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- 24 May, 2010 4 commits
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cvs2git authored
Sprout from master 2010-05-24 12:52:11 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Punish stable IDs that change biotype harder.' 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/add_species_aliases.pl misc-scripts/alternative_splicing/AltSplicingToolkit/AUTHORS misc-scripts/alternative_splicing/AltSplicingToolkit/BUGS misc-scripts/alternative_splicing/AltSplicingToolkit/COPYING misc-scripts/alternative_splicing/AltSplicingToolkit/ChangeLog misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL misc-scripts/alternative_splicing/AltSplicingToolkit/INSTALL.configure misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.am misc-scripts/alternative_splicing/AltSplicingToolkit/Makefile.in misc-scripts/alternative_splicing/AltSplicingToolkit/NEWS misc-scripts/alternative_splicing/AltSplicingToolkit/README misc-scripts/alternative_splicing/AltSplicingToolkit/THANKS misc-scripts/alternative_splicing/AltSplicingToolkit/aclocal.m4 misc-scripts/alternative_splicing/AltSplicingToolkit/configure.ac misc-scripts/alternative_splicing/AltSplicingToolkit/depcomp misc-scripts/alternative_splicing/AltSplicingToolkit/release_notes.txt misc-scripts/alternative_splicing/AltSplicingToolkit/src/Constants.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/Main.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.am misc-scripts/alternative_splicing/AltSplicingToolkit/src/Makefile.in misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Coordinates.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Coordinates.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/ExonChunk.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/ExonChunk.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Feature.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Feature.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Gene.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Gene.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/GeneFeature.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/GeneFeature.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/RegionChunk.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/RegionChunk.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEvent.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEvent.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventContainer.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventContainer.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventMatrix.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingEventMatrix.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingGraph.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingGraph.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingVertex.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/SplicingVertex.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Transcript.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/Transcript.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/as/TranscriptFeature.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/BioMartGffHandler.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffEventModel.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffParser.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffParser.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffSimpleHandler.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/GffSimpleHandler.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/SplicingEventGffGenerator.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/gff/SplicingEventGffGenerator.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/Logger.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/Logger.h misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.cpp misc-scripts/alternative_splicing/AltSplicingToolkit/src/util/StringUtil.h misc-scripts/alternative_splicing/Fetch_gff.pl misc-scripts/alternative_splicing/README.txt misc-scripts/alternative_splicing/load_alt_splice_gff.pl misc-scripts/analysis_description/analysis.descriptions misc-scripts/analysis_description/apply_rules.pl misc-scripts/analysis_description/chech_web_data_column.pl misc-scripts/analysis_description/load_analysis_descriptions.pl 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/cleanup_tmp_tables.sql 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/assembly_patches/README.TXT misc-scripts/assembly_patches/assembly_patch_load.pl misc-scripts/attribute_types/attrib_type.txt misc-scripts/attribute_types/upload_attributes.pl misc-scripts/canonical_transcripts/set_canonical_transcripts.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/constitutive_exon.pl misc-scripts/db-space.pl 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/ebi_search_dump/count_entries.sh misc-scripts/ebi_search_dump/dump_44.sh misc-scripts/ebi_search_dump/dump_ebi.pl misc-scripts/ebi_search_dump/ebi_search_dump.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/meta_coord/update_meta_coord.pl misc-scripts/meta_levels.pl misc-scripts/misc_feature/misc_set.descriptions misc-scripts/misc_feature/update_misc_set_descripitons.pl misc-scripts/ontology/README misc-scripts/ontology/scripts/add_subset_maps.pl misc-scripts/ontology/scripts/compute_closure.pl misc-scripts/ontology/scripts/demo1.pl misc-scripts/ontology/scripts/demo2.pl misc-scripts/ontology/scripts/load_OBO_file.pl misc-scripts/ontology/sql/table.sql misc-scripts/overlapping_regions.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/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/translation_attribs.pl misc-scripts/translation_attribs_wrapper.pl misc-scripts/unmapped_reason/unmapped_reason.txt misc-scripts/unmapped_reason/update_unmapped_reasons.pl misc-scripts/update_mapping_set.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/variation/nonsense_transcript_attribs.pl misc-scripts/web_stats.sh misc-scripts/xref_mapping/FAQ.txt misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm misc-scripts/xref_mapping/XrefMapper/CoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/CoreInfo.pm misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm misc-scripts/xref_mapping/XrefMapper/Interpro.pm misc-scripts/xref_mapping/XrefMapper/LoadMapper.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/ExonerateGappedBest1_culex.pm misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest_100_perc_id.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/ProcessMappings.pm misc-scripts/xref_mapping/XrefMapper/ProcessPaired.pm misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm misc-scripts/xref_mapping/XrefMapper/TestMappings.pm misc-scripts/xref_mapping/XrefMapper/VBCoordinateMapper.pm misc-scripts/xref_mapping/XrefMapper/XrefLoader.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/culex_pipiens.pm misc-scripts/xref_mapping/XrefMapper/danio_rerio.pm misc-scripts/xref_mapping/XrefMapper/db.pm misc-scripts/xref_mapping/XrefMapper/drosophila_ananassae.pm misc-scripts/xref_mapping/XrefMapper/drosophila_erecta.pm misc-scripts/xref_mapping/XrefMapper/drosophila_grimshawi.pm misc-scripts/xref_mapping/XrefMapper/drosophila_melanogaster.pm misc-scripts/xref_mapping/XrefMapper/drosophila_mojavensis.pm misc-scripts/xref_mapping/XrefMapper/drosophila_persimilis.pm misc-scripts/xref_mapping/XrefMapper/drosophila_pseudoobscura.pm misc-scripts/xref_mapping/XrefMapper/drosophila_sechellia.pm misc-scripts/xref_mapping/XrefMapper/drosophila_simulans.pm misc-scripts/xref_mapping/XrefMapper/drosophila_virilis.pm misc-scripts/xref_mapping/XrefMapper/drosophila_willistoni.pm misc-scripts/xref_mapping/XrefMapper/drosophila_yakuba.pm misc-scripts/xref_mapping/XrefMapper/fugu_rubripes.pm misc-scripts/xref_mapping/XrefMapper/homo_sapiens.pm misc-scripts/xref_mapping/XrefMapper/ixodes_scapularis.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/AedesCAPParser.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/DBASSParser.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/FantomParser.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/GOSlimParser.pm misc-scripts/xref_mapping/XrefParser/HGNCParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_CCDSParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm misc-scripts/xref_mapping/XrefParser/HGNC_curated_transcriptParser.pm misc-scripts/xref_mapping/XrefParser/HPAParser.pm misc-scripts/xref_mapping/XrefParser/IPIParser.pm misc-scripts/xref_mapping/XrefParser/IlluminaParser.pm misc-scripts/xref_mapping/XrefParser/IlluminaWGParser.pm misc-scripts/xref_mapping/XrefParser/InterproGoParser.pm misc-scripts/xref_mapping/XrefParser/InterproParser.pm misc-scripts/xref_mapping/XrefParser/IxodesCAPParser.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/MGI_CCDS_Parser.pm misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm misc-scripts/xref_mapping/XrefParser/MGI_Vega_Parser.pm misc-scripts/xref_mapping/XrefParser/MGI_curated_transcriptParser.pm misc-scripts/xref_mapping/XrefParser/MIMParser.pm misc-scripts/xref_mapping/XrefParser/Mim2GeneParser.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/UniProtDirectParser.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/VBCommunitySymbolParser.pm misc-scripts/xref_mapping/XrefParser/VbDirectParser.pm misc-scripts/xref_mapping/XrefParser/VbGFF3Parser.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/XrefParser/ncRNA_DBParser.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/core_vega_link_check.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/xref_tracker.pl misc-scripts/xref_mapping/xrefs_detailed_docs.txt misc-scripts/xref_mapping/xrefs_overview.txt misc-scripts/xref_projection/README misc-scripts/xref_projection/project_display_xrefs.pl misc-scripts/xref_projection/projection_db.sql misc-scripts/xref_projection/release_48.ini misc-scripts/xref_projection/submit_projections.pl modules/Bio/EnsEMBL/AlignStrainSlice.pm modules/Bio/EnsEMBL/Analysis.pm modules/Bio/EnsEMBL/Analysis/PairAlign.pm modules/Bio/EnsEMBL/Analysis/Programs.pm modules/Bio/EnsEMBL/ArchiveStableId.pm modules/Bio/EnsEMBL/AssemblyExceptionFeature.pm modules/Bio/EnsEMBL/AssemblyMapper.pm modules/Bio/EnsEMBL/Attribute.pm modules/Bio/EnsEMBL/BaseAlignFeature.pm modules/Bio/EnsEMBL/ChainedAssemblyMapper.pm modules/Bio/EnsEMBL/Collection.pm modules/Bio/EnsEMBL/Collection/Exon.pm modules/Bio/EnsEMBL/Collection/Gene.pm modules/Bio/EnsEMBL/Collection/RepeatFeature.pm modules/Bio/EnsEMBL/Collection/Transcript.pm modules/Bio/EnsEMBL/CoordSystem.pm modules/Bio/EnsEMBL/DB/ExternalFeatureFactoryI.pm modules/Bio/EnsEMBL/DBEntry.pm modules/Bio/EnsEMBL/DBLoader.pm modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm modules/Bio/EnsEMBL/DBSQL/AssemblyExceptionFeatureAdaptor.pm modules/Bio/EnsEMBL/DBSQL/AssemblyMapperAdaptor.pm modules/Bio/EnsEMBL/DBSQL/AssemblySliceAdaptor.pm modules/Bio/EnsEMBL/DBSQL/AttributeAdaptor.pm modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm modules/Bio/EnsEMBL/DBSQL/CompressedSequenceAdaptor.pm modules/Bio/EnsEMBL/DBSQL/CoordSystemAdaptor.pm modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm 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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 sql/patch_38_39_b.sql sql/patch_38_39_c.sql sql/patch_38_39_d.sql sql/patch_38_39_e.sql sql/patch_39_40_a.sql sql/patch_39_40_b.sql sql/patch_39_40_c.sql sql/patch_39_40_d.sql sql/patch_39_40_e.sql sql/patch_39_40_f.sql sql/patch_39_40_g.sql sql/patch_39_40_h.sql sql/patch_39_40_i.sql sql/patch_39_40_j.sql sql/patch_40_41_a.sql sql/patch_40_41_b.sql sql/patch_40_41_c.sql sql/patch_40_41_d.sql sql/patch_40_41_e.sql sql/patch_40_41_f.sql sql/patch_41_42_a.sql sql/patch_41_42_b.sql sql/patch_41_42_c.sql sql/patch_41_42_d.sql sql/patch_41_42_e.sql sql/patch_41_42_f.sql sql/patch_41_42_g.sql sql/patch_42_43_a.sql sql/patch_42_43_b.sql sql/patch_42_43_c.sql sql/patch_42_43_d.sql sql/patch_42_43_e.sql sql/patch_42_43_f.sql sql/patch_43_44_a.sql sql/patch_43_44_b.sql sql/patch_43_44_c.sql sql/patch_43_44_d.sql sql/patch_43_44_e.sql sql/patch_43_44_f.sql sql/patch_44_45_a.sql sql/patch_44_45_b.sql sql/patch_44_45_c.sql sql/patch_45_46_a.sql sql/patch_45_46_b.sql sql/patch_45_46_c.sql 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/patch_49_50_a.sql sql/patch_49_50_b.sql sql/patch_49_50_c.sql sql/patch_49_50_d.sql sql/patch_49_50_e.sql sql/patch_50_51_a.sql sql/patch_50_51_b.sql sql/patch_50_51_c.sql sql/patch_50_51_d.sql sql/patch_50_51_e.sql sql/patch_50_51_f.sql sql/patch_50_51_g.sql sql/patch_50_51_h.sql sql/patch_50_51_i.sql sql/patch_51_52_a.sql sql/patch_51_52_b.sql sql/patch_51_52_c.sql sql/patch_51_52_d.sql sql/patch_52_53_a.sql sql/patch_52_53_b.sql sql/patch_52_53_c.sql sql/patch_52_53_d.sql sql/patch_53_54_a.sql sql/patch_53_54_b.sql sql/patch_53_54_c.sql sql/patch_54_55_a.sql sql/patch_54_55_b.sql sql/patch_54_55_c.sql sql/patch_54_55_d.sql sql/patch_54_55_e.sql sql/patch_54_55_f.sql sql/patch_54_55_g.sql sql/patch_54_55_h.sql sql/patch_55_56_a.sql sql/patch_55_56_b.sql sql/patch_55_56_c.sql sql/patch_55_56_d.sql sql/patch_56_57_a.sql sql/patch_56_57_b.sql sql/patch_56_57_c.sql sql/patch_56_57_d.sql sql/patch_56_57_e.sql sql/patch_56_57_f.sql sql/patch_57_58_a.sql sql/populate_meta_coord.pl sql/table.sql sql/transfer_misc_affy.pl sql/vega_latest_schema.sql sql/vega_specific_tables.sql -
Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
to flush index data to file before copying. Add new flag: --noopt (Optional) Skip the optimization step. The database tables are optimized (as with "OPTIMIZE TABLE") to flush the index data onto disk. This may be a time consuming operation for very large tables. The --noopt flag disables the optimization.
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- 21 May, 2010 4 commits
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Ian Longden authored
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Nick Langridge authored -
Ian Longden authored
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Ian Longden authored
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- 20 May, 2010 1 commit
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Bronwen Aken authored
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- 19 May, 2010 3 commits
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Arnaud Kerhornou authored
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Arnaud Kerhornou authored
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Ian Longden authored
make LRGSlice inherit from Slice as the lrg regions are now strored in the asembly differently so can now inherit
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- 17 May, 2010 3 commits
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Ian Longden authored
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William McLaren authored
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Glenn Proctor authored
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- 14 May, 2010 1 commit
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Ian Longden authored
Get sequence using mfetch as fasta file has fasta of the pathced region and not of the contigs that make up this region
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- 12 May, 2010 1 commit
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Ian Longden authored
many changes but the most important is to only add seq_region mapping if the seq_region_ids are different
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- 11 May, 2010 1 commit
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Susan Fairley authored
Fixed bug that showed up on Y chromosome and problem with not deleting entries when no analysis description was present, see release 58 notes for more details.
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- 07 May, 2010 1 commit
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Ian Longden authored
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- 06 May, 2010 5 commits
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Andreas Kusalananda Kähäri authored
Arg [SPECIES]: (optional) string By default, all databases that are found on the server and that corresponds to the correct release are probed for aliases etc. For some people, depending on where they are in the world, this might be a slow operation. With the '-species' argument, one may reduce the startup time by restricting the set of databases that are probed to those of a particular species. Note that the latin name of the species is required, e.g., 'homo sapiens', 'gallus gallus', 'callithrix jacchus' etc. It may be the whole species name, or only the first part of the name, e.g. 'homo', 'gallus', or 'callithrix'. This will be used in matching against the name of the databases. -
Eugene Kulesha authored
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Eugene Kulesha authored
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Ian Longden authored
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Ian Longden authored
fixes for LRGSlices and new methods to find nearest gene to a feature (this will change greatly as this is a very simple case)
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- 05 May, 2010 3 commits
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
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- 04 May, 2010 4 commits
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Andy Yates authored
Regular expressions expanded to allow for 0-9 in the second portion of a database name. Original patch only allowed this in the first scan of names. Passed by Andreas
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Glenn Proctor authored
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Glenn Proctor authored
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Glenn Proctor authored
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- 23 Apr, 2010 1 commit
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Simon White authored
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- 22 Apr, 2010 4 commits
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Simon White authored
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Andreas Kusalananda Kähäri authored
We know that fetch_all_by_Transcript() (on a TranslationAdaptor) will return a list of translations, where the first one will always be the canonical translation (if there is one). Make use of this fact to make the routine slightly quicker.
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Andreas Kusalananda Kähäri authored
* Use fetch_all_by_Transcript() rather than translation() on the transcript to get the canonical translation (and any alternative translations). * ... then store the translation and any alternative translations. Solves a problem stopping genebuilders from copying genes from one database to another. -
Andreas Kusalananda Kähäri authored
* Correct documentation. * Use fetch_by_Transcript() to get canonical translation. * Modify SQL not to get canonical translation.
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- 21 Apr, 2010 1 commit
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Andreas Kusalananda Kähäri authored
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- 20 Apr, 2010 3 commits
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Gautier Koscielny authored
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Andreas Kusalananda Kähäri authored
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Andreas Kusalananda Kähäri authored
get_all_alternative_translations().
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