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collapse: Collapse features by their taxonomy at the specified levelΒΆ

Docstring:

Usage: qiime taxa collapse [OPTIONS]

  Collapse groups of features that have the same taxonomic assignment
  through the specified level. The frequencies of all features will be
  summed when they are collapsed.

Inputs:
  --i-table ARTIFACT FeatureTable[Frequency]
                         Feature table to be collapsed.             [required]
  --i-taxonomy ARTIFACT FeatureData[Taxonomy]
                         Taxonomic annotations for features in the provided
                         feature table. All features in the feature table must
                         have a corresponding taxonomic annotation. Taxonomic
                         annotations that are not present in the feature table
                         will be ignored.                           [required]
Parameters:
  --p-level INTEGER      The taxonomic level at which the features should be
                         collapsed. All ouput features will have exactly this
                         many levels of taxonomic annotation.       [required]
Outputs:
  --o-collapsed-table ARTIFACT FeatureTable[Frequency]
                         The resulting feature table, where all features are
                         now taxonomic annotations with the user-specified
                         number of levels.                          [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).
  --citations            Show citations and exit.
  --help                 Show this message and exit.

Import:

from qiime2.plugins.taxa.methods import collapse

Docstring:

Collapse features by their taxonomy at the specified level

Collapse groups of features that have the same taxonomic assignment through
the specified level. The frequencies of all features will be summed when
they are collapsed.

Parameters
----------
table : FeatureTable[Frequency]
    Feature table to be collapsed.
taxonomy : FeatureData[Taxonomy]
    Taxonomic annotations for features in the provided feature table. All
    features in the feature table must have a corresponding taxonomic
    annotation. Taxonomic annotations that are not present in the feature
    table will be ignored.
level : Int
    The taxonomic level at which the features should be collapsed. All
    ouput features will have exactly this many levels of taxonomic
    annotation.

Returns
-------
collapsed_table : FeatureTable[Frequency]
    The resulting feature table, where all features are now taxonomic
    annotations with the user-specified number of levels.