augur.filter package
Filter and subsample a sequence set.
SeqKit is used behind the scenes to handle FASTA files, but this should be considered an implementation detail that may change in the future. The CLI program seqkit must be available. If it’s not on PATH (or you want to use a version different from what’s on PATH), set the SEQKIT environment variable to path of the desired seqkit executable.
VCFtools is used behind the scenes to handle VCF files, but this should be considered an implementation detail that may change in the future. The CLI program vcftools must be available on PATH.
- 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_ids()
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