augur export¶
Note
The behavior of augur export
has changed in v6. Please see here for more details.
Export JSON files suitable for visualization with auspice.
usage: augur export [-h]
Augur export now needs you to define the JSON version you
want, e.g. `augur export v2`. ...
JSON SCHEMA¶
- Augur export now needs you to define the JSON version you want, e.g. `augur export v2`.
Possible choices: v2, v1
Sub-commands:¶
v2¶
Export version 2 JSON schema
augur export v2 [-h] --tree newick --node-data JSON [JSON ...] --output JSON
[--auspice-config JSON] [--title title]
[--maintainers name [name ...]] [--build-url url]
[--description description.md]
[--geo-resolutions trait [trait ...]]
[--color-by-metadata trait [trait ...]]
[--panels panels [panels ...]] [--metadata TSV] [--colors TSV]
[--lat-longs TSV] [--minify-json] [--include-root-sequence]
REQUIRED¶
- --tree, -t
Phylogenetic tree, usually output from augur refine
- --node-data
JSON files containing metadata for nodes in the tree
- --output
Ouput file (typically for visualisation in auspice)
DISPLAY CONFIGURATION¶
These control the display settings for auspice. You can supply a config JSON (which has all available options) or command line arguments (which are more limited but great to get started). Supplying both is fine too, command line args will overrule what is set in the config file!
- --auspice-config
Auspice configuration file
- --title
Title to be displayed by auspice
- --maintainers
Analysis maintained by, in format ‘Name <URL>’ ‘Name2 <URL>’, …
- --build-url
Build URL/repository to be displayed by Auspice
- --description
Markdown file with description of build and/or acknowledgements to be displayed by Auspice
- --geo-resolutions
Geographic traits to be displayed on map
- --color-by-metadata
Metadata columns to include as coloring options
- --panels
Possible choices: tree, map, entropy, frequencies
Restrict panel display in auspice. Options are [‘tree’, ‘map’, ‘entropy’, ‘frequencies’]. Ignore this option to display all available panels.
OPTIONAL INPUT FILES¶
- --metadata
Additional metadata for strains in the tree
- --colors
Custom color definitions
- --lat-longs
Latitudes and longitudes for geography traits (overrides built in mappings)
OPTIONAL SETTINGS¶
- --minify-json
export JSONs without indentation or line returns
Default: False
- --include-root-sequence
Export an additional JSON containing the root sequence (reference sequence for vcf) used to identify mutations. The filename will follow the pattern of <OUTPUT>_root-sequence.json for a main auspice JSON of <OUTPUT>.json
Default: False
v1¶
Export version 1 JSON schema (separate meta and tree JSONs)
augur export v1 [-h] --tree TREE --metadata METADATA --node-data NODE_DATA
[NODE_DATA ...] [--output-tree OUTPUT_TREE]
[--output-meta OUTPUT_META] [--auspice-config AUSPICE_CONFIG]
[--colors COLORS] [--lat-longs LAT_LONGS]
[--tree-name TREE_NAME] [--minify-json]
[--output-sequence OUTPUT_SEQUENCE] [--reference REFERENCE]
[--reference-translations REFERENCE_TRANSLATIONS]
REQUIRED¶
- --tree, -t
tree to perform trait reconstruction on
- --metadata
tsv file with sequence meta data
- --node-data
JSON files with meta data for each node
- --output-tree
JSON file name that is passed on to auspice (e.g., zika_tree.json).
- --output-meta
JSON file name that is passed on to auspice (e.g., zika_meta.json).
- --auspice-config
file with auspice configuration
OPTIONS¶
- --colors
file with color definitions
- --lat-longs
file latitudes and longitudes, overrides built in mappings
- --tree-name
Tree name (needed for tangle tree functionality)
Default: False
- --minify-json
export JSONs without indentation or line returns
Default: False
- --output-sequence
JSON file name that is passed on to auspice (e.g., zika_seq.json).
- --reference
reference sequence for export to browser, only vcf
- --reference-translations
reference translations for export to browser, only vcf