Docstring:
Usage: qiime feature-table tabulate-seqs [OPTIONS]
Generate tabular view of feature identifier to sequence mapping, including
links to BLAST each sequence against the NCBI nt database.
Inputs:
--i-data ARTIFACT FeatureData[Sequence | AlignedSequence]
The feature sequences to be tabulated. [required]
--i-taxonomy ARTIFACTS... Collection[FeatureData[Taxonomy]]
The taxonomic classifications of the tabulated
features. [optional]
Parameters:
--m-metadata-file METADATA...
(multiple Any additional metadata for the tabulated features.
arguments will be
merged) [optional]
--p-merge-method TEXT Choices('strict', 'union', 'intersect')
Method that joins data sets [default: 'strict']
Outputs:
--o-visualization VISUALIZATION
[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: feature table tabulate seqs
qiime feature-table tabulate-seqs \
--i-data rep-seqs.qza \
--o-visualization rep-seqs.qzv
# ### example: feature table tabulate seqs single taxon
qiime feature-table tabulate-seqs \
--i-data rep-seqs-single-taxon.qza \
--i-taxonomy single-taxonomy.qza \
--o-visualization rep-seqs.qzv
# ### example: feature table tabulate seqs multi taxon
qiime feature-table tabulate-seqs \
--i-data rep-seqs-multi-taxon.qza \
--i-taxonomy multi-taxonomy/ \
--o-visualization rep-seqs.qzv
Import:
from qiime2.plugins.feature_table.visualizers import tabulate_seqs
Docstring:
View sequence associated with each feature
Generate tabular view of feature identifier to sequence mapping, including
links to BLAST each sequence against the NCBI nt database.
Parameters
----------
data : FeatureData[Sequence | AlignedSequence]
The feature sequences to be tabulated.
taxonomy : Collection[FeatureData[Taxonomy]], optional
The taxonomic classifications of the tabulated features.
metadata : Metadata, optional
Any additional metadata for the tabulated features.
merge_method : Str % Choices('strict', 'union', 'intersect'), optional
Method that joins data sets
Returns
-------
visualization : Visualization