augur.export_v2 module¶
Export JSON files suitable for visualization with auspice.
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exception
augur.export_v2.
InvalidOption
¶ Bases:
Exception
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augur.export_v2.
are_clades_defined
(node_attrs)¶
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augur.export_v2.
are_dates_defined
(node_attrs)¶
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augur.export_v2.
are_mutations_defined
(node_attrs)¶
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augur.export_v2.
configure_warnings
()¶
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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
Gather the authors which appear in the metadata and create the author info structure with unique keys
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augur.export_v2.
deprecated
(message)¶
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augur.export_v2.
fatal
(message)¶
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augur.export_v2.
get_config
(args)¶
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augur.export_v2.
get_config_colorings_as_dict
(config)¶
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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
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augur.export_v2.
get_values_across_nodes
(node_attrs, key)¶
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augur.export_v2.
is_valid
(value)¶
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augur.export_v2.
node_data_prop_is_normal_trait
(name)¶
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augur.export_v2.
parse_node_data_and_metadata
(T, node_data_files, metadata_file)¶
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augur.export_v2.
register_arguments_v2
(subparsers)¶
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augur.export_v2.
run_v2
(args)¶
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augur.export_v2.
set_annotations
(data_json, node_data)¶
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augur.export_v2.
set_build_url
(data_json, config, cmd_line_build_url)¶
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augur.export_v2.
set_colorings
(data_json, config, command_line_colorings, metadata_names, node_data_colorings, provided_colors, node_attrs)¶
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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.
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augur.export_v2.
set_display_defaults
(data_json, config)¶
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augur.export_v2.
set_filters
(data_json, config)¶
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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.
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augur.export_v2.
set_maintainers
(data_json, config, cmd_line_maintainers)¶
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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)
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augur.export_v2.
set_panels
(data_json, config, cmd_line_panels)¶
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augur.export_v2.
set_title
(data_json, config, cmd_line_title)¶
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augur.export_v2.
update_deprecated_names
(name)¶
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augur.export_v2.
validate_data_json
(filename)¶
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augur.export_v2.
warning
(message)¶