augur.export_v2 module

Export JSON files suitable for visualization with auspice.

exception augur.export_v2.InvalidOption

Bases: Exception

augur.export_v2.are_clades_defined(node_attrs)
augur.export_v2.are_dates_defined(node_attrs)
augur.export_v2.are_mutations_defined(node_attrs)
augur.export_v2.configure_warnings()
augur.export_v2.convert_tree_to_json_structure(node, metadata, div=0)

converts the Biopython tree structure to a dictionary that can be written to file as a json. This is called recursively. Creates the name property & divergence on each node

input

node – node for which top level dict is produced. div – cumulative divergence (root = 0). False → divergence won’t be exported.

returns

tree in JSON structure list of strains

augur.export_v2.create_author_data(node_attrs)

Gather the authors which appear in the metadata and create the author info structure with unique keys

augur.export_v2.deprecated(message)
augur.export_v2.fatal(message)
augur.export_v2.get_config(args)
augur.export_v2.get_config_colorings_as_dict(config)
augur.export_v2.get_root_sequence(root_node, ref=None, translations=None)

create a json structure that contains the sequence of the root, both as nucleotide and as translations. This allows look-up of the sequence for all states, including those that are not variable.

Parameters

  • root_node (dict) – data associated with the node

  • ref (str, optional) – filename of the root sequence

  • translations (str, optional) – file name of translations

Returns

dict of nucleotide sequence and translations

Return type

dict

augur.export_v2.get_values_across_nodes(node_attrs, key)
augur.export_v2.is_valid(value)
augur.export_v2.node_data_prop_is_normal_trait(name)
augur.export_v2.parse_node_data_and_metadata(T, node_data_files, metadata_file)
augur.export_v2.register_arguments_v2(subparsers)
augur.export_v2.run_v2(args)
augur.export_v2.set_annotations(data_json, node_data)
augur.export_v2.set_build_url(data_json, config, cmd_line_build_url)
augur.export_v2.set_colorings(data_json, config, command_line_colorings, metadata_names, node_data_colorings, provided_colors, node_attrs)
augur.export_v2.set_description(data_json, cmd_line_description_file)

Read Markdown file provided by cmd_line_description_file and set meta.description in data_json to the text provided.

augur.export_v2.set_display_defaults(data_json, config)
augur.export_v2.set_filters(data_json, config)
augur.export_v2.set_geo_resolutions(data_json, config, command_line_traits, lat_long_mapping, node_attrs)

appropriately combine provided geo resolutions from command line & config files and associate with lat/longs.

augur.export_v2.set_maintainers(data_json, config, cmd_line_maintainers)
augur.export_v2.set_node_attrs_on_tree(data_json, node_attrs)

Assign desired colorings, metadata etc to the tree structure

Parameters

  • data_json (dict) –

  • node_attrs (dict) – keys: strain names. values: dict with keys -> all available metadata (even “excluded” keys), values -> data (string / numeric / bool)

augur.export_v2.set_panels(data_json, config, cmd_line_panels)
augur.export_v2.set_title(data_json, config, cmd_line_title)
augur.export_v2.update_deprecated_names(name)
augur.export_v2.validate_data_json(filename)
augur.export_v2.warning(message)