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

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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.taxa.methods import filter_seqs

Docstring:

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.