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 ...]]
                [--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]
                [--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

--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 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

--include-root-sequence-inline

Export the root sequence (reference sequence for vcf) used to identify mutations as part of the main dataset JSON. This should only be used for small genomes for file size reasons.

Default: False

--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