Docstring:
Usage: qiime phylogeny filter-table [OPTIONS]
Remove features from a feature table if their identifiers are not tip
identifiers in tree.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency² |
PresenceAbsence³] Feature table that features should be filtered from.
[required]
--i-tree ARTIFACT Phylogeny[Rooted | Unrooted]
Tree where tip identifiers are the feature
identifiers that should be retained in the table.
[required]
Outputs:
--o-filtered-table ARTIFACT FeatureTable[Frequency¹ | RelativeFrequency²
| PresenceAbsence³] The resulting feature table. [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.phylogeny.methods import filter_table
Docstring:
Remove features from table if they're not present in tree.
Remove features from a feature table if their identifiers are not tip
identifiers in tree.
Parameters
----------
table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³]
Feature table that features should be filtered from.
tree : Phylogeny[Rooted | Unrooted]
Tree where tip identifiers are the feature identifiers that should be
retained in the table.
Returns
-------
filtered_table : FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³]
The resulting feature table.