# 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.

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.