qiime taxa filter-seqs (version 2019.4)

--i-sequences: ARTIFACT FeatureData[Sequence] Feature sequences to be filtered. [required]:

--p-include: TEXT One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included. [optional]:

--p-exclude: TEXT One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded. [optional]:

--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']:

--p-mode: :

Taxonomy-based feature sequence filter.

This method filters sequences based on their taxonomic annotations. Features can be retained in the result by specifying one or more include search terms, and can be filtered out of the result by specifying one or more exclude search terms. If both include and exclude are provided, the inclusion critera will be applied before the exclusion critera. Either include or exclude terms (or both) must be provided.

Parameters

sequences : FeatureData[Sequence]: Feature sequences to be filtered.
taxonomy : FeatureData[Taxonomy]: Taxonomic annotations for features in the provided feature sequences. All features in the feature sequences must have a corresponding taxonomic annotation. Taxonomic annotations for features that are not present in the feature sequences will be ignored.
include : Str, optional: One or more search terms that indicate which taxa should be included in the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.
exclude : Str, optional: One or more search terms that indicate which taxa should be excluded from the resulting sequences. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.
query_delimiter : Str, optional: The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations.
mode : Str % Choices('exact', 'contains'), optional: Mode for determining if a search term matches a taxonomic annotation. "contains" requires that the annotation has the term as a substring; "exact" requires that the annotation is a perfect match to a search term.

Returns

filtered_sequences : FeatureData[Sequence]: The taxonomy-filtered feature sequences.