augur exportļ
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 SCHEMAļ
- Augur export now needs you to define the JSON version you want, e.g. `augur export v2`.
Possible choices: v2, v1
Sub-commandsļ
v2ļ
Export version 2 JSON schema for visualization with Auspice
augur export v2 [-h] --tree newick --output JSON
[--auspice-config JSON [JSON ...]] [--title title]
[--maintainers name [name ...]] [--build-url url]
[--description description.md] [--warning text or file]
[--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]
[--output-auspice-config JSON]
REQUIREDļ
- --tree, -t
Phylogenetic tree, usually output from augur refine
- --output
Output file (typically for visualisation in auspice)
DISPLAY CONFIGURATIONļ
These control the display settings for auspice. Config JSON(s) allow customisation of all available options whereas individual command line arguments 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. Multiple JSONs will be merged together, and lists present in multiple configs will be merged by extending the original list.
- --auspice-config
Auspice configuration file(s)
Default:
[]
- --title
Title to be displayed by auspice
- --maintainers
Analysis maintained by, in format āName <URL>ā āName2 <URL>ā, ā¦
- --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
- --warning
Text or file in Markdown format to be displayed as a warning banner by Auspice
- --geo-resolutions
Geographic traits to be displayed on map
- --color-by-metadata
Metadata columns to include as coloring options. Ignores columns named ānoneā, so please rename them if you would like to include them as colorings.
- --metadata-columns
Metadata columns to export in addition to columns provided by ācolor-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. Ignores columns named ānoneā, so please rename them if you would like to include them as metadata fields.
- --panels
Possible choices: tree, map, entropy, frequencies, measurements
Restrict panel display in auspice. Options are [ātreeā, āmapā, āentropyā, āfrequenciesā, āmeasurementsā]. Ignore this option to display all available panels.
OPTIONAL INPUT FILESļ
- --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. See this file for the format:
<https://github.com/nextstrain/augur/blob/30.0.1/augur/data/lat_longs.tsv>. This file provides the default set of latitudes and longitudes. An additional file specified by this option will extend the default set. Duplicates based on the first two columns will be resolved by taking the coordinates from the user-provided file.
OPTIONAL MINIFY SETTINGSļ
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 SETTINGSļ
The root-sequences describe the sequences (nuc + aa) for the parent of the treeās 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 SETTINGSļ
- --validation-mode
Possible choices: error, warn, skip
Control if optional validation checks are performed and what happens if they fail.
āerrorā and āwarnā modes perform validation and emit messages about failed validation checks. āerrorā mode causes a non-zero exit status if any validation checks failed, while āwarnā does not.
āskipā 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 āvalidation-mode=skip. Use at your own risk!
- --output-auspice-config
Write out the merged auspice configuration file for debugging purposes etc. File is only written if you provide multiple config files via āauspice-config.
v1ļ
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]
REQUIREDļ
- --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
OPTIONSļ
- --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