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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]
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.
  --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

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.

Returns
-------
visualization : Visualization