filter-seqs: Taxonomy-based feature sequence filter.¶

Docstring:

Usage: qiime taxa filter-seqs [OPTIONS]

  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.

Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                          Feature sequences to be filtered.         [required]
  --i-taxonomy ARTIFACT 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.                                  [required]
Parameters:
  --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 TEXT Choices('exact', 'contains')
                          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.                   [default: 'contains']
Outputs:
  --o-filtered-sequences ARTIFACT FeatureData[Sequence]
                          The taxonomy-filtered feature sequences.  [required]
Miscellaneous:
  --output-dir PATH       Output unspecified results to a directory
  --verbose / --quiet     Display verbose output to stdout and/or stderr
                          during execution of this action. Or silence output
                          if execution is successful (silence is golden).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --use-cache DIRECTORY   Specify the cache to be used for the intermediate
                          work of this action. If not provided, the default
                          cache under $TMP/qiime2/ will be used.
                          IMPORTANT FOR HPC USERS: If you are on an HPC system
                          and are using parallel execution it is important to
                          set this to a location that is globally accessible
                          to all nodes in the cluster.
  --help                  Show this message and exit.