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 for visualization with Auspice
augur export v2 [-h] --tree newick --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 ...]]
[--metadata-columns METADATA_COLUMNS [METADATA_COLUMNS ...]]
[--panels panels [panels ...]] [--node-data JSON [JSON ...]]
[--metadata FILE]
[--metadata-delimiters METADATA_DELIMITERS [METADATA_DELIMITERS ...]]
[--metadata-id-columns METADATA_ID_COLUMNS [METADATA_ID_COLUMNS ...]]
[--colors FILE] [--lat-longs TSV]
[--minify-json | --no-minify-json]
[[--include-root-sequence | --include-root-sequence-inline]]
[--validation-mode {error,warn,skip}] [--skip-validation]
REQUIRED
- --tree, -t
Phylogenetic tree, usually output from augur refine
- --output
Output 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
- --metadata-columns
Metadata columns to export in addition to columns provided by –color-by-metadata or colorings in the Auspice configuration file. These columns will not be used as coloring options in Auspice but will be visible in the tree.
- --panels
Possible choices: tree, map, entropy, frequencies, measurements
Restrict panel display in auspice. Options are [‘tree’, ‘map’, ‘entropy’, ‘frequencies’, ‘measurements’]. Ignore this option to display all available panels.
OPTIONAL INPUT FILES
- --node-data
JSON files containing metadata for nodes in the tree
- --metadata
Additional metadata for strains in the tree
- --metadata-delimiters
delimiters to accept when reading a metadata file. Only one delimiter will be inferred.
Default:
(',', '\t')
- --metadata-id-columns
names of possible metadata columns containing identifier information, ordered by priority. Only one ID column will be inferred.
Default:
('strain', 'name')
- --colors
Custom color definitions, one per line in the format TRAIT_TYPEtTRAIT_VALUEtHEX_CODE
- --lat-longs
Latitudes and longitudes for geography traits (overrides built in mappings)
OPTIONAL MINIFY SETTINGS
By default, output JSON files (both main and sidecar) are automatically minimized if the size of the un-minified main JSON file exceeds 5 MB. Use these options to override that behavior.
- --minify-json
always export JSONs without indentation or line returns.
Default:
False
- --no-minify-json
always export JSONs to be human readable.
Default:
False
OPTIONAL ROOT-SEQUENCE SETTINGS
The root-sequences describe the sequences (nuc + aa) for the parent of the tree’s root-node. They may represent a reference sequence or the inferred sequence at the root node, depending on how they were generated. The data is taken directly from the reference key within the provided node-data JSONs. These arguments are mutually exclusive.
- --include-root-sequence
Export as an additional JSON. The filename will follow the pattern of <OUTPUT>_root-sequence.json for a main auspice JSON of <OUTPUT>.json
Default:
False
- --include-root-sequence-inline
Export the root sequence within the dataset JSON. This should only be used for small genomes for file size reasons.
Default:
False
OTHER OPTIONAL SETTINGS
- --validation-mode
Possible choices: error, warn, skip
Control if optional validation checks are performed and what happens if they fail.
‘error’ and ‘warn’ modes perform validation and emit messages about failed validation checks. ‘error’ mode causes a non-zero exit status if any validation checks failed, while ‘warn’ does not.
‘skip’ mode performs no validation.
Note that some validation checks are non-optional and as such are not affected by this setting.
Default:
error
- --skip-validation
Skip validation of input/output files, equivalent to –validation-mode=skip. Use at your own risk!
v1
Export version 1 JSON schema (separate meta and tree JSONs) for visualization with Auspice
augur export v1 [-h] --tree TREE --metadata FILE
[--metadata-delimiters METADATA_DELIMITERS [METADATA_DELIMITERS ...]]
--node-data NODE_DATA [NODE_DATA ...]
[--output-tree OUTPUT_TREE] [--output-meta OUTPUT_META]
[--auspice-config AUSPICE_CONFIG] [--colors FILE]
[--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
sequence metadata
- --metadata-delimiters
delimiters to accept when reading a metadata file. Only one delimiter will be inferred.
Default:
(',', '\t')
- --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
Custom color definitions, one per line in the format TRAIT_TYPEtTRAIT_VALUEtHEX_CODE
- --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