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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.           [required]
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).
  --example-data PATH    Write example data and exit.
  --citations            Show citations and exit.
  --use-cache DIRECTORY  Specify the cache to be used for the intermediate
                         work of this action. If not provided, the default
                         cache under $TMP/qiime2/ will be used.
                         IMPORTANT FOR HPC USERS: If you are on an HPC system
                         and are using parallel execution it is important to
                         set this to a location that is globally accessible to
                         all nodes in the cluster.
  --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]
    Reference taxonomic table that maps every OTU-ID into a taxonomic
    lineage string.

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