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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/s
                       epp-tutorial.md#sample-datasets-default-parameters.
                                                               [default: 5000]
  --p-threads INTEGER  The number of threads to use.              [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).
  --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 : Int, optional
    The number of threads to use.
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.