Docstring:
Usage: qiime quality-control decontam-identify-batches [OPTIONS]
This method breaks an ASV table into batches based on the given metadata and
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]
--i-rep-seqs ARTIFACT FeatureData[Sequence]
Representative Sequences table which contaminate
seqeunces will be removed from [optional]
Parameters:
--m-metadata-file METADATA...
(multiple arguments metadata file indicating which samples in the
will be merged) experiment are control samples, assumes sample names
in file correspond to the `table` input parameter
[required]
--p-split-column TEXT input metadata columns that you wish to subset the
ASV table byNote: Column names must be in quotes and
delimited by a space [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 [required]
--p-filter-empty-features / --p-no-filter-empty-features
If true, features which are not present in a split
feature table are dropped. [optional]
--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]
--p-threshold NUMBER Select threshold cutoff for decontam algorithm
scores [default: 0.1]
--p-weighted / --p-no-weighted
weight the decontam scores by their associated read
number [default: True]
--p-bin-size NUMBER Select bin size for the histogram [default: 0.02]
Outputs:
--o-batch-subset-tables ARTIFACTS... Collection[FeatureTable[Frequency]]
Directory where feature tables split based on
metadata and parameter split-column values should be
written. [required]
--o-decontam-scores ARTIFACTS... Collection[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]
--o-score-histograms VISUALIZATION
The vizulaizer histograms for all decontam score
objects generated from the pipeline [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).
--recycle-pool TEXT Use a cache pool for pipeline resumption. QIIME 2
will cache your results in this pool for reuse by
future invocations. These pool are retained until
deleted by the user. If not provided, QIIME 2 will
create a pool which is automatically reused by
invocations of the same action and removed if the
action is successful. Note: these pools are local to
the cache you are using.
--no-recycle Do not recycle results from a previous failed
pipeline run or save the results from this run for
future recycling.
--parallel Execute your action in parallel. This flag will use
your default parallel config.
--parallel-config FILE Execute your action in parallel using a config at
the indicated path.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this pipeline. 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.
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.quality_control.pipelines import decontam_identify_batches
Docstring:
Identify contaminants in Batch Mode
This method breaks an ASV table into batches based on the given metadata
and 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
split_column : Str
input metadata columns that you wish to subset the ASV table byNote:
Column names must be in quotes and delimited by a space
method : Str % 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
rep_seqs : FeatureData[Sequence], optional
Representative Sequences table which contaminate seqeunces will be
removed from
filter_empty_features : Bool, optional
If true, features which are not present in a split feature table are
dropped.
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")
threshold : Float, optional
Select threshold cutoff for decontam algorithm scores
weighted : Bool, optional
weight the decontam scores by their associated read number
bin_size : Float, optional
Select bin size for the histogram
Returns
-------
batch_subset_tables : Collection[FeatureTable[Frequency]]
Directory where feature tables split based on metadata and parameter
split_column values should be written.
decontam_scores : Collection[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
score_histograms : Visualization
The vizulaizer histograms for all decontam score objects generated from
the pipeline
