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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.

Options:
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  Feature table to be collapsed.  [required]
  --i-taxonomy ARTIFACT PATH 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]
  --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]
  --o-collapsed-table ARTIFACT PATH FeatureTable[Frequency]
                                  The resulting feature table, where all
                                  features are now taxonomic annotations with
                                  the user-specified number of levels.
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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.