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.
--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 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.
