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sepp: Insert fragment sequences using SEPP into reference phylogenies.ΒΆ

Docstring:

Usage: qiime fragment-insertion sepp [OPTIONS]

  Perform fragment insertion of sequences using the SEPP algorithm.

Inputs:
  --i-representative-sequences ARTIFACT FeatureData[Sequence]
                        The sequences to insert into the reference tree.
                                                                    [required]
  --i-reference-database ARTIFACT SeppReferenceDatabase
                        The reference database to insert the representative
                        sequences into.                             [required]
Parameters:
  --p-alignment-subset-size INTEGER
                        Each placement subset is further broken into subsets
                        of at most these many sequences and a separate HMM is
                        trained on each subset.                [default: 1000]
  --p-placement-subset-size INTEGER
                        The tree is divided into subsets such that each
                        subset includes at most these many subsets. The
                        placement step places the fragment on only one subset,
                        determined based on alignment scores. Further reading:
                        https://github.com/smirarab/sepp/blob/master/tutorial/
                        sepp-tutorial.md#sample-datasets-default-parameters.
                                                               [default: 5000]
  --p-threads NTHREADS  The number of threads to use. Pass 0 to use one per
                        available core.                           [default: 1]
  --p-debug / --p-no-debug
                        Collect additional run information to STDOUT for
                        debugging. Temporary directories will not be removed
                        if run fails.                         [default: False]
Outputs:
  --o-tree ARTIFACT     The tree with inserted feature data.
    Phylogeny[Rooted]                                               [required]
  --o-placements ARTIFACT
    Placements          Information about the feature placements within the
                        reference tree.                             [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.
  --help                Show this message and exit.

Import:

from qiime2.plugins.fragment_insertion.methods import sepp

Docstring:

Insert fragment sequences using SEPP into reference phylogenies.

Perform fragment insertion of sequences using the SEPP algorithm.

Parameters
----------
representative_sequences : FeatureData[Sequence]
    The sequences to insert into the reference tree.
reference_database : SeppReferenceDatabase
    The reference database to insert the representative sequences into.
alignment_subset_size : Int, optional
    Each placement subset is further broken into subsets of at most these
    many sequences and a separate HMM is trained on each subset.
placement_subset_size : Int, optional
    The tree is divided into subsets such that each subset includes at most
    these many subsets. The placement step places the fragment on only one
    subset, determined based on alignment scores. Further reading:
    https://github.com/smirarab/sepp/blob/master/tutorial/sepp-
    tutorial.md#sample-datasets-default-parameters.
threads : Threads, optional
    The number of threads to use. Pass 0 to use one per available core.
debug : Bool, optional
    Collect additional run information to STDOUT for debugging. Temporary
    directories will not be removed if run fails.

Returns
-------
tree : Phylogeny[Rooted]
    The tree with inserted feature data.
placements : Placements
    Information about the feature placements within the reference tree.