 10080 22 | 51492 10080 23 | 51493 10080 24 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/core/assembly.txt: -------------------------------------------------------------------------------- 1 | 20580 11185 13510019 13617508 1 107490 -1 2 | 20602 11185 20323634 20431123 1 107490 -1 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/core/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 contig \N 3 default_version,sequence_level 2 | 2 1 scaffold GRCm38 2 default_version 3 | 3 1 chromosome GRCm38 1 default_version 4 | 11 1 chromosome NCBIM37 4 5 | 12 1 supercontig NCBIM37 5 6 | 111 1 chromosome NCBIM36 6 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/core/external_db.txt: -------------------------------------------------------------------------------- 1 | 0 GeneCards XREF 50 GeneCards MISC \N \N \N 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/core/gene.txt: -------------------------------------------------------------------------------- 1 | 18256 protein_coding 1282 20602 30274334 30300924 1 \N ensembl DJ310O13.1.2 (NOVEL PROTEIN SIMILAR DROSOPHILA PROTEIN CG7474, ISOFORM 2 ) (FRAGMENT). [Source:SPTREMBL;Acc:Q9BR18] 1 21716 ENSMUSG00000088524 1 2004-12-06 12:00:00 2004-12-06 12:00:00 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/core/seq_region.txt: -------------------------------------------------------------------------------- 1 | 11185 AC158775.9 1 177241 2 | 20602 19 3 61431566 3 | 13705553 1 3 195471971 4 | 13705555 8 3 129401213 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/core/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 20602 6 1 2 | 20602 10 1973105 3 | 20602 64 708 4 | 20602 67 73 5 | 20602 353 250 6 | 20602 367 19 7 | 20602 389 131 8 | 20602 390 103 9 | 20602 408 8 10 | 20602 444 16 11 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql: -------------------------------------------------------------------------------- 1 | BEGIN TRANSACTION; 2 | 3 | COMMIT; 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/allele_code.txt: -------------------------------------------------------------------------------- 1 | 685938 G 2 | 685939 A 3 | 685940 C 4 | 685941 T 5 | 685942 - 6 | 685943 CA 7 | 685944 TAAAAATCCC 8 | 685945 AAATCCCAAC 9 | 685946 AAAAAAAAAA 10 | 685947 TT 11 | 685948 GAAAA 12 | 685949 AAAAAAA 13 | 685950 AAAAA 14 | 685951 GA 15 | 685952 AT 16 | 685953 AC 17 | 685954 CG 18 | 685955 GCTTAGATGAAATGC 19 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/genotype_code.txt: -------------------------------------------------------------------------------- 1 | 1 685939 1 0 2 | 1 685939 2 0 3 | 2 685941 1 0 4 | 2 685941 2 0 5 | 3 685940 1 0 6 | 3 685940 2 0 7 | 4 685938 1 0 8 | 4 685938 2 0 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/individual_type.txt: -------------------------------------------------------------------------------- 1 | 1 fully_inbred multiple organisms have the same genome sequence 2 | 2 partly_inbred single organisms have reduced genome variability due to human intervention 3 | 3 outbred a single organism which breeds freely 4 | 4 mutant a single or multiple organisms with the same genome sequence that have a natural or experimentally induced mutation 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/meta_coord.txt: -------------------------------------------------------------------------------- 1 | variation_feature 3 500 2 | transcript_variation 1 0 3 | structural_variation_feature 3 13018700 4 | compressed_genotype_region 1 100001 5 | compressed_genotype_region 3 100001 6 | phenotype_feature 1 4563513 7 | phenotype_feature 3 4563513 8 | read_coverage 3 107158 9 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/read_coverage.txt: -------------------------------------------------------------------------------- 1 | 20602 20380190 20384180 1 4 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/sample.txt: -------------------------------------------------------------------------------- 1 | 6 6 129X1/SVJ \N \N DEFAULT 1 \N 2 | 79 79 PWD/PHJ \N \N DISPLAYABLE 0 \N 3 | 32 32 WSB/EIJ 001145 \N DISPLAYABLE 0 \N 4 | 22 22 CAST/EIJ \N \N DISPLAYABLE 0 \N 5 | 4 4 A/J \N \N DEFAULT 1 \N 6 | 2 2 NOD/LTJ NOD/LtJ \N DISPLAYABLE 0 \N 7 | 47 47 NZW/LACJ \N \N DISPLAYABLE 0 \N 8 | 23 23 LG/J 000675 \N DISPLAYABLE 0 \N 9 | 113 113 KK/HLJ 002106 \N DISPLAYABLE 0 \N 10 | 13 13 BALB/CBYJ \N \N DEFAULT 0 \N 11 | 28 28 129S1/SVIMJ \N \N DEFAULT 1 \N 12 | 35 35 BTBR T+ TF/J 002282 \N DISPLAYABLE 0 \N 13 | 33 33 C57BL/6J \N \N REFERENCE 0 \N 14 | 66 66 FVB/NJ 001800 \N DEFAULT 0 \N 15 | 7 7 MOLF/EIJ 000550 \N DISPLAYABLE 0 \N 16 | 53 53 SM/J 000687 \N DISPLAYABLE 0 \N 17 | 40 40 C3H/HEJ \N \N DEFAULT 1 \N 18 | 43 43 DBA/2J \N \N DEFAULT 1 \N 19 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/seq_region.txt: -------------------------------------------------------------------------------- 1 | 11185 AC158775.9 1 2 | 20602 19 3 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/mus_musculus/variation/source.txt: -------------------------------------------------------------------------------- 1 | 1 dbSNP 142 Variants (including SNPs and indels) imported from dbSNP http://www.ncbi.nlm.nih.gov/projects/SNP/ \N mixed variation 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/nameless/core/external_db.txt: -------------------------------------------------------------------------------- 1 | 0 GeneCards XREF 50 GeneCards MISC \N \N \N 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/ontology/ontology/alt_id.txt: -------------------------------------------------------------------------------- 1 | 1 2688 GO:0005554 2 | 2 2702 GO:0003695 3 | 3 2704 GO:0003698 4 | 4 2704 GO:0003699 5 | 5 2811 GO:0009387 6 | 6 13423 GO:0032134 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/ontology/ontology/aux_GO_Cross_product_review_map.txt: -------------------------------------------------------------------------------- 1 | 882 882 0 2 | 883 882 1 3 | 883 883 0 4 | 884 882 2 5 | 884 883 1 6 | 885 882 2 7 | 885 883 1 8 | 13583 13588 2 9 | 13584 13588 1 10 | 13586 13586 0 11 | 13587 13587 0 12 | 13588 13588 0 13 | 18641 13588 2 14 | 21541 13588 2 15 | 25166 13588 1 16 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/ontology/ontology/aux_GO_mf_needs_review_map.txt: -------------------------------------------------------------------------------- 1 | 193 13957 1 2 | 3020 3020 0 3 | 3285 3285 0 4 | 3477 3477 0 5 | 6188 6188 0 6 | 9572 9572 0 7 | 9790 9790 0 8 | 9914 13957 1 9 | 10540 10540 0 10 | 12638 12638 0 11 | 13957 13957 0 12 | 16093 16093 0 13 | 16100 16100 0 14 | 16338 23937 1 15 | 16339 23937 1 16 | 16411 13957 1 17 | 16412 13957 1 18 | 16413 13957 1 19 | 19246 19246 0 20 | 19294 13957 1 21 | 19295 13957 1 22 | 19540 13957 1 23 | 20632 20632 0 24 | 21919 21919 0 25 | 22124 22124 0 26 | 23082 23082 0 27 | 23937 23937 0 28 | 24056 24056 0 29 | 24484 24484 0 30 | 25519 25519 0 31 | 25615 25615 0 32 | 25683 25683 0 33 | 25685 24056 1 34 | 26952 13957 1 35 | 26952 26952 0 36 | 30396 30396 0 37 | 32742 13957 1 38 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/ontology/ontology/aux_SO_DBVAR_map.txt: -------------------------------------------------------------------------------- 1 | 37409 37409 0 2 | 37846 37846 0 3 | 38338 37846 1 4 | 38852 38852 0 5 | 38853 38853 0 6 | 38854 38854 0 7 | 38855 38854 1 8 | 38856 38854 1 9 | 38893 38893 0 10 | 38893 38894 1 11 | 38894 38894 0 12 | 38895 38895 0 13 | 38946 37846 1 14 | 38947 37846 1 15 | 38981 38894 1 16 | 38982 38894 2 17 | 38983 38894 2 18 | 39037 37846 2 19 | 39105 37846 1 20 | 39106 39106 0 21 | 39109 37846 3 22 | 39109 39146 1 23 | 39110 37846 3 24 | 39110 39146 1 25 | 39146 37846 2 26 | 39146 39146 0 27 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/ontology/ontology/ontology.txt: -------------------------------------------------------------------------------- 1 | 1 GO biological_process releases/2016-03-30 \N 2 | 2 GO cellular_component releases/2016-03-30 \N 3 | 3 GO molecular_function releases/2016-03-30 \N 4 | 5 SO sequence so-xp/releases/2015-11-24/so-xp.owl \N 5 | 6 EFO BrendaTissueOBO \N \N 6 | 7 EFO EFO \N \N 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/ontology/ontology/subset.txt: -------------------------------------------------------------------------------- 1 | 1 Cross_product_review Involved_in 2 | 2 goslim_aspergillus Aspergillus GO slim 3 | 3 goslim_candida Candida GO slim 4 | 4 goslim_generic Generic GO slim 5 | 5 goslim_metagenomics Metagenomics GO slim 6 | 6 goslim_pir PIR GO slim 7 | 7 goslim_plant Plant GO slim 8 | 8 goslim_pombe Fission yeast GO slim 9 | 9 goslim_yeast Yeast GO slim 10 | 10 gosubset_prok Prokaryotic GO subset 11 | 11 high_level_annotation_qc High-level terms not to be used for direct annotation 12 | 12 mf_needs_review Catalytic activity terms in need of attention 13 | 13 termgenie_unvetted Terms created by TermGenie that do not follow a template and require additional vetting by editors 14 | 14 virus_checked Viral overhaul terms 15 | 15 DBVAR database of genomic structural variation 16 | 16 SOFA SO feature annotation 17 | 17 biosapiens biosapiens protein feature ontology 18 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/parus_major1/core/coord_system.txt: -------------------------------------------------------------------------------- 1 | 1 1 primary_assembly Parus_major1.1 1 default_version,sequence_level 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/parus_major1/core/seq_region.txt: -------------------------------------------------------------------------------- 1 | 1 1 1 114059860 2 | 27 25LG2 1 809223 3 | 40 JRXK01022146.1 1 9743 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/parus_major1/core/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 1 367 1 2 | 1 6 1 3 | 1 64 1152 4 | 1 67 1 5 | 1 444 9 6 | 1 389 43 7 | 1 390 372 8 | 1 353 424 9 | 27 367 27 10 | 27 6 1 11 | 27 64 80 12 | 27 67 4 13 | 27 390 9 14 | 27 353 9 15 | 40 6 1 16 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/parus_major1/core/seq_region_synonym.txt: -------------------------------------------------------------------------------- 1 | 1 1 CM003709.1 50710 -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/assembly.txt: -------------------------------------------------------------------------------- 1 | 3495644 3309354 1 4562 1 4562 1 2 | 3495727 3355688 1 18301 1 18301 1 3 | 3495794 3116582 1 5428 1 5428 1 4 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/coord_system.txt: -------------------------------------------------------------------------------- 1 | 10 1 scaffold IWGSP1 4 \N 2 | 7 1 contig \N 3 default_version,sequence_level 3 | 8 1 scaffold IWGSC2 2 default_version 4 | 9 1 chromosome IWGSC2 1 default_version 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/density_type.txt: -------------------------------------------------------------------------------- 1 | 22 156 0 150 sum 2 | 8 149 0 150 sum 3 | 21 150 0 150 sum 4 | 16 151 0 150 sum 5 | 20 153 0 150 ratio 6 | 19 152 0 150 sum 7 | 17 148 0 150 ratio 8 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/exon_transcript.txt: -------------------------------------------------------------------------------- 1 | 243045 79141 1 2 | 243046 79141 2 3 | 243998 79459 1 4 | 247713 80726 1 5 | 357233 116850 3 6 | 357234 116850 4 7 | 357235 116850 5 8 | 357236 116850 6 9 | 357240 116850 2 10 | 357242 116850 1 11 | 357243 116850 7 12 | 379407 123920 1 13 | 382466 124987 1 14 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/external_db.txt: -------------------------------------------------------------------------------- 1 | 0 GeneCards XREF 50 GeneCards MISC \N \N \N 2 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/gene.txt: -------------------------------------------------------------------------------- 1 | 23688 protein_coding 119 3495727 898 1416 -1 \N ensembl \N 1 79141 Traes_6DS_3B68FB2E11 1 2014-01-21 14:05:47 2014-01-21 14:05:47 2 | 23830 protein_coding 119 3495727 8829 9015 1 \N ensembl \N 1 79459 Traes_6DS_F1A510F0D1 1 2014-01-21 14:05:48 2014-01-21 14:05:48 3 | 24399 protein_coding 119 3495727 1853 2068 1 462285 ensembl 30S ribosomal protein S19, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:P60577] 1 80726 Traes_6DS_262C704652 1 2014-01-21 14:05:56 2014-01-21 14:05:56 4 | 37263 protein_coding 119 3495794 323 5415 -1 \N ensembl \N 1 116850 Traes_5AL_7256A9F19 1 2014-01-21 14:17:38 2014-01-21 14:17:38 5 | 39717 protein_coding 119 3495644 2408 2611 -1 \N ensembl \N 1 123920 Traes_6BS_5FDE5650B 1 2014-01-21 14:18:24 2014-01-21 14:18:24 6 | 40233 protein_coding 119 3495644 2030 2272 -1 \N ensembl \N 1 124987 Traes_6BS_48A5D59CE 1 2014-01-21 14:18:30 2014-01-21 14:18:30 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/gene_attrib.txt: -------------------------------------------------------------------------------- 1 | 23830 142 32.09 2 | 37263 142 38.66 3 | 23688 142 55.11 4 | 39717 142 41.18 5 | 24399 142 41.20 6 | 40233 142 35.80 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/genome_statistics.txt: -------------------------------------------------------------------------------- 1 | 4 ref_length 4294967295 1 405 2014-11-25 16:03:21 2 | 39 lnoncoding_cnt 14 1 390 2014-11-25 16:03:21 3 | 7 total_length 4294967295 1 406 2014-11-25 16:03:21 4 | 43 PredictionTranscript 39237 1 424 2014-11-25 16:09:37 5 | 15 transcript 111488 1 403 2014-12-02 16:27:20 6 | 40 snoncoding_cnt 10128 1 389 2014-11-25 16:03:21 7 | 38 coding_cnt 99926 1 64 2014-11-25 16:03:21 8 | 44 SNPCount 10960049 1 10 2014-12-02 16:27:20 9 | 42 PredictionTranscript 83160 1 423 2014-11-25 16:09:37 10 | 41 pseudogene_cnt 1420 1 67 2014-11-25 16:03:21 11 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/identity_xref.txt: -------------------------------------------------------------------------------- 1 | 3508135 76 100 23 93 1 71 71M 374 \N 2 | 3506965 76 100 23 93 1 71 71M 374 \N 3 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/meta_coord.txt: -------------------------------------------------------------------------------- 1 | gene 8 35335 2 | transcript 8 35059 3 | repeat_feature 8 18170 4 | exon 8 7827 5 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/repeat_consensus.txt: -------------------------------------------------------------------------------- 1 | 1163918 trf trf Tandem repeats CTGCAATATTCACTTGCTCTC 2 | 1163915 trf trf Tandem repeats ACTTGTTCTGCTCTTGT 3 | 1163913 trf trf Tandem repeats TAGTAAAATTCAAAAGAAAA 4 | 1163911 trf trf Tandem repeats ATTCACTTGCTCTGCTCTTGTACTGAACTGAAC 5 | 1163907 trf trf Tandem repeats ACCAAAAGGACATAGTTCAGTACATGATA 6 | 1163894 trf trf Tandem repeats AATCCTCATCAGAAGAAT 7 | 1022815 trf trf Tandem repeats TGTACTTATGAAATCACAATC 8 | 1022812 trf trf Tandem repeats ATAGTATAAGAAAAACAA 9 | 1022810 trf trf Tandem repeats TTTATTTCATTTCTATAGTATAAGAAAAACAA 10 | 1022807 trf trf Tandem repeats TACTTGTCTTTCTAGGCATTTCAAATGACTATCACATACGGATGTATGTAGACATATTTTAGAGTGTAGATTCACTCATTTTACTCCGTATGTAGTCACTTGTTGAAATGCCTAGAAAGACAAGTATTTAGGAACGGAGGGAG 11 | 942309 dust dust Dust N 12 | 941541 HADES_TA DNA/TcMar-Stowaway Type II Transposons N 13 | 941900 gnl|TREP|TREP3092 Unknown Unknown N 14 | 941902 gnl|TREP|TREP3081 Unknown Unknown N 15 | 941943 gnl|TREP|TREP3528 Unknown Unknown N 16 | 941955 gnl|TREP|TREP3107 Unknown Unknown N 17 | 941971 gnl|TREP|TREP3051 Unknown Unknown N 18 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/seq_region.txt: -------------------------------------------------------------------------------- 1 | 3116582 IWGSC_CSS_5AL_contig_316991 7 5428 2 | 3309354 IWGSC_CSS_6BS_contig_3758 7 4562 3 | 3355688 IWGSC_CSS_6DS_contig_94739 7 18301 4 | 3495644 IWGSC_CSS_6BS_scaff_233977 8 4562 5 | 3495727 IWGSC_CSS_6DS_scaff_2121653 8 18301 6 | 3495794 IWGSC_CSS_5AL_scaff_2697823 8 5428 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/seq_region_attrib.txt: -------------------------------------------------------------------------------- 1 | 3495794 425 A 2 | 3495644 425 B 3 | 3495794 6 1 4 | 3495727 6 1 5 | 3495644 6 1 6 | 3495644 64 2 7 | 3495727 64 3 8 | 3495794 64 1 9 | 3495727 425 D 10 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/transcript.txt: -------------------------------------------------------------------------------- 1 | 79141 23688 119 3495727 898 1416 -1 \N ensembl protein_coding \N 1 79141 Traes_6DS_3B68FB2E11.1 1 2014-01-21 14:05:47 2014-01-21 14:05:47 2 | 79459 23830 119 3495727 8829 9015 1 \N ensembl protein_coding \N 1 79459 Traes_6DS_F1A510F0D1.1 1 2014-01-21 14:05:48 2014-01-21 14:05:48 3 | 80726 24399 119 3495727 1853 2068 1 665630 ensembl protein_coding \N 1 80726 Traes_6DS_262C704652.1 1 2014-01-21 14:05:56 2014-01-21 14:05:56 4 | 116850 37263 119 3495794 506 4791 -1 \N ensembl protein_coding \N 1 116850 Traes_5AL_7256A9F19.3 1 2014-01-21 14:17:38 2014-01-21 14:17:38 5 | 123920 39717 119 3495644 2408 2611 -1 \N ensembl protein_coding \N 1 123920 Traes_6BS_5FDE5650B.1 1 2014-01-21 14:18:24 2014-01-21 14:18:24 6 | 124987 40233 119 3495644 2030 2272 -1 \N ensembl protein_coding \N 1 124987 Traes_6BS_48A5D59CE.1 1 2014-01-21 14:18:30 2014-01-21 14:18:30 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/translation.txt: -------------------------------------------------------------------------------- 1 | 79141 79141 1 243045 143 243046 Traes_6DS_3B68FB2E11.1 1 2014-01-21 14:05:47 2014-01-21 14:05:47 2 | 79459 79459 23 243998 187 243998 Traes_6DS_F1A510F0D1.1 1 2014-01-21 14:05:48 2014-01-21 14:05:48 3 | 80726 80726 1 247713 216 247713 Traes_6DS_262C704652.1 1 2014-01-21 14:05:56 2014-01-21 14:05:56 4 | 116850 116850 150 357242 211 357243 Traes_5AL_7256A9F19.3 1 2014-01-21 14:17:38 2014-01-21 14:17:38 5 | 123920 123920 1 379407 204 379407 Traes_6BS_5FDE5650B.1 1 2014-01-21 14:18:24 2014-01-21 14:18:24 6 | 124987 124987 1 382466 243 382466 Traes_6BS_48A5D59CE.1 1 2014-01-21 14:18:30 2014-01-21 14:18:30 7 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/polyploidy/core/translation_attrib.txt: -------------------------------------------------------------------------------- 1 | 124987 166 9566.19 2 | 124987 168 118.101 3 | 124987 165 7.5 4 | 124987 164 10.2248 5 | 124987 167 81 6 | 80726 166 8194.45 7 | 80726 168 115.415 8 | 80726 165 7.0 9 | 80726 164 10.6220 10 | 80726 167 71 11 | 79459 168 116.792 12 | 79459 165 0.5 13 | 79459 164 7.5424 14 | 79459 167 54 15 | 79459 166 6306.76 16 | 116850 165 2.5 17 | 116850 164 6.8239 18 | 116850 167 310 19 | 116850 166 33595.74 20 | 116850 168 108.373 21 | 79141 166 12775.81 22 | 79141 168 108.270 23 | 79141 165 6.5 24 | 79141 164 11.2305 25 | 79141 167 118 26 | 123920 167 68 27 | 123920 164 5.5837 28 | 123920 165 -1.0 29 | 123920 168 117.178 30 | 123920 166 7968.14 31 | -------------------------------------------------------------------------------- /modules/t/test-genome-DBs/test_collection/core/external_db.txt: -------------------------------------------------------------------------------- 1 | 0 GeneCards XREF 50 GeneCards MISC \N \N \N 2 | -------------------------------------------------------------------------------- /sql/patch_111_112_b.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_111_112_b.sql 17 | # 18 | # Title: Allow meta_value to be null 19 | # 20 | # Description: 21 | # Allow meta_value to be null 22 | 23 | ALTER TABLE meta MODIFY COLUMN meta_value VARCHAR(255); 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_111_112_b.sql|Allow meta_value to be null'); 28 | -------------------------------------------------------------------------------- /sql/patch_111_112_c.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_111_112_c.sql 17 | # 18 | # Title: Extend meta_key length 19 | # 20 | # Description: 21 | # Extend meta_key length to 64 22 | 23 | ALTER TABLE meta MODIFY COLUMN meta_key VARCHAR(64) NOT NULL; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_111_112_c.sql|Extend meta_key length to 64'); -------------------------------------------------------------------------------- /sql/patch_28_29.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # there were no schema changes on the core databases between release 28 and 29 17 | # :-) 18 | -------------------------------------------------------------------------------- /sql/patch_29_30.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # there were no schema changes on the core databases between release 29 and 30 17 | # :-) 18 | -------------------------------------------------------------------------------- /sql/patch_32_33.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # SQL to patch a release 32 Ensembl database schema to release 33 17 | 18 | # Add db_display_name column to external_db 19 | ALTER TABLE external_db ADD COLUMN db_display_name VARCHAR(255); 20 | -------------------------------------------------------------------------------- /sql/patch_34_35.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # There were no schema changes on the core databases between release 34 and 35 17 | # 18 | # Just update the schema_version in the meta table 19 | UPDATE meta set meta_value="35" where meta_key="schema_version"; 20 | -------------------------------------------------------------------------------- /sql/patch_38_39_d.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_38_39_d 17 | # 18 | # title: schema version 19 | # 20 | # description: 21 | # this patch updates the schema version 22 | 23 | # update schema version 24 | UPDATE meta set meta_value = 39 where meta_key = 'schema_version'; 25 | 26 | # patch identifier 27 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_38_39_d.sql|schema_version'); 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_39_40_d.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_39_40_d 17 | # 18 | # title: stable id event score column 19 | # 20 | # description: 21 | # Add stable_id_event.score column 22 | 23 | ALTER TABLE stable_id_event ADD COLUMN score FLOAT NOT NULL DEFAULT 0; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_39_40_d.sql|stable_id_event_score_column'); 27 | 28 | -------------------------------------------------------------------------------- /sql/patch_39_40_i.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_39_40_i 17 | # 18 | # title: schema version 19 | # 20 | # description: 21 | # this patch updates the schema version 22 | 23 | # update schema version 24 | UPDATE meta set meta_value = 40 where meta_key = 'schema_version'; 25 | 26 | # patch identifier 27 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_39_40_i.sql|schema_version'); 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_39_40_j.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_39_40_e 17 | # 18 | # title: marker_synonym name 19 | # 20 | # description: 21 | # this patch widens the name column in marker_synonym to 50 characters. 22 | 23 | ALTER TABLE marker_synonym CHANGE name name VARCHAR(50); 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_39_40_j.sql|marker_synonym_name'); 27 | 28 | -------------------------------------------------------------------------------- /sql/patch_40_41_c.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_40_41_c 17 | # 18 | # title: xref priority 19 | # 20 | # description: 21 | # Add a priority column to the xref table 22 | 23 | ALTER TABLE xref ADD COLUMN priority INT DEFAULT 1 NOT NULL; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_40_41_c.sql|xref_priority'); 27 | -------------------------------------------------------------------------------- /sql/patch_40_41_d.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_40_41_d 17 | # 18 | # title: ditag primary key type 19 | # 20 | # description: 21 | # Make ditag.ditag_id be INT(10) 22 | 23 | ALTER TABLE ditag CHANGE COLUMN ditag_id ditag_id INT(10) UNSIGNED; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_40_41_d.sql|ditag_primary_key_type'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_40_41_e.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_40_41_e 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 41 22 | 23 | UPDATE meta SET meta_value='41' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_40_41_e.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_41_42_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_41_42_a 17 | # 18 | # title: remove xref.priority 19 | # 20 | # description: 21 | # Remove the priority column in xref 22 | 23 | ALTER TABLE xref DROP COLUMN priority; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_41_42_a.sql|remove_xref_priority'); 27 | -------------------------------------------------------------------------------- /sql/patch_41_42_d.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_40_41_d 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 42 22 | 23 | UPDATE meta SET meta_value='42' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_41_42_d.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_41_42_e.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_40_41_e 17 | # 18 | # title: ditag correction from patch_40_41_d 19 | # 20 | # description: put auto increment back in the table 21 | 22 | alter table ditag change column ditag_id ditag_id int(10) unsigned NOT NULL auto_increment; 23 | 24 | # patch identifier 25 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_41_42_e.sql|ditag_autoincrement'); 26 | -------------------------------------------------------------------------------- /sql/patch_41_42_f.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_40_41_f 17 | # 18 | # title: Analysis_description.web_data 19 | # 20 | # description: Add web_data column to analysis_description. 21 | 22 | ALTER TABLE analysis_description ADD COLUMN web_data TEXT; 23 | 24 | # patch identifier 25 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_41_42_f.sql|analysis_description_web_data'); 26 | -------------------------------------------------------------------------------- /sql/patch_42_43_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_42_43_a 17 | # 18 | # title: unmapped_object.parent 19 | # 20 | # description: 21 | # Add parent column to unmapped_object 22 | 23 | ALTER TABLE unmapped_object ADD COLUMN parent VARCHAR(255) DEFAULT NULL; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_42_43_a.sql|unmapped_object.parent'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_42_43_f.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_42_43_f 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 43 22 | 23 | UPDATE meta SET meta_value='43' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_42_43_f.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_43_44_e.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_43_44_e 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 44 22 | 23 | UPDATE meta SET meta_value='44' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_43_44_e.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_44_45_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_44_45_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 45 22 | 23 | UPDATE meta SET meta_value='45' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_44_45_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_44_45_b.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_44_45_b.sql 17 | # 18 | # title: Marker index 19 | # 20 | # description: 21 | # Add index to marker.display_marker_synonym_id 22 | 23 | ALTER TABLE marker ADD INDEX display_idx (display_marker_synonym_id); 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_44_45_b.sql|marker_index'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_45_46_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_45_46_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 46 22 | 23 | UPDATE meta SET meta_value='46' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_45_46_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_45_46_d.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_45_46_d.sql 17 | # 18 | # title: Meta unique key 19 | # 20 | # description: 21 | # Add unique key to meta_key/meta_value columns in meta table. 22 | 23 | ALTER TABLE meta ADD UNIQUE key_value (meta_key, meta_value); 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_45_46_d.sql|meta_unique_key'); 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /sql/patch_46_47_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_46_47_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 47 22 | 23 | UPDATE meta SET meta_value='47' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_46_47_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_47_48_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_47_48_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 48 22 | 23 | UPDATE meta SET meta_value='48' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_47_48_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_48_49_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_48_49_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 49 22 | 23 | UPDATE meta SET meta_value='49' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_48_49_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_49_50_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_49_50_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 50 22 | 23 | UPDATE meta SET meta_value='50' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_49_50_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_50_51_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_50_51_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 51 22 | 23 | UPDATE meta SET meta_value='51' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (meta_key, meta_value) VALUES ('patch', 'patch_50_51_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_51_52_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_51_52_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 52 22 | 23 | UPDATE meta SET meta_value='52' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_51_52_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_51_52_d.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_51_52_d.sql 17 | # 18 | # title: External_db description 19 | # 20 | # description: 21 | # Add a description column to external_db 22 | 23 | ALTER TABLE external_db ADD COLUMN description TEXT; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_51_52_d.sql|external_db_description'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_52_53_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_52_53_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 53 22 | 23 | UPDATE meta SET meta_value='53' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_52_53_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_53_54_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_53_54_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 54 22 | 23 | UPDATE meta SET meta_value='54' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_53_54_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_54_55_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_54_55_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 55 22 | 23 | UPDATE meta SET meta_value='55' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_54_55_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_55_56_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_55_56_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 56 22 | 23 | UPDATE meta SET meta_value='56' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_55_56_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_56_57_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_56_57_a.sql 17 | # 18 | # title: update schema version 19 | # 20 | # description: 21 | # Update schema_version in meta table to 57 22 | 23 | UPDATE meta SET meta_value='57' WHERE meta_key='schema_version'; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_56_57_a.sql|schema_version'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_57_58_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_57_58_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 58. 22 | 23 | UPDATE meta SET meta_value='58' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_57_58_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_58_59_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_58_59_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 59. 22 | 23 | UPDATE meta SET meta_value='59' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_58_59_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_59_60_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_59_60_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 60. 22 | 23 | UPDATE meta SET meta_value='60' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_59_60_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_73_74_b.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_73_74_b.sql 17 | # 18 | # title: dnac removal 19 | # 20 | # description: 21 | # Removal dnac table which is not used any more 22 | 23 | DROP TABLE dnac; 24 | 25 | # patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) VALUES (NULL, 'patch', 'patch_73_74_b.sql|remove_dnac'); 27 | 28 | 29 | -------------------------------------------------------------------------------- /sql/patch_84_85_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_84_85_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 85. 22 | 23 | UPDATE meta SET meta_value='85' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_84_85_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_84_85_b.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_84_85_b.sql 17 | # 18 | # Title: Duplicate key in genome_statistics table 19 | # 20 | # Description: 21 | # Remove duplicated keys 22 | 23 | ALTER TABLE genome_statistics DROP KEY stats_idx; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_84_85_b.sql|remove_duplicated_key'); 28 | -------------------------------------------------------------------------------- /sql/patch_85_86_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_85_86_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 86. 22 | 23 | UPDATE meta SET meta_value='86' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_85_86_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_86_87_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_86_87_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 87. 22 | 23 | UPDATE meta SET meta_value='87' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_86_87_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_87_88_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_87_88_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 88. 22 | 23 | UPDATE meta SET meta_value='88' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_87_88_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_88_89_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_88_89_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 89. 22 | 23 | UPDATE meta SET meta_value='89' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_88_89_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_89_90_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_89_90_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 90. 22 | 23 | UPDATE meta SET meta_value='90' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_89_90_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_90_91_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_90_91_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 91. 22 | 23 | UPDATE meta SET meta_value='91' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_90_91_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_91_92_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_91_92_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 92. 22 | 23 | UPDATE meta SET meta_value='92' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_91_92_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_92_93_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_92_93_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 93. 22 | 23 | UPDATE meta SET meta_value='93' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_92_93_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_93_94_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_93_94_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 94. 22 | 23 | UPDATE meta SET meta_value='94' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_93_94_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_94_95_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_94_95_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 95. 22 | 23 | UPDATE meta SET meta_value='95' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_94_95_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_95_96_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_95_96_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 96. 22 | 23 | UPDATE meta SET meta_value='96' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_95_96_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_96_97_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_96_97_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 96. 22 | 23 | UPDATE meta SET meta_value='97' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_96_97_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_97_98_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_97_98_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 98. 22 | 23 | UPDATE meta SET meta_value='98' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_97_98_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /sql/patch_98_99_a.sql: -------------------------------------------------------------------------------- 1 | -- See the NOTICE file distributed with this work for additional information 2 | -- regarding copyright ownership. 3 | -- 4 | -- Licensed under the Apache License, Version 2.0 (the "License"); 5 | -- you may not use this file except in compliance with the License. 6 | -- You may obtain a copy of the License at 7 | -- 8 | -- http://www.apache.org/licenses/LICENSE-2.0 9 | -- 10 | -- Unless required by applicable law or agreed to in writing, software 11 | -- distributed under the License is distributed on an "AS IS" BASIS, 12 | -- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | -- See the License for the specific language governing permissions and 14 | -- limitations under the License. 15 | 16 | # patch_98_99_a.sql 17 | # 18 | # Title: Update schema version. 19 | # 20 | # Description: 21 | # Update schema_version in meta table to 99. 22 | 23 | UPDATE meta SET meta_value='99' WHERE meta_key='schema_version'; 24 | 25 | # Patch identifier 26 | INSERT INTO meta (species_id, meta_key, meta_value) 27 | VALUES (NULL, 'patch', 'patch_98_99_a.sql|schema_version'); 28 | -------------------------------------------------------------------------------- /travisci/MultiTestDB.conf.gitlabci.mysql: -------------------------------------------------------------------------------- 1 | { 2 | 'driver' => 'mysql', 3 | 'host' => 'mysqldb', 4 | 'port' => '3306', 5 | 'user' => 'root', 6 | 'pass' => 'n0t4t4l1s3cur3!', 7 | } 8 | -------------------------------------------------------------------------------- /travisci/MultiTestDB.conf.travisci.SQLite: -------------------------------------------------------------------------------- 1 | { 2 | 'driver' => 'SQLite', 3 | 'dbdir' => '/var/tmp/MultiTestDB', 4 | 'user' => 'travis', 5 | } 6 | -------------------------------------------------------------------------------- /travisci/MultiTestDB.conf.travisci.mysql: -------------------------------------------------------------------------------- 1 | { 2 | 'port' => '3306', 3 | 'driver' => 'mysql', 4 | 'user' => 'travis', 5 | 'host' => '127.0.0.1', 6 | } 7 | -------------------------------------------------------------------------------- /travisci/api_build_run_last_hour.py: -------------------------------------------------------------------------------- 1 | import sys 2 | import time 3 | from datetime import datetime, date 4 | import json 5 | 6 | def api_build_run_last_hour(x): 7 | return x['state'] != 'canceled' and \ 8 | x['event_type'] == 'api' and \ 9 | (x['finished_at'] == None or \ 10 | float((datetime.fromtimestamp(time.time()) - datetime.strptime(x['finished_at'],'%Y-%m-%dT%H:%M:%SZ')).total_seconds())/3600 < 1.0) 11 | 12 | builds = list(filter(api_build_run_last_hour, json.load(sys.stdin)['builds'])) 13 | print(len(builds) > 0) 14 | -------------------------------------------------------------------------------- /travisci/testdb.conf.gitlabci.mysql: -------------------------------------------------------------------------------- 1 | driver = mysql 2 | host = mysqldb 3 | port = 3306 4 | user = root 5 | pass = n0t4t4l1s3cur3! 6 | -------------------------------------------------------------------------------- /travisci/testdb.conf.travisci.SQLite: -------------------------------------------------------------------------------- 1 | driver = SQLite 2 | file = /var/tmp/xref_testdb.sqlite 3 | -------------------------------------------------------------------------------- /travisci/testdb.conf.travisci.mysql: -------------------------------------------------------------------------------- 1 | driver = mysql 2 | host = 127.0.0.1 3 | port = 3306 4 | user = travis 5 | pass = 6 | --------------------------------------------------------------------------------