augur.export module¶
Export JSON files suitable for visualization with auspice.
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augur.export.
add_metadata_to_tree
(node, metadata)¶
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augur.export.
add_tsv_metadata_to_nodes
(nodes, meta_tsv, meta_json, extra_fields=['authors', 'url', 'accession'])¶ Only used for nextflu 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
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augur.export.
collect_strain_info
(node_data, tsv_path)¶ Integrate TSV metadata to the per-node metadata structure
For each node, gather the relevant author information (returned) and create a unique key inside node_metadata
author info maps the “authors” property present on tree nodes to further information about the paper etc
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augur.export.
convert_tree_to_json_structure
(node, metadata, div=0, nextflu_schema=False, 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) nextflu_schema – use nexflu schema (e.g. node[“attr”]). This is deprecated.
- returns
tree in JSON structure list of strains
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augur.export.
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.
get_traits
(node_data)¶
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augur.export.
process_annotations
(node_data)¶
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augur.export.
process_colorings
(jsn, color_mapping, nodes=None, node_metadata=None, nextflu=False)¶
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augur.export.
process_geographic_info
(jsn, lat_long_mapping, nextflu=False, node_metadata=None, nodes=None)¶
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augur.export.
process_panels
(user_panels, meta_json, nextflu=False)¶
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augur.export.
recursively_decorate_tree_json_nextflu_schema
(node, node_metadata, decorations)¶ This function is deprecated and is used to produce the nextflu-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.
register_arguments
(parser)¶
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augur.export.
run
(args)¶
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augur.export.
transfer_metadata_to_strains
(strains, raw_strain_info, traits)¶
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augur.export.
tree_layout
(T)¶ calculate tree layout. This function is deprecated, and only used for the nextflu JSON format