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classify-otus-experimental: Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.ΒΆ

Docstring:

Usage: qiime fragment-insertion classify-otus-experimental
           [OPTIONS]

  Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
  for every inserted fragment. Then, look up the reference lineage string in
  the reference taxonomy.

Inputs:
  --i-representative-sequences ARTIFACT FeatureData[Sequence]
                       The sequences used for a 'sepp' run to produce the
                       'tree'.                                      [required]
  --i-tree ARTIFACT    The tree resulting from inserting fragments into a
    Phylogeny[Rooted]  reference phylogeny, i.e. the output of function 'sepp'
                                                                    [required]
  --i-reference-taxonomy ARTIFACT FeatureData[Taxonomy]
                       Reference taxonomic table that maps every OTU-ID into
                       a taxonomic lineage string.                  [optional]
Outputs:
  --o-classification ARTIFACT FeatureData[Taxonomy]
                       Taxonomic lineages for inserted fragments.   [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.fragment_insertion.methods import classify_otus_experimental

Docstring:

Experimental: Obtain taxonomic lineages, by finding closest OTU in
reference phylogeny.

Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
for every inserted fragment. Then, look up the reference lineage string in
the reference taxonomy.

Parameters
----------
representative_sequences : FeatureData[Sequence]
    The sequences used for a 'sepp' run to produce the 'tree'.
tree : Phylogeny[Rooted]
    The tree resulting from inserting fragments into a reference phylogeny,
    i.e. the output of function 'sepp'
reference_taxonomy : FeatureData[Taxonomy], optional
    Reference taxonomic table that maps every OTU-ID into a taxonomic
    lineage string.

Returns
-------
classification : FeatureData[Taxonomy]
    Taxonomic lineages for inserted fragments.