augur

The top-level augur command which dispatches to subcommands.

augur.add_version_alias(parser)

Add –version as a (hidden) alias for the version command.

It’s not uncommon to blindly run a command with –version as the sole argument, so its useful to make that Just Work.

augur.make_parser()

augur.run(argv)

• augur.align
  • AlignmentError
  • analyse_insertions()
  • check_arguments()
  • check_duplicates()
  • ensure_reference_strain_present()
  • generate_alignment_cmd()
  • make_gaps_ambiguous()
  • postprocess()
  • prepare()
  • prettify_alignment()
  • prune_seqs_matching_alignment()
  • read_alignment()
  • read_reference()
  • read_sequences()
  • register_arguments()
  • register_parser()
  • remove_reference_sequence()
  • run()
  • strip_non_reference()
  • write_seqs()
• augur.ancestral
  • ancestral_sequence_inference()
  • collect_mutations()
  • collect_sequences()
  • create_mask()
  • register_parser()
  • run()
  • run_ancestral()
  • validate_arguments()
• augur.clades
  • assign_clades()
  • ensure_no_multiple_mutations()
  • get_reference_sequence_from_root_node()
  • is_node_in_clade()
  • parse_nodes()
  • read_in_clade_definitions()
  • register_parser()
  • run()
  • warn_if_clades_not_found()
• augur.dates
  • get_iso_year_week()
  • get_numerical_date_from_value()
  • get_numerical_dates()
  • is_date_ambiguous()
  • numeric_date()
  • numeric_date_type()
  • augur.dates.ambiguous_date
    • AmbiguousDate
      • AmbiguousDate.assert_only_less_significant_uncertainty()
      • AmbiguousDate.fmt_components
      • AmbiguousDate.range()
      • AmbiguousDate.regex
      • AmbiguousDate.uncertain_date_components
    • get_bounds()
    • max_day_for_year_month()
    • resolve_uncertain_int()
    • tuple_to_date()
  • augur.dates.errors
    • InvalidDate
    • InvalidYearBounds
• augur.distance
  • get_distance_between_nodes()
  • get_distances_to_all_pairs()
  • get_distances_to_last_ancestor()
  • get_distances_to_root()
  • read_distance_map()
  • register_parser()
  • run()
• augur.errors
  • AugurError
• augur.export
  • register_parser()
• augur.export_v1
  • add_core_args()
  • add_option_args()
  • add_tsv_metadata_to_nodes()
  • construct_author_info_v1()
  • convert_tree_to_json_structure()
  • ensure_config_is_v1()
  • get_root_sequence()
  • process_annotations()
  • process_colorings()
  • process_geographic_info()
  • process_panels()
  • recursively_decorate_tree_json_v1_schema()
  • register_parser()
  • run()
  • tree_layout()
• augur.export_v2
  • CustomOrderedDict
    • CustomOrderedDict.move_to_end_if_present()
    • CustomOrderedDict.set_order()
  • InvalidOption
  • are_mutations_defined()
  • configure_warnings()
  • convert_tree_to_json_structure()
  • counter_to_disambiguation_suffix()
  • create_author_data()
  • create_branch_labels()
  • create_branch_mutations()
  • deprecated()
  • fatal()
  • get_additional_metadata_columns()
  • get_config()
  • get_config_colorings_as_dict()
  • get_values_across_nodes()
  • is_node_attr_defined()
  • is_valid()
  • node_data_prop_is_normal_trait()
  • node_div()
  • orderKeys()
  • parse_node_data_and_metadata()
  • register_parser()
  • run()
  • set_annotations()
  • set_branch_attrs_on_tree()
  • set_build_url()
  • set_colorings()
  • set_data_provenance()
  • set_description()
  • set_display_defaults()
  • set_filters()
  • set_geo_resolutions()
  • set_maintainers()
  • set_node_attrs_on_tree()
  • set_panels()
  • set_title()
  • update_deprecated_names()
  • validate_data_json()
  • validation_failure()
  • warning()
• augur.filenames
• augur.filter
  • register_arguments()
  • register_parser()
  • run()
  • augur.filter._run
    • run()
  • augur.filter.include_exclude_rules
    • apply_filters()
    • construct_filters()
    • extract_variables()
    • filter_by_ambiguous_date()
    • filter_by_exclude()
    • filter_by_exclude_all()
    • filter_by_exclude_where()
    • filter_by_max_date()
    • filter_by_max_length()
    • filter_by_min_date()
    • filter_by_min_length()
    • filter_by_non_nucleotide()
    • filter_by_query()
    • filter_by_sequence_index()
    • force_include_strains()
    • force_include_where()
    • parse_filter_query()
    • skip_group_by_with_ambiguous_day()
    • skip_group_by_with_ambiguous_month()
    • skip_group_by_with_ambiguous_year()
  • augur.filter.io
    • cleanup_outputs()
    • column_type_pair()
    • get_useful_metadata_columns()
    • read_priority_scores()
    • write_metadata_based_outputs()
  • augur.filter.subsample
    • PriorityQueue
      • PriorityQueue.add()
      • PriorityQueue.get_items()
    • TooManyGroupsError
    • calculate_sequences_per_group()
    • create_queues_by_group()
    • get_groups_for_subsampling()
  • augur.filter.validate_arguments
    • validate_arguments()
• augur.frequencies
  • format_frequencies()
  • register_parser()
  • run()
• augur.frequency_estimators
  • AlignmentKdeFrequencies
    • AlignmentKdeFrequencies.estimate()
  • KdeFrequencies
    • KdeFrequencies.estimate_frequencies()
    • KdeFrequencies.from_json()
    • KdeFrequencies.get_densities_for_observations()
    • KdeFrequencies.get_density_for_observation()
    • KdeFrequencies.get_params()
    • KdeFrequencies.normalize_to_frequencies()
    • KdeFrequencies.to_json()
  • TreeKdeFrequencies
    • TreeKdeFrequencies.estimate()
    • TreeKdeFrequencies.estimate_tip_frequencies_to_proportion()
    • TreeKdeFrequencies.tip_passes_filters()
  • TreeKdeFrequenciesError
  • alignment_frequencies
    • alignment_frequencies.calc_confidence()
    • alignment_frequencies.estimate_genotype_frequency()
    • alignment_frequencies.mutation_frequencies()
  • count_observations()
  • fix_freq()
  • float_to_datestring()
  • freq_est_clipped
    • freq_est_clipped.dtps
    • freq_est_clipped.fe
    • freq_est_clipped.good_pivots
    • freq_est_clipped.good_tps
    • freq_est_clipped.obs
    • freq_est_clipped.pivot_freq
    • freq_est_clipped.pivot_lower_cutoff
    • freq_est_clipped.pivot_upper_cutoff
    • freq_est_clipped.pivots
    • freq_est_clipped.tps
    • freq_est_clipped.valid
    • freq_est_clipped.learn()
  • frequency_estimator
    • frequency_estimator.initial_guess()
    • frequency_estimator.learn()
    • frequency_estimator.stiffLH()
  • get_pivots()
  • logit_inv()
  • logit_transform()
  • make_pivots()
  • nested_frequencies
    • nested_frequencies.calc_freqs()
  • pq()
  • running_average()
  • test_nested_estimator()
  • test_simple_estimator()
  • timestamp_to_float()
  • tree_frequencies
    • tree_frequencies.calc_confidence()
    • tree_frequencies.estimate_clade_frequencies()
    • tree_frequencies.prepare()
• augur.import
  • register_parser()
• augur.index
  • index_sequence()
  • index_sequences()
  • index_vcf()
  • register_parser()
  • run()
• augur.io
  • augur.io.file
    • open_file()
  • augur.io.json
    • JSONDecodeError
      • JSONDecodeError.CONTEXT_LENGTH
    • JsonEncoder
      • JsonEncoder.default()
    • as_json()
    • contextualize_char()
    • dump_ndjson()
    • load_json()
    • load_ndjson()
    • mark_char()
    • shorten_as_json()
    • shorten_left()
  • augur.io.metadata
    • InvalidDelimiter
    • Metadata
      • Metadata.columns
      • Metadata.delimiter
      • Metadata.id_column
      • Metadata.open()
      • Metadata.path
      • Metadata.rows()
    • read_metadata()
    • read_metadata_with_sequences()
    • read_table_to_dict()
    • write_records_to_tsv()
  • augur.io.print
    • print_err()
  • augur.io.sequences
    • read_sequences()
    • write_records_to_fasta()
    • write_sequences()
  • augur.io.shell_command_runner
    • ShellCommandRunner
      • ShellCommandRunner.invoke_command()
      • ShellCommandRunner.modified_env
      • ShellCommandRunner.print_error()
      • ShellCommandRunner.print_error_message()
      • ShellCommandRunner.run()
      • ShellCommandRunner.shell_args
      • ShellCommandRunner.shell_executable
      • ShellCommandRunner.signal_from_error()
    • run_shell_command()
  • augur.io.vcf
    • is_vcf()
    • write_VCF_translation()
    • write_vcf()
• augur.lbi
  • calculate_LBI()
  • register_parser()
  • run()
  • select_nodes_in_season()
• augur.mask
  • get_chrom_name()
  • mask_fasta()
  • mask_sequence()
  • mask_vcf()
  • register_arguments()
  • register_parser()
  • run()
• augur.measurements
  • register_parser()
  • augur.measurements.concat
    • register_parser()
    • run()
  • augur.measurements.export
    • register_parser()
    • run()
• augur.parse
  • fix_dates()
  • parse_sequence()
  • prettify()
  • register_parser()
  • run()
• augur.reconstruct_sequences
  • get_sequence()
  • load_alignments()
  • register_parser()
  • run()
• augur.refine
  • collect_node_data()
  • refine()
  • register_parser()
  • run()
• augur.sequence_traits
  • annotate_strains()
  • annotate_strains_by_gene()
  • attach_features()
  • read_in_features()
  • read_in_translate_vcf()
  • register_parser()
  • run()
• augur.titer_model
  • InsufficientDataException
  • SubstitutionModel
    • SubstitutionModel.annotate_tree()
    • SubstitutionModel.collapse_colinear_mutations()
    • SubstitutionModel.compile_substitution_effects()
    • SubstitutionModel.determine_relevant_mutations()
    • SubstitutionModel.get_mutations()
    • SubstitutionModel.make_seqgraph()
    • SubstitutionModel.predict_titer()
    • SubstitutionModel.prepare()
    • SubstitutionModel.train()
  • TiterCollection
    • TiterCollection.count_strains()
    • TiterCollection.determine_autologous_titers()
    • TiterCollection.filter_strains()
    • TiterCollection.load_from_file()
    • TiterCollection.normalize()
    • TiterCollection.normalize_titers()
    • TiterCollection.read_titers()
    • TiterCollection.strain_census()
  • TiterModel
    • TiterModel.assign_titers()
    • TiterModel.compile_potencies()
    • TiterModel.compile_titers()
    • TiterModel.compile_virus_effects()
    • TiterModel.fit_func()
    • TiterModel.fit_l1reg()
    • TiterModel.fit_nnl1reg()
    • TiterModel.fit_nnl2reg()
    • TiterModel.fit_nnls()
    • TiterModel.make_training_set()
    • TiterModel.reference_virus_statistic()
    • TiterModel.titer_stats()
    • TiterModel.validate()
  • TreeModel
    • TreeModel.cross_validate()
    • TreeModel.find_titer_splits()
    • TreeModel.get_path_no_terminals()
    • TreeModel.make_treegraph()
    • TreeModel.predict_titer()
    • TreeModel.prepare()
    • TreeModel.prepare_tree()
    • TreeModel.train()
• augur.titers
  • infer_substitution_model
    • infer_substitution_model.run()
  • infer_tree_model
    • infer_tree_model.run()
  • register_parser()
• augur.traits
  • mugration_inference()
  • register_parser()
  • run()
• augur.translate
  • MismatchNodeError
  • MissingNodeError
  • NoVariationError
  • assign_aa_fasta()
  • assign_aa_vcf()
  • check_arg_combinations()
  • construct_mut()
  • register_parser()
  • run()
  • safe_translate()
  • sequences_json()
  • sequences_vcf()
  • translate_feature()
  • translate_vcf_feature()
• augur.tree
  • ConflictingArgumentsException
  • build_fasttree()
  • build_iqtree()
  • build_raxml()
  • check_conflicting_args()
  • find_executable()
  • mask_sites_in_multiple_sequence_alignment()
  • register_parser()
  • run()
  • write_out_informative_fasta()
• augur.types
  • ArgparseEnum
    • ArgparseEnum.argtype()
  • DataErrorMethod
    • DataErrorMethod.ERROR_ALL
    • DataErrorMethod.ERROR_FIRST
    • DataErrorMethod.SILENT
    • DataErrorMethod.WARN
  • EmptyOutputReportingMethod
    • EmptyOutputReportingMethod.ERROR
    • EmptyOutputReportingMethod.SILENT
    • EmptyOutputReportingMethod.WARN
  • ValidationMode
    • ValidationMode.ERROR
    • ValidationMode.SKIP
    • ValidationMode.WARN
• augur.util_support
  • augur.util_support.color_parser
    • ColorParser
      • ColorParser.mapping
      • ColorParser.parse_file()
  • augur.util_support.color_parser_line
    • ColorParserLine
      • ColorParserLine.fields
      • ColorParserLine.hex_code
      • ColorParserLine.is_comment_or_blank()
      • ColorParserLine.pair()
      • ColorParserLine.trait
      • ColorParserLine.trait_value
  • augur.util_support.node_data
    • DuplicatedNonDictAttributeError
    • NodeData
      • NodeData.deep_add_or_update()
      • NodeData.update()
  • augur.util_support.node_data_file
    • NodeDataFile
      • NodeDataFile.annotations
      • NodeDataFile.branches
      • NodeDataFile.generated_by
      • NodeDataFile.is_generated_by_incompatible_augur
      • NodeDataFile.items()
      • NodeDataFile.nodes
      • NodeDataFile.validate()
    • NodeDataObject
  • augur.util_support.node_data_reader
    • NodeDataReader
      • NodeDataReader.build_node_data()
      • NodeDataReader.check_against_tree_file()
      • NodeDataReader.node_data_files
      • NodeDataReader.node_names_from_tree_file
      • NodeDataReader.read()
• augur.utils
  • AugurJSONEncoder
    • AugurJSONEncoder.default()
  • BytesWrittenCounterIO
    • BytesWrittenCounterIO.write()
    • BytesWrittenCounterIO.written
  • InvalidTreeError
  • annotate_parents_for_tree()
  • available_cpu_cores()
  • first_line()
  • genome_features_to_auspice_annotation()
  • get_augur_version()
  • get_json_name()
  • get_parent_name_by_child_name_for_tree()
  • json_size()
  • json_to_tree()
  • load_features()
  • load_mask_sites()
  • nthreads_value()
  • parse_genes_argument()
  • read_bed_file()
  • read_colors()
  • read_config()
  • read_entries()
  • read_lat_longs()
  • read_mask_file()
  • read_node_data()
  • read_strains()
  • read_tree()
  • write_json()
• augur.validate
  • ValidateError
  • auspice_config_v2()
  • elide_path()
  • export_v1()
  • export_v2()
  • fatal()
  • format_path()
  • get_unique_keys()
  • grouped()
  • load_json()
  • load_json_schema()
  • measurements()
  • measurements_collection_config()
  • register_parser()
  • run()
  • validate()
  • validate_collection_config_fields()
  • validate_collection_display_defaults()
  • validate_json()
  • validate_measurements_config()
• augur.validate_export
  • collectAAMutationGenesV1()
  • collectBranchLabels()
  • collectMutationGenes()
  • collectTreeAttrsV1()
  • collectTreeAttrsV2()
  • ensure_no_duplicate_names()
  • verifyMainJSONIsInternallyConsistent()
  • verifyMetaAndOrTreeJSONsAreInternallyConsistent()
• augur.version
  • register_parser()
  • run()