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collapse: Collapse features by their taxonomy at the specified level¶
Docstring:
Usage: qiime taxa collapse [OPTIONS]
Collapse groups of features that have the same taxonomic assignment through
the specified level. The frequencies of all features will be summed when
they are collapsed.
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
Feature table to be collapsed. [required]
--i-taxonomy ARTIFACT FeatureData[Taxonomy]
Taxonomic annotations for features in the provided
feature table. All features in the feature table must
have a corresponding taxonomic annotation. Taxonomic
annotations that are not present in the feature table
will be ignored. [required]
Parameters:
--p-level INTEGER The taxonomic level at which the features should be
collapsed. All ouput features will have exactly this
many levels of taxonomic annotation. [required]
Outputs:
--o-collapsed-table ARTIFACT FeatureTable[Frequency]
The resulting feature table, where all features are
now taxonomic annotations with the user-specified
number of levels. [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.
Examples:
# ### example: collapse
qiime taxa collapse \
--i-table table.qza \
--i-taxonomy taxonomy.qza \
--p-level 6 \
--o-collapsed-table collapsed-table-l6.qza
Import:
from qiime2.plugins.taxa.methods import collapse
Docstring:
Collapse features by their taxonomy at the specified level
Collapse groups of features that have the same taxonomic assignment through
the specified level. The frequencies of all features will be summed when
they are collapsed.
Parameters
----------
table : FeatureTable[Frequency]
Feature table to be collapsed.
taxonomy : FeatureData[Taxonomy]
Taxonomic annotations for features in the provided feature table. All
features in the feature table must have a corresponding taxonomic
annotation. Taxonomic annotations that are not present in the feature
table will be ignored.
level : Int
The taxonomic level at which the features should be collapsed. All
ouput features will have exactly this many levels of taxonomic
annotation.
Returns
-------
collapsed_table : FeatureTable[Frequency]
The resulting feature table, where all features are now taxonomic
annotations with the user-specified number of levels.