Docstring:
Usage: qiime vsearch cluster-features-de-novo [OPTIONS]
Given a feature table and the associated feature sequences, cluster the
features based on user-specified percent identity threshold of their
sequences. This is not a general-purpose de novo clustering method, but
rather is intended to be used for clustering the results of quality-
filtering/dereplication methods, such as DADA2, or for re-clustering a
FeatureTable at a lower percent identity than it was originally clustered
at. When a group of features in the input table are clustered into a single
feature, the frequency of that single feature in a given sample is the sum
of the frequencies of the features that were clustered in that sample.
Feature identifiers and sequences will be inherited from the centroid
feature of each cluster. See the vsearch documentation for details on how
sequence clustering is performed.
Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
The sequences corresponding to the features in
table. [required]
--i-table ARTIFACT FeatureTable[Frequency]
The feature table to be clustered. [required]
Parameters:
--p-perc-identity PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True) The percent identity at which clustering should be
performed. This parameter maps to vsearch's --id
parameter. [required]
--p-strand TEXT Choices('plus', 'both')
Search plus (i.e., forward) or both (i.e., forward
and reverse complement) strands. [default: 'plus']
--p-threads NTHREADS The number of threads to use for computation.
Passing 0 will launch one thread per CPU core.
[default: 1]
Outputs:
--o-clustered-table ARTIFACT FeatureTable[Frequency]
The table following clustering of features.
[required]
--o-clustered-sequences ARTIFACT FeatureData[Sequence]
Sequences representing clustered features.
[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.
Examples:
# ### example: cluster features de novo
qiime vsearch cluster-features-de-novo \
--i-sequences seqs1.qza \
--i-table table1.qza \
--p-perc-identity 0.97 \
--p-strand plus \
--p-threads 1 \
--o-clustered-table clustered-table.qza \
--o-clustered-sequences clustered-sequences.qza
Import:
from qiime2.plugins.vsearch.methods import cluster_features_de_novo
Docstring:
De novo clustering of features.
Given a feature table and the associated feature sequences, cluster the
features based on user-specified percent identity threshold of their
sequences. This is not a general-purpose de novo clustering method, but
rather is intended to be used for clustering the results of quality-
filtering/dereplication methods, such as DADA2, or for re-clustering a
FeatureTable at a lower percent identity than it was originally clustered
at. When a group of features in the input table are clustered into a single
feature, the frequency of that single feature in a given sample is the sum
of the frequencies of the features that were clustered in that sample.
Feature identifiers and sequences will be inherited from the centroid
feature of each cluster. See the vsearch documentation for details on how
sequence clustering is performed.
Parameters
----------
sequences : FeatureData[Sequence]
The sequences corresponding to the features in table.
table : FeatureTable[Frequency]
The feature table to be clustered.
perc_identity : Float % Range(0, 1, inclusive_start=False, inclusive_end=True)
The percent identity at which clustering should be performed. This
parameter maps to vsearch's --id parameter.
strand : Str % Choices('plus', 'both'), optional
Search plus (i.e., forward) or both (i.e., forward and reverse
complement) strands.
threads : Threads, optional
The number of threads to use for computation. Passing 0 will launch one
thread per CPU core.
Returns
-------
clustered_table : FeatureTable[Frequency]
The table following clustering of features.
clustered_sequences : FeatureData[Sequence]
Sequences representing clustered features.
