Docstring:
Usage: qiime quality-control decontam-identify [OPTIONS]
This method identifies contaminant sequences from an OTU or ASV table and
reports them to the user
Inputs:
--i-table ARTIFACT FeatureTable[Frequency]
Feature table which contaminate sequences will be
identified from [required]
Parameters:
--m-metadata-file METADATA...
(multiple metadata file indicating which samples in the
arguments will be experiment are control samples, assumes sample names
merged) in file correspond to the `table` input parameter
[required]
--p-method TEXT Choices('combined', 'frequency', 'prevalence')
Select how to which method to id contaminants with;
Prevalence: Utilizes control ASVs/OTUs to identify
contaminants, Frequency: Utilizes sample
concentration information to identify contaminants,
Combined: Utilizes both Prevalence and Frequency
methods when identifying contaminants
[default: 'prevalence']
--p-freq-concentration-column TEXT
Input column name that has concentration information
for the samples [optional]
--p-prev-control-column TEXT
Input column name containing experimental or control
sample metadata [optional]
--p-prev-control-indicator TEXT
indicate the control sample identifier (e.g.
"control" or "blank") [optional]
Outputs:
--o-decontam-scores ARTIFACT FeatureData[DecontamScore]
The resulting table of scores from the decontam
algorithm which scores each feature on how likely
they are to be a contaminant sequence [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.quality_control.methods import decontam_identify
Docstring:
Identify contaminants
This method identifies contaminant sequences from an OTU or ASV table and
reports them to the user
Parameters
----------
table : FeatureTable[Frequency]
Feature table which contaminate sequences will be identified from
metadata : Metadata
metadata file indicating which samples in the experiment are control
samples, assumes sample names in file correspond to the `table` input
parameter
method : Str % Choices('combined', 'frequency', 'prevalence'), optional
Select how to which method to id contaminants with; Prevalence:
Utilizes control ASVs/OTUs to identify contaminants, Frequency:
Utilizes sample concentration information to identify contaminants,
Combined: Utilizes both Prevalence and Frequency methods when
identifying contaminants
freq_concentration_column : Str, optional
Input column name that has concentration information for the samples
prev_control_column : Str, optional
Input column name containing experimental or control sample metadata
prev_control_indicator : Str, optional
indicate the control sample identifier (e.g. "control" or "blank")
Returns
-------
decontam_scores : FeatureData[DecontamScore]
The resulting table of scores from the decontam algorithm which scores
each feature on how likely they are to be a contaminant sequence
