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.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency¹ | PresenceAbsence²]
Feature table to be filtered. [required]
--i-taxonomy ARTIFACT 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]
Parameters:
--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 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-table ARTIFACT FeatureTable[Frequency¹ | PresenceAbsence²]
The taxonomy-filtered feature table. [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).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--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[Frequency¹ | PresenceAbsence²]
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('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_table : FeatureTable[Frequency¹ | PresenceAbsence²]
The taxonomy-filtered feature table.
