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.
Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
Feature sequences to be filtered. [required]
--i-taxonomy ARTIFACT 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]
Parameters:
--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 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-sequences ARTIFACT FeatureData[Sequence]
The taxonomy-filtered feature sequences. [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_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('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_sequences : FeatureData[Sequence]
The taxonomy-filtered feature sequences.
