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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.

Options:
  --i-sequences ARTIFACT PATH FeatureData[Sequence]
                                  Feature sequences to be filtered.
                                  [required]
  --i-taxonomy ARTIFACT PATH 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]
  --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 [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]
  --o-filtered-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The taxonomy-filtered feature sequences.
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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({'contains', 'exact'}), 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.