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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.

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