augur package
The top-level augur command which dispatches to subcommands.
- augur.add_default_command(parser)
Sets the default command to run when none is provided.
- augur.add_version_alias(parser)
Add –version as a (hidden) alias for the version command.
It’s not uncommon to blindly run a command with –version as the sole argument, so its useful to make that Just Work.
- augur.command_name(command)
Returns a short name for a command module.
- augur.make_parser()
- augur.run(argv)
Subpackages
- augur.util_support package
- Submodules
- augur.util_support.color_parser module
- augur.util_support.color_parser_line module
- augur.util_support.date_disambiguator module
- augur.util_support.metadata_file module
- augur.util_support.node_data module
- augur.util_support.node_data_file module
- augur.util_support.node_data_reader module
- augur.util_support.shell_command_runner module
- Submodules
Submodules
- augur.align module
- augur.ancestral module
- augur.clades module
- augur.distance module
- augur.export module
- augur.export_v1 module
- augur.export_v2 module
- augur.filenames module
- augur.filter module
- augur.frequencies module
- augur.frequency_estimators module
- augur.import module
- augur.import_beast module
- augur.index module
- augur.lbi module
- augur.mask module
- augur.parse module
- augur.reconstruct_sequences module
- augur.refine module
- augur.sequence_traits module
- augur.titer_model module
- augur.titers module
- augur.traits module
- augur.translate module
- augur.tree module
- augur.utils module
- augur.validate module
- augur.validate_export module
- augur.version module