augur.export_v1 module¶
Augur Version 1-specific helpers for exporting JSON files suitable for visualization with auspice.
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augur.export_v1.
add_core_args
(parser)¶
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augur.export_v1.
add_option_args
(parser)¶
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augur.export_v1.
add_tsv_metadata_to_nodes
(nodes, meta_tsv, meta_json, extra_fields=['authors', 'url', 'accession'])¶ Only used for v1 schema compatability
Add the relevent fields from meta_tsv to the nodes (both are dictionaries keyed off of strain names) * the relevent fields are found by scanning the meta json together with the extra_fields param
author info maps the “authors” property present on tree nodes to further information about the paper etc
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augur.export_v1.
convert_tree_to_json_structure
(node, metadata, div=0, strains=None)¶ converts the Biopython tree structure to a dictionary that can be written to file as a json. This is called recursively. Creates the strain property & divergence on each node
- input
node – node for which top level dict is produced. div – cumulative divergence (root = 0)
- returns
tree in JSON structure list of strains
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augur.export_v1.
ensure_config_is_v1
(config)¶ Check the provided config file is intended for augur export v1 (not v2, v3 etc) Side effects: may print a warning & exit
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augur.export_v1.
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_v1.
process_annotations
(node_data)¶
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augur.export_v1.
process_colorings
(jsn, color_mapping, nodes=None, node_metadata=None)¶
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augur.export_v1.
process_geographic_info
(jsn, lat_long_mapping, node_metadata=None, nodes=None)¶
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augur.export_v1.
process_panels
(user_panels, meta_json)¶
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augur.export_v1.
recursively_decorate_tree_json_v1_schema
(node, node_metadata, decorations)¶ This function is deprecated and is used to produce the v1-compatable JSON format
For given decorations, add information from node_metadata to each node in the tree. * decorations must have property “key” which is the key used to insert into the node and the default key used to access node_metadata * if decorations has property “lookup_key”, this is used to access node meta_data instead * if decorations has property “is_attr” (and it’s value is True) then the result is inserted into node[“attr”]
returns Null
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augur.export_v1.
register_arguments_v1
(subparsers)¶
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augur.export_v1.
run_v1
(args)¶
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augur.export_v1.
tree_layout
(T)¶ calculate tree layout. This function is deprecated, and only used for the v1 JSON format