# filter-table: Taxonomy-based feature table filter.¶

#### 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.