augur package
The top-level augur command which dispatches to subcommands.
- 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.make_parser()
- augur.run(argv)
Subpackages
- augur.curate package
create_shared_parser()
register_parser()
run()
validate_records()
- Submodules
- augur.curate.abbreviate_authors module
- augur.curate.apply_geolocation_rules module
- augur.curate.apply_record_annotations module
- augur.curate.format_dates module
- augur.curate.format_dates_directives module
- augur.curate.normalize_strings module
- augur.curate.parse_genbank_location module
- augur.curate.passthru module
- augur.curate.rename module
- augur.curate.titlecase module
- augur.curate.transform_strain_name module
- augur.data package
- augur.dates package
- augur.filter package
register_arguments()
register_parser()
run()
- Submodules
- augur.filter.constants module
- augur.filter.include_exclude_rules module
apply_filters()
construct_filters()
extract_variables()
filter_by_ambiguous_date()
filter_by_exclude()
filter_by_exclude_all()
filter_by_exclude_where()
filter_by_max_date()
filter_by_max_length()
filter_by_min_date()
filter_by_min_length()
filter_by_non_nucleotide()
filter_by_query()
filter_by_sequence_index()
force_include_strains()
force_include_where()
parse_filter_query()
skip_group_by_with_ambiguous_day()
skip_group_by_with_ambiguous_month()
skip_group_by_with_ambiguous_year()
- augur.filter.io module
- augur.filter.subsample module
- augur.filter.validate_arguments module
- augur.filter.weights_file module
- augur.import_ package
- augur.io package
- augur.measurements package
- augur.util_support package
Submodules
- augur.align module
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 module
- augur.argparse_ module
- augur.clades module
- augur.debug module
- augur.distance module
- augur.errors module
- augur.export module
- augur.export_v1 module
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 module
ConfidenceCategorical
ConfidenceNumeric
CustomOrderedDict
EmptyDict
InvalidOption
are_mutations_defined()
attr_confidence()
configure_warnings()
convert_tree_to_json_structure()
counter_to_disambiguation_suffix()
create_author_data()
create_branch_labels()
create_branch_mutations()
deprecated()
fatal()
format_number()
get_additional_metadata_columns()
get_config()
get_config_colorings_as_dict()
get_values_across_nodes()
is_node_attr_defined()
is_numeric()
is_valid()
node_data_prop_is_normal_trait()
node_div()
orderKeys()
parse_node_data_and_metadata()
register_parser()
run()
set_annotations()
set_branch_attrs_on_tree()
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.frequencies module
- augur.frequency_estimators module
AlignmentKdeFrequencies
KdeFrequencies
TreeKdeFrequencies
TreeKdeFrequenciesError
alignment_frequencies
count_observations()
fix_freq()
float_to_datestring()
freq_est_clipped
freq_est_clipped.dtps
freq_est_clipped.fe
freq_est_clipped.good_pivots
freq_est_clipped.good_tps
freq_est_clipped.obs
freq_est_clipped.pivot_freq
freq_est_clipped.pivot_lower_cutoff
freq_est_clipped.pivot_upper_cutoff
freq_est_clipped.pivots
freq_est_clipped.tps
freq_est_clipped.valid
freq_est_clipped.learn()
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.index module
- augur.lbi module
- augur.mask module
- augur.merge module
- augur.parse module
- augur.read_file module
- augur.reconstruct_sequences module
- augur.refine module
- augur.sequence_traits module
- augur.titer_model module
InsufficientDataException
SubstitutionModel
SubstitutionModel.annotate_tree()
SubstitutionModel.collapse_colinear_mutations()
SubstitutionModel.compile_substitution_effects()
SubstitutionModel.determine_relevant_mutations()
SubstitutionModel.get_mutations()
SubstitutionModel.make_seqgraph()
SubstitutionModel.predict_titer()
SubstitutionModel.prepare()
SubstitutionModel.train()
TiterCollection
TiterModel
TiterModel.assign_titers()
TiterModel.compile_potencies()
TiterModel.compile_titers()
TiterModel.compile_virus_effects()
TiterModel.fit_func()
TiterModel.fit_l1reg()
TiterModel.fit_nnl1reg()
TiterModel.fit_nnl2reg()
TiterModel.fit_nnls()
TiterModel.make_training_set()
TiterModel.reference_virus_statistic()
TiterModel.titer_stats()
TiterModel.validate()
TreeModel
- augur.titers module
- augur.traits module
- augur.translate module
- augur.tree module
- augur.types module
- augur.utils module
AugurJSONEncoder
BytesWrittenCounterIO
InvalidTreeError
annotate_parents_for_tree()
available_cpu_cores()
first_line()
genome_features_to_auspice_annotation()
get_augur_version()
get_json_name()
get_parent_name_by_child_name_for_tree()
json_size()
json_to_tree()
load_features()
load_mask_sites()
nthreads_value()
parse_genes_argument()
read_bed_file()
read_colors()
read_config()
read_entries()
read_lat_longs()
read_mask_file()
read_node_data()
read_strains()
read_tree()
write_json()
- augur.validate module
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 module
- augur.version module
- augur.write_file module