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filter-table: Taxonomy-based feature table filter.ΒΆ

Docstring:

Usage: qiime taxa filter-table [OPTIONS]

  This method filters features from a table based on their taxonomic
  annotations. Features can be retained in the resulting table by specifying
  one or more include search terms, and can be filtered out of the resulting
  table 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. Any samples that have a total frequency of zero after filtering
  will be removed from the resulting table.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  Feature table to be filtered.  [required]
  --i-taxonomy ARTIFACT PATH FeatureData[Taxonomy]
                                  Taxonomic annotations for features in the
                                  provided feature table. All features in the
                                  feature table must have a corresponding
                                  taxonomic annotation. Taxonomic annotations
                                  for features that are not present in the
                                  feature table will be ignored.  [required]
  --p-include TEXT                One or more search terms that indicate which
                                  taxa should be included in the resulting
                                  table. 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
                                  table. 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-table ARTIFACT PATH FeatureTable[Frequency]
                                  The taxonomy-filtered feature table.
                                  [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_table

Docstring:

Taxonomy-based feature table filter.

This method filters features from a table based on their taxonomic
annotations. Features can be retained in the resulting table by specifying
one or more include search terms, and can be filtered out of the resulting
table 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. Any samples that have a total frequency of zero after filtering
will be removed from the resulting table.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to be filtered.
taxonomy : FeatureData[Taxonomy]
    Taxonomic annotations for features in the provided feature table. All
    features in the feature table must have a corresponding taxonomic
    annotation. Taxonomic annotations for features that are not present in
    the feature table will be ignored.
include : Str, optional
    One or more search terms that indicate which taxa should be included in
    the resulting table. 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 table. 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_table : FeatureTable[Frequency]
    The taxonomy-filtered feature table.