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assign-ids: Assigns ids on internal nodes in the tree, and makes sure that they are consistent with the table columns.ΒΆ

Docstring:

Usage: qiime gneiss assign-ids [OPTIONS]

  Assigns UUIDs to uniquely identify internal nodes in the tree.  Also
  corrects for polytomies to create strictly bifurcating trees and aligns
  the table columns with the tree tip names

Inputs:
  --i-input-table ARTIFACT FeatureTable[Frequency]
                       The input table of counts.                   [required]
  --i-input-tree ARTIFACT
    Phylogeny[Rooted]  The input tree with potential missing ids.   [required]
Outputs:
  --o-output-table ARTIFACT FeatureTable[Frequency]
                       A table with features matching the tree tips.
                                                                    [required]
  --o-output-tree ARTIFACT
    Hierarchy          A tree with uniquely identifying ids.        [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.gneiss.methods import assign_ids

Docstring:

Assigns ids on internal nodes in the tree, and makes sure that they are
consistent with the table columns.

Assigns UUIDs to uniquely identify internal nodes in the tree.  Also
corrects for polytomies to create strictly bifurcating trees and aligns the
table columns with the tree tip names

Parameters
----------
input_table : FeatureTable[Frequency]
    The input table of counts.
input_tree : Phylogeny[Rooted]
    The input tree with potential missing ids.

Returns
-------
output_table : FeatureTable[Frequency]
    A table with features matching the tree tips.
output_tree : Hierarchy
    A tree with uniquely identifying ids.