Developer API
Warning
If you are importing Augur in your Python scripts, use the public API.
While anything in this API can be imported from an external script, changes are not guaranteed to be versioned or included in the changelog.
These pages contain documentation automatically generated from docstrings within the Augur codebase. They are intended for people developing Augur.
- augur
add_version_alias()make_parser()run()- augur.align
AlignmentErroranalyse_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
- augur.clades
- augur.dates
- augur.distance
- augur.errors
- augur.export
- 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
CustomOrderedDictInvalidOptionare_clades_defined()are_dates_defined()are_mutations_defined()configure_warnings()convert_tree_to_json_structure()counter_to_disambiguation_suffix()create_author_data()deprecated()fatal()get_config()get_config_colorings_as_dict()get_values_across_nodes()is_valid()node_data_prop_is_normal_trait()orderKeys()parse_node_data_and_metadata()register_parser()run()set_annotations()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
- augur.frequencies
- augur.frequency_estimators
AlignmentKdeFrequenciesKdeFrequenciesTreeKdeFrequenciesTreeKdeFrequenciesErroralignment_frequenciescount_observations()fix_freq()float_to_datestring()freq_est_clippedfrequency_estimatorget_pivots()logit_inv()logit_transform()make_pivots()nested_frequenciespq()running_average()test_nested_estimator()test_simple_estimator()timestamp_to_float()tree_frequencies
- augur.import
- augur.index
- augur.io
- augur.lbi
- augur.mask
- augur.measurements
- augur.parse
- augur.reconstruct_sequences
- augur.refine
- augur.sequence_traits
- augur.titer_model
- augur.titers
- augur.traits
- augur.translate
- augur.tree
- augur.types
- augur.util_support
- augur.utils
InvalidTreeErrorNumpyJSONEncoderannotate_parents_for_tree()available_cpu_cores()first_line()get_augur_version()get_json_name()get_parent_name_by_child_name_for_tree()json_to_tree()load_features()load_mask_sites()nthreads_value()read_bed_file()read_colors()read_config()read_lat_longs()read_mask_file()read_node_data()read_strains()read_tree()write_json()
- augur.validate
ValidateErrorauspice_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
- augur.version