Developer API
Warning
If you are importing Augur in your Python scripts, use the public API.
While anything in this API can be imported from an external script, changes are not guaranteed to be versioned or included in the changelog.
These pages contain documentation automatically generated from docstrings within the Augur codebase. They are intended for people developing Augur.
- augur
add_version_alias()
make_parser()
run()
- augur.align
AlignmentError
analyse_insertions()
check_arguments()
check_duplicates()
ensure_reference_strain_present()
generate_alignment_cmd()
make_gaps_ambiguous()
postprocess()
prepare()
prettify_alignment()
prune_seqs_matching_alignment()
read_alignment()
read_reference()
read_sequences()
register_arguments()
register_parser()
remove_reference_sequence()
run()
strip_non_reference()
write_seqs()
- augur.ancestral
- augur.clades
- augur.dates
- augur.distance
- augur.errors
- augur.export
- augur.export_v1
add_core_args()
add_option_args()
add_tsv_metadata_to_nodes()
construct_author_info_v1()
convert_tree_to_json_structure()
ensure_config_is_v1()
get_root_sequence()
process_annotations()
process_colorings()
process_geographic_info()
process_panels()
recursively_decorate_tree_json_v1_schema()
register_parser()
run()
tree_layout()
- augur.export_v2
CustomOrderedDict
InvalidOption
are_clades_defined()
are_dates_defined()
are_mutations_defined()
configure_warnings()
convert_tree_to_json_structure()
counter_to_disambiguation_suffix()
create_author_data()
deprecated()
fatal()
get_config()
get_config_colorings_as_dict()
get_values_across_nodes()
is_valid()
node_data_prop_is_normal_trait()
orderKeys()
parse_node_data_and_metadata()
register_parser()
run()
set_annotations()
set_build_url()
set_colorings()
set_data_provenance()
set_description()
set_display_defaults()
set_filters()
set_geo_resolutions()
set_maintainers()
set_node_attrs_on_tree()
set_panels()
set_title()
update_deprecated_names()
validate_data_json()
validation_failure()
warning()
- augur.filenames
- augur.filter
- augur.frequencies
- augur.frequency_estimators
AlignmentKdeFrequencies
KdeFrequencies
TreeKdeFrequencies
TreeKdeFrequenciesError
alignment_frequencies
count_observations()
fix_freq()
float_to_datestring()
freq_est_clipped
frequency_estimator
get_pivots()
logit_inv()
logit_transform()
make_pivots()
nested_frequencies
pq()
running_average()
test_nested_estimator()
test_simple_estimator()
timestamp_to_float()
tree_frequencies
- augur.import
- augur.index
- augur.io
- augur.lbi
- augur.mask
- augur.measurements
- augur.parse
- augur.reconstruct_sequences
- augur.refine
- augur.sequence_traits
- augur.titer_model
- augur.titers
- augur.traits
- augur.translate
- augur.tree
- augur.types
- augur.util_support
- augur.utils
InvalidTreeError
NumpyJSONEncoder
annotate_parents_for_tree()
available_cpu_cores()
first_line()
get_augur_version()
get_json_name()
get_parent_name_by_child_name_for_tree()
json_to_tree()
load_features()
load_mask_sites()
nthreads_value()
read_bed_file()
read_colors()
read_config()
read_lat_longs()
read_mask_file()
read_node_data()
read_strains()
read_tree()
write_json()
- augur.validate
ValidateError
auspice_config_v2()
elide_path()
export_v1()
export_v2()
fatal()
format_path()
get_unique_keys()
grouped()
load_json()
load_json_schema()
measurements()
measurements_collection_config()
register_parser()
run()
validate()
validate_collection_config_fields()
validate_collection_display_defaults()
validate_json()
validate_measurements_config()
- augur.validate_export
- augur.version