This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git.
Pull mirroring updated .
- 15 Feb, 2008 2 commits
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
RepeatFeature as the test case for now. Won't do anything useful just yet.
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- 14 Feb, 2008 3 commits
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Andreas Kusalananda Kähäri authored
AssemblyExceptionFeatureAdaptor).
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Andreas Kusalananda Kähäri authored
Add the methods _create_feature() and _create_feature_fast() that returns a feature created by calling new() and new_fast() respectively, of the given type and with the given argument hashes. In the various feature adaptors: Create features using the two new methods above instead of new() and new_fast(). This allows for hijacking feature creation in the feature collection "adaptor" later.
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cvs2git authored
featurecollection-dev'. Sprout from master 2008-02-07 11:53:09 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Fixup POD for method translation().' Delete: LICENSE docs/ensembl_changes_spec.txt docs/ensembl_das/Homo_sapiens.ini docs/ensembl_das/demo.ini docs/ensembl_das/demo.pm docs/ensembl_das/ensembl-das.pdf docs/ensembl_das/ensembl-das.sxw docs/schema_description/README docs/schema_description/process-saxon.bat docs/schema_description/process-saxon.sh docs/schema_description/schema_description.dtd docs/schema_description/schema_description.html docs/schema_description/tables.html docs/schema_description/tables.txt docs/schema_description/tables.xml docs/schema_description/xml2html.xsl docs/schema_description/xml2wiki.xsl docs/tutorial/ensembl_tutorial.pdf docs/tutorial/ensembl_tutorial.sxw docs/tutorial/ensembl_tutorial.txt misc-scripts/CopyDBoverServer.pl misc-scripts/CreateFile4CopyDBoverServer.pl misc-scripts/README.schema_patching misc-scripts/anopheles_scripts/check_bad_regions.pl misc-scripts/anopheles_scripts/check_stops.pl misc-scripts/anopheles_scripts/dump_genbank_45.pl misc-scripts/anopheles_scripts/dump_genebank.pl misc-scripts/anopheles_scripts/dump_genebank_38.pl misc-scripts/anopheles_scripts/format_bacs.pl misc-scripts/anopheles_scripts/format_blat.pl misc-scripts/anopheles_scripts/format_matepairs.pl misc-scripts/anopheles_scripts/get_est_supporting_evidences.pl misc-scripts/anopheles_scripts/get_freqs.pl misc-scripts/anopheles_scripts/get_good_matepairs.pl misc-scripts/anopheles_scripts/get_transposon_repeats.pl misc-scripts/anopheles_scripts/load_karyotype.pl misc-scripts/anopheles_scripts/location_check_for_dump.pl misc-scripts/anopheles_scripts/produce_snap_training_set.pl misc-scripts/anopheles_scripts/protein_annotation_from_embl.pl misc-scripts/anopheles_scripts/remove_proteins_from_db.pl misc-scripts/anopheles_scripts/split_fasta_in_subslices_anopheles.pl misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm misc-scripts/assembly/EXAMPLE.use_mapping.pl misc-scripts/assembly/README misc-scripts/assembly/align_by_clone_identity.pl misc-scripts/assembly/align_nonident_regions.pl misc-scripts/assembly/align_nonident_regions_wrapper.pl misc-scripts/assembly/blastz_matrix.txt misc-scripts/assembly/check_mapping.pl misc-scripts/assembly/compare_assemblies.pl misc-scripts/assembly/find_overlaps.pl misc-scripts/assembly/fix_overlaps.pl misc-scripts/assembly/load_alternative_assembly.pl misc-scripts/assembly/mapping_stats.pl misc-scripts/attribute_types/attrib_type.txt misc-scripts/attribute_types/upload_attributes.pl misc-scripts/chain/axt2assembly.pl misc-scripts/chain/chain2assembly.pl misc-scripts/chimp/Deletion.pm misc-scripts/chimp/Gene.pm misc-scripts/chimp/Insertion.pm misc-scripts/chimp/InterimExon.pm misc-scripts/chimp/InterimTranscript.pm misc-scripts/chimp/Length.pm misc-scripts/chimp/README misc-scripts/chimp/StatLogger.pm misc-scripts/chimp/StatMsg.pm misc-scripts/chimp/Transcript.pm misc-scripts/chimp/Utils.pm misc-scripts/chimp/chimp_chr_ctg_assembly.pl misc-scripts/chimp/get_stats.pl misc-scripts/chimp/human2chimp.pl misc-scripts/chimp/lift_assembly.pl misc-scripts/chimp/run_hum2chimp.sh misc-scripts/db/cleanup_tmp_tables.pl misc-scripts/db/multidb_sql.pl misc-scripts/density_feature/DensityCalc.sh misc-scripts/density_feature/densities_multi_db.pl misc-scripts/density_feature/density_feature_fetch.pl misc-scripts/density_feature/gene_density_calc.pl misc-scripts/density_feature/glovar_snp_density.pl misc-scripts/density_feature/logicname_density_calc.pl misc-scripts/density_feature/percent_gc_calc.pl misc-scripts/density_feature/repeat_coverage_calc.pl misc-scripts/density_feature/seq_region_stats.pl misc-scripts/density_feature/variation_density.pl misc-scripts/density_feature/vega_gene_density.pl misc-scripts/density_feature/vega_percent_gc_calc.pl misc-scripts/density_feature/vega_repeat_coverage_calc.pl misc-scripts/ebi_search_dump/dump_44.sh misc-scripts/ebi_search_dump/dump_ebi.pl misc-scripts/external_db/README misc-scripts/external_db/convert_external_dbs.pl misc-scripts/external_db/external_dbs.txt misc-scripts/external_db/load_additional_human_affy_xrefs.pl misc-scripts/external_db/load_additional_human_gkb_xrefs.pl misc-scripts/external_db/update_external_dbs.pl misc-scripts/frameshift_transcript_attribs.pl misc-scripts/gene_gc.pl misc-scripts/generate_stable_ids.pl misc-scripts/golden_path/check_sum.pl misc-scripts/golden_path/fin_agp2ensembl misc-scripts/golden_path/get_contig.pl misc-scripts/golden_path/gp_contig_mismatch.pl misc-scripts/golden_path/gp_incons_test.pl misc-scripts/golden_path/gp_parse.pl misc-scripts/golden_path/makeunique.pl misc-scripts/golden_path/ncbi2ensembl misc-scripts/golden_path/nt_crossmatch.pl misc-scripts/golden_path/pfetch2ensembl misc-scripts/golden_path/rat_agp2ensembl misc-scripts/id_mapping/README misc-scripts/id_mapping/default.conf misc-scripts/id_mapping/dump_by_seq_region.pl misc-scripts/id_mapping/dump_cache.pl misc-scripts/id_mapping/fake_stable_id_mapping.pl misc-scripts/id_mapping/id_mapping.pl misc-scripts/id_mapping/run.pl misc-scripts/id_mapping/utils/batch_id_history.pl misc-scripts/id_mapping/utils/compare_results.pl misc-scripts/id_mapping/utils/dump_scores.pl misc-scripts/id_mapping/utils/id_mapping_clean.sql misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl misc-scripts/meta_coord/update_meta_coord.pl misc-scripts/meta_levels.pl misc-scripts/probe_mapping/compare_mappings.pl misc-scripts/probe_mapping/probe2transcript.pl misc-scripts/protein_match/process_pmach.pl misc-scripts/qtl/extract_rat_map_ids.pl misc-scripts/qtl/qtl_feature_calculation.pl misc-scripts/qtl/rat_qtl_import.pl misc-scripts/qtl/run_rat_import.pl misc-scripts/regulatory_regions/RegulatoryFeatureParser/BaseParser.pm misc-scripts/regulatory_regions/RegulatoryFeatureParser/cisred.pm misc-scripts/regulatory_regions/RegulatoryFeatureParser/enhancer.pm misc-scripts/regulatory_regions/RegulatoryFeatureParser/miranda.pm misc-scripts/regulatory_regions/gene_coverage.pl misc-scripts/regulatory_regions/load_regulatory.pl misc-scripts/regulatory_regions/parse_cisred.pl misc-scripts/repeats/repeat-libraries.pl misc-scripts/repeats/repeat-types.pl misc-scripts/repeats/repeats.txt misc-scripts/repeats/shrink_trfs.pl misc-scripts/repeats/vega_repeat_libraries.pl misc-scripts/schema_patch.pl misc-scripts/search_dbs.pl misc-scripts/surgery/SchemaConverter.pm misc-scripts/surgery/SeqStoreConverter/AnophelesGambiae.pm misc-scripts/surgery/SeqStoreConverter/ApisMellifera.pm misc-scripts/surgery/SeqStoreConverter/BasicConverter.pm misc-scripts/surgery/SeqStoreConverter/CaenorhabditisBriggsae.pm misc-scripts/surgery/SeqStoreConverter/CaenorhabditisElegans.pm misc-scripts/surgery/SeqStoreConverter/CanisFamiliaris.pm misc-scripts/surgery/SeqStoreConverter/DanioRerio.pm misc-scripts/surgery/SeqStoreConverter/DrosophilaMelanogaster.pm misc-scripts/surgery/SeqStoreConverter/FuguRubripes.pm misc-scripts/surgery/SeqStoreConverter/GallusGallus.pm misc-scripts/surgery/SeqStoreConverter/HomoSapiens.pm misc-scripts/surgery/SeqStoreConverter/MusMusculus.pm misc-scripts/surgery/SeqStoreConverter/PanTroglodytes.pm misc-scripts/surgery/SeqStoreConverter/RattusNorvegicus.pm misc-scripts/surgery/SeqStoreConverter/vega/CanisFamiliaris.pm misc-scripts/surgery/SeqStoreConverter/vega/DanioRerio.pm misc-scripts/surgery/SeqStoreConverter/vega/HomoSapiens.pm misc-scripts/surgery/SeqStoreConverter/vega/MusMusculus.pm misc-scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm misc-scripts/surgery/convert120_130.pl misc-scripts/surgery/convert_6_main.pl misc-scripts/surgery/convert_7a_main.pl misc-scripts/surgery/convert_seqstore.pl misc-scripts/surgery/converter.input misc-scripts/surgery/create_fixsql.pl misc-scripts/surgery/dump_seq_in_region misc-scripts/surgery/fuller_test_genome_9_chr20.pl misc-scripts/surgery/push_align_features.pl misc-scripts/surgery/set_nonredundant_attribs.pl misc-scripts/surgery/shortintrons2frameshifts.pl misc-scripts/surgery/table_column_munge misc-scripts/transfer_karyotype.pl misc-scripts/unmapped_reason/unmapped_reason.txt misc-scripts/unmapped_reason/update_unmapped_reasons.pl misc-scripts/utilities/dna_compress.pl misc-scripts/utilities/parse_embl.pl misc-scripts/utilities/show_method_status.pl misc-scripts/utilities/split_fasta.pl misc-scripts/web_stats.sh misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_agam.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_90_perc_id.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateUngappedBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/LocalExonerateGappedBest1.pm misc-scripts/xref_mapping/XrefMapper/Methods/PBSExonerateGappedBest1.pm misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/aedes_aegypti.pm misc-scripts/xref_mapping/XrefMapper/anopheles_gambiae.pm misc-scripts/xref_mapping/XrefMapper/caenorhabditis_elegans.pm misc-scripts/xref_mapping/XrefMapper/canis_familiaris.pm misc-scripts/xref_mapping/XrefMapper/ciona_intestinalis.pm misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm misc-scripts/xref_mapping/XrefMapper/db.pm misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm misc-scripts/xref_mapping/XrefMapper/macaca_mulatta.pm misc-scripts/xref_mapping/XrefMapper/monodelphis_domestica.pm misc-scripts/xref_mapping/XrefMapper/mus_musculus.pm misc-scripts/xref_mapping/XrefMapper/ornithorhynchus_anatinus.pm misc-scripts/xref_mapping/XrefMapper/rattus_norvegicus.pm misc-scripts/xref_mapping/XrefMapper/tetraodon_nigroviridis.pm misc-scripts/xref_mapping/XrefMapper/xenopus_tropicalis.pm misc-scripts/xref_mapping/XrefParser/AedesGenBankParser.pm misc-scripts/xref_mapping/XrefParser/AgilentParser.pm misc-scripts/xref_mapping/XrefParser/AnophelesSymbolParser.pm misc-scripts/xref_mapping/XrefParser/BaseParser.pm misc-scripts/xref_mapping/XrefParser/CCDSParser.pm misc-scripts/xref_mapping/XrefParser/CeleraParser.pm misc-scripts/xref_mapping/XrefParser/CeleraProteinParser.pm misc-scripts/xref_mapping/XrefParser/CeleraTranscriptParser.pm misc-scripts/xref_mapping/XrefParser/CodelinkParser.pm misc-scripts/xref_mapping/XrefParser/CoordinateParser.pm misc-scripts/xref_mapping/XrefParser/DatabaseParser.pm misc-scripts/xref_mapping/XrefParser/DirectParser.pm misc-scripts/xref_mapping/XrefParser/EntrezGeneParser.pm misc-scripts/xref_mapping/XrefParser/FastaParser.pm misc-scripts/xref_mapping/XrefParser/FlybaseParser.pm misc-scripts/xref_mapping/XrefParser/Flybase_dmel_GFFv3_Parser.pm misc-scripts/xref_mapping/XrefParser/GOParser.pm misc-scripts/xref_mapping/XrefParser/HGNCParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_ENSGParser.pm misc-scripts/xref_mapping/XrefParser/IPIParser.pm misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm misc-scripts/xref_mapping/XrefParser/InterproParser.pm misc-scripts/xref_mapping/XrefParser/JGI_Parser.pm misc-scripts/xref_mapping/XrefParser/JGI_ProteinParser.pm misc-scripts/xref_mapping/XrefParser/MGDParser.pm misc-scripts/xref_mapping/XrefParser/MIMParser.pm misc-scripts/xref_mapping/XrefParser/OTTTParser.pm misc-scripts/xref_mapping/XrefParser/RGDParser.pm misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm misc-scripts/xref_mapping/XrefParser/RefSeq_CCDSParser.pm misc-scripts/xref_mapping/XrefParser/SGDParser.pm misc-scripts/xref_mapping/XrefParser/SegmentParser.pm misc-scripts/xref_mapping/XrefParser/UCSCParser.pm misc-scripts/xref_mapping/XrefParser/UniGeneParser.pm misc-scripts/xref_mapping/XrefParser/UniProtParser.pm misc-scripts/xref_mapping/XrefParser/UniProtParser_descriptions_only.pm misc-scripts/xref_mapping/XrefParser/UniProtVarSplicParser.pm misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.pm misc-scripts/xref_mapping/XrefParser/VegaParser.pm misc-scripts/xref_mapping/XrefParser/WilsonAffyParser.pm misc-scripts/xref_mapping/XrefParser/WormPepParser.pm misc-scripts/xref_mapping/XrefParser/WormbaseDatabaseStableIDParser.pm misc-scripts/xref_mapping/XrefParser/XenopusJamboreeParser.pm misc-scripts/xref_mapping/XrefParser/ZFINParser.pm misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm misc-scripts/xref_mapping/compare_mapping.pl misc-scripts/xref_mapping/compare_xrefs_by_source.pl misc-scripts/xref_mapping/convert_xrefs_to_all_translations.pl misc-scripts/xref_mapping/ensembl_xrefs.pdf misc-scripts/xref_mapping/ensembl_xrefs.sxw misc-scripts/xref_mapping/gen_perc_file.pl misc-scripts/xref_mapping/generate_csv_graph_file.pl misc-scripts/xref_mapping/parsing_information.txt misc-scripts/xref_mapping/sql/table.sql misc-scripts/xref_mapping/test_mapping_files.pl misc-scripts/xref_mapping/test_xref_mapper.pl misc-scripts/xref_mapping/xref_config.ini misc-scripts/xref_mapping/xref_config2sql.pl misc-scripts/xref_mapping/xref_mapper.input misc-scripts/xref_mapping/xref_mapper.pl misc-scripts/xref_mapping/xref_parser.pl misc-scripts/xref_mapping/xrefs_overview.txt misc-scripts/xref_projection/README misc-scripts/xref_projection/README_projection.txt misc-scripts/xref_projection/project_display_xrefs.pl misc-scripts/xref_projection/projection_db.sql misc-scripts/xref_projection/release_37.conf misc-scripts/xref_projection/release_38.conf misc-scripts/xref_projection/release_47.ini misc-scripts/xref_projection/release_48.ini misc-scripts/xref_projection/submit_projections.pl modules/Bio/EnsEMBL/Collection.pm modules/Bio/EnsEMBL/Collection/DnaAlignFeature.pm modules/Bio/EnsEMBL/Collection/Exon.pm modules/Bio/EnsEMBL/Collection/Gene.pm modules/Bio/EnsEMBL/Collection/ProteinAlignFeature.pm modules/Bio/EnsEMBL/Collection/RepeatFeature.pm modules/Bio/EnsEMBL/Collection/Transcript.pm modules/t/MultiTestDB.conf.example modules/t/MultiTestDB.t modules/t/README modules/t/TestUtils.pm modules/t/affy.t modules/t/affyAdaptors.t modules/t/analysis.t modules/t/archiveStableId.t modules/t/argument.t modules/t/assemblyException.t modules/t/assemblyExceptionFeature.t modules/t/assemblyMapper.t modules/t/attribute.t modules/t/attributeAdaptor.t modules/t/canonicalDBAdaptor.t modules/t/chainedAssemblyMapper.t modules/t/compressedSequenceAdaptor.t modules/t/coordSystem.t modules/t/coordSystemAdaptor.t modules/t/dbConnection.t modules/t/dbEntries.t modules/t/densityFeature.t modules/t/densityFeatureAdaptor.t modules/t/densityType.t modules/t/densityTypeAdaptor.t modules/t/ditag.t modules/t/ditagAdaptor.t modules/t/ditagFeature.t modules/t/ditagFeatureAdaptor.t modules/t/dnaAlignFeatureAdaptor.t modules/t/dnaDnaAlignFeature.t modules/t/dnaPepAlignFeature.t modules/t/easyargv.t modules/t/exception.t modules/t/exon.t modules/t/externalFeatureAdaptor.t modules/t/feature.t modules/t/featurePair.t modules/t/gene.t modules/t/geneview.t modules/t/info_testdb.pl modules/t/intron.t modules/t/karyotypeBand.t modules/t/karyotypeBandAdaptor.t modules/t/mapLocation.t modules/t/mapper.t modules/t/marker.t modules/t/markerAdaptor.t modules/t/markerFeature.t modules/t/markerFeatureAdaptor.t modules/t/markerSynonym.t modules/t/metaContainer.t modules/t/metaCoordContainer.t modules/t/miscFeature.t modules/t/miscFeatureAdaptor.t modules/t/miscSet.t modules/t/miscSetAdaptor.t modules/t/oligo.t modules/t/oligoAdaptors.t modules/t/predictionTranscript.t modules/t/proteinAlignFeatureAdaptor.t modules/t/proteinFeature.t modules/t/proteinFeatureAdaptor.t modules/t/qtl.t modules/t/rangeRegistry.t modules/t/repeatConsensus.t modules/t/repeatConsensusAdaptor.t modules/t/repeatFeature.t modules/t/repeatFeatureAdaptor.t modules/t/repeatMaskedSlice.t modules/t/seqDumper.t modules/t/seqEdit.t modules/t/sequenceAdaptor.t modules/t/simpleFeature.t modules/t/slice.t modules/t/sliceAdaptor.t modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.sql modules/t/test-genome-DBs/homo_sapiens/core/alt_allele.txt modules/t/test-genome-DBs/homo_sapiens/core/analysis.sql modules/t/test-genome-DBs/homo_sapiens/core/analysis.txt modules/t/test-genome-DBs/homo_sapiens/core/analysis_description.sql modules/t/test-genome-DBs/homo_sapiens/core/analysis_description.txt modules/t/test-genome-DBs/homo_sapiens/core/assembly.sql modules/t/test-genome-DBs/homo_sapiens/core/assembly.txt modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.sql modules/t/test-genome-DBs/homo_sapiens/core/assembly_exception.txt modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.sql modules/t/test-genome-DBs/homo_sapiens/core/attrib_type.txt modules/t/test-genome-DBs/homo_sapiens/core/coord_system.sql modules/t/test-genome-DBs/homo_sapiens/core/coord_system.txt modules/t/test-genome-DBs/homo_sapiens/core/density_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/density_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/density_type.sql modules/t/test-genome-DBs/homo_sapiens/core/density_type.txt modules/t/test-genome-DBs/homo_sapiens/core/ditag.sql modules/t/test-genome-DBs/homo_sapiens/core/ditag.txt modules/t/test-genome-DBs/homo_sapiens/core/ditag_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/ditag_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/dna.sql modules/t/test-genome-DBs/homo_sapiens/core/dna.txt modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/dnac.sql modules/t/test-genome-DBs/homo_sapiens/core/dnac.txt modules/t/test-genome-DBs/homo_sapiens/core/exon.sql modules/t/test-genome-DBs/homo_sapiens/core/exon.txt modules/t/test-genome-DBs/homo_sapiens/core/exon_stable_id.sql modules/t/test-genome-DBs/homo_sapiens/core/exon_stable_id.txt modules/t/test-genome-DBs/homo_sapiens/core/exon_transcript.sql modules/t/test-genome-DBs/homo_sapiens/core/exon_transcript.txt modules/t/test-genome-DBs/homo_sapiens/core/external_db.sql modules/t/test-genome-DBs/homo_sapiens/core/external_db.txt modules/t/test-genome-DBs/homo_sapiens/core/external_synonym.sql modules/t/test-genome-DBs/homo_sapiens/core/external_synonym.txt modules/t/test-genome-DBs/homo_sapiens/core/gene.sql modules/t/test-genome-DBs/homo_sapiens/core/gene.txt modules/t/test-genome-DBs/homo_sapiens/core/gene_archive.sql modules/t/test-genome-DBs/homo_sapiens/core/gene_archive.txt modules/t/test-genome-DBs/homo_sapiens/core/gene_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/gene_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/gene_stable_id.sql modules/t/test-genome-DBs/homo_sapiens/core/gene_stable_id.txt modules/t/test-genome-DBs/homo_sapiens/core/go_xref.sql modules/t/test-genome-DBs/homo_sapiens/core/go_xref.txt modules/t/test-genome-DBs/homo_sapiens/core/identity_xref.sql modules/t/test-genome-DBs/homo_sapiens/core/identity_xref.txt modules/t/test-genome-DBs/homo_sapiens/core/interpro.sql modules/t/test-genome-DBs/homo_sapiens/core/interpro.txt modules/t/test-genome-DBs/homo_sapiens/core/karyotype.sql modules/t/test-genome-DBs/homo_sapiens/core/karyotype.txt modules/t/test-genome-DBs/homo_sapiens/core/map.sql modules/t/test-genome-DBs/homo_sapiens/core/map.txt modules/t/test-genome-DBs/homo_sapiens/core/mapping_session.sql modules/t/test-genome-DBs/homo_sapiens/core/mapping_session.txt modules/t/test-genome-DBs/homo_sapiens/core/marker.sql modules/t/test-genome-DBs/homo_sapiens/core/marker.txt modules/t/test-genome-DBs/homo_sapiens/core/marker_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/marker_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/marker_map_location.sql modules/t/test-genome-DBs/homo_sapiens/core/marker_map_location.txt modules/t/test-genome-DBs/homo_sapiens/core/marker_synonym.sql modules/t/test-genome-DBs/homo_sapiens/core/marker_synonym.txt modules/t/test-genome-DBs/homo_sapiens/core/meta.sql modules/t/test-genome-DBs/homo_sapiens/core/meta.txt modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.sql modules/t/test-genome-DBs/homo_sapiens/core/meta_coord.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_attrib.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_attrib.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_feature_misc_set.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_feature_misc_set.txt modules/t/test-genome-DBs/homo_sapiens/core/misc_set.sql modules/t/test-genome-DBs/homo_sapiens/core/misc_set.txt modules/t/test-genome-DBs/homo_sapiens/core/object_xref.sql modules/t/test-genome-DBs/homo_sapiens/core/object_xref.txt modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.sql modules/t/test-genome-DBs/homo_sapiens/core/oligo_array.txt modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.sql modules/t/test-genome-DBs/homo_sapiens/core/oligo_feature.txt modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.sql modules/t/test-genome-DBs/homo_sapiens/core/oligo_probe.txt modules/t/test-genome-DBs/homo_sapiens/core/peptide_archive.sql modules/t/test-genome-DBs/homo_sapiens/core/peptide_archive.txt 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modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.sql modules/t/test-genome-DBs/homo_sapiens/core/unmapped_object.txt modules/t/test-genome-DBs/homo_sapiens/core/unmapped_reason.sql modules/t/test-genome-DBs/homo_sapiens/core/unmapped_reason.txt modules/t/test-genome-DBs/homo_sapiens/core/xref.sql modules/t/test-genome-DBs/homo_sapiens/core/xref.txt modules/t/topLevelAssemblyMapper.t modules/t/transcript.t modules/t/translation.t modules/t/unconventionalTranscriptAssociation.t modules/t/unconventionalTranscriptAssociationAdaptor.t modules/t/unmappedObject.t modules/t/unmappedObjectAdaptor.t sql/README sql/foreign_keys.sql sql/patch_21_22.sql sql/patch_23_24.sql sql/patch_24_25.sql sql/patch_25_26.sql sql/patch_26_27.sql sql/patch_27_28.sql sql/patch_28_29.sql sql/patch_29_30.sql sql/patch_30_31.sql sql/patch_31_32.sql sql/patch_32_33.sql sql/patch_33_34.sql sql/patch_34_35.sql sql/patch_35_36.sql sql/patch_36_37.sql sql/patch_37_38.sql sql/patch_38_39_a.sql 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sql/patch_45_46_d.sql sql/patch_45_46_e.sql sql/patch_45_46_f.sql sql/patch_45_46_g.sql sql/patch_46_47_a.sql sql/patch_46_47_b.sql sql/patch_46_47_c.sql sql/patch_47_48_a.sql sql/patch_48_49_a.sql sql/patch_48_49_b.sql sql/patch_48_49_c.sql sql/patch_48_49_d.sql sql/patch_48_49_e.sql sql/populate_meta_coord.pl sql/table.sql sql/transfer_misc_affy.pl sql/vega_latest_schema.sql sql/vega_specific_tables.sql
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- 07 Feb, 2008 2 commits
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Andreas Kusalananda Kähäri authored
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Patrick Meidl authored
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- 06 Feb, 2008 1 commit
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Patrick Meidl authored
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- 05 Feb, 2008 1 commit
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Andreas Kusalananda Kähäri authored
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- 01 Feb, 2008 1 commit
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Nathan Johnson authored
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- 31 Jan, 2008 1 commit
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Glenn Proctor authored
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- 29 Jan, 2008 12 commits
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Ian Longden authored
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Ian Longden authored
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Daniel Rios authored
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Andreas Kusalananda Kähäri authored
fetchrow_arrayref().
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Andreas Kusalananda Kähäri authored
decrease the amount of code (slightly) in most of the feature-specific sub-classes.
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Ian Longden authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
Add missing ':' to 'RefSeq_dna:equus_caballus' in species section. Remove (comment out) non-existant source 'ncRNA::equus_caballus' from species section. For pongo_pygmaeus: Replace non-existant source 'UniGene::pongo_pygmaeus' with 'UniGene::MULTI' in species section.
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Glenn Proctor authored
Skip genes that are listed in Compara but aren't in the relevant core databases. Shouldn't be necessary in production runs but makes testing with previous Compara versions easier.
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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- 28 Jan, 2008 15 commits
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Ian Longden authored
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Jan-hinnerk Vogel authored
info for options added
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Simon White authored
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Andreas Kusalananda Kähäri authored
default external_db_id to 11000 ('UCSC') manually. -
Andreas Kusalananda Kähäri authored
Formatting.
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Glenn Proctor authored
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Glenn Proctor authored
Removed regulatory feature tables.
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Glenn Proctor authored
Added patch identifiers to meta table.
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Ian Longden authored
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- 25 Jan, 2008 2 commits
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Jan-hinnerk Vogel authored
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Will Spooner authored
fetch_all_by_feature_class method now throws if there is an orphen analysis_id foreign key in the "feature_class" table
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