augur.filter package
Filter and subsample a sequence set.
- augur.filter.register_arguments(parser)
Add arguments to parser. Kept as a separate function than register_parser to continue to support unit tests that use this function to create argparser.
- augur.filter.register_parser(parent_subparsers)
- augur.filter.run(args)
filter and subsample a set of sequences into an analysis set
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