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tabulate-seqs: View sequence associated with each feature

Citations

  • NCBI Resource Coordinators. Database resources of the national center for biotechnology information. Nucleic Acids Research, 45(D1):D12–D17, 2017. doi:10.1093/nar/gkw1071.

  • Mark Johnson, Irena Zaretskaya, Yan Raytselis, Yuri Merezhuk, Scott McGinnis, and Thomas L. Madden. Ncbi blast: a better web interface. Nucleic Acids Research, 36(suppl_2):W5–W9, 2008. doi:10.1093/nar/gkn201.

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