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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

Options:
  --i-input-table ARTIFACT PATH FeatureTable[Frequency]
                                  The input table of counts.  [required]
  --i-input-tree ARTIFACT PATH Phylogeny[Rooted]
                                  The input tree with potential missing ids.
                                  [required]
  --o-output-table ARTIFACT PATH FeatureTable[Frequency]
                                  A table with features matching the tree
                                  tips.  [required if not passing --output-
                                  dir]
  --o-output-tree ARTIFACT PATH Hierarchy
                                  A tree with uniquely identifying ids.
                                  [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.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.