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summarize: Summarize counts per sample.¶
Docstring:
Usage: qiime demux summarize [OPTIONS]
Summarize counts per sample for all samples, and generate interactive
positional quality plots based on `n` randomly selected sequences.
Inputs:
--i-data ARTIFACT SampleData[SequencesWithQuality |
PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
The demultiplexed sequences to be summarized.
[required]
Parameters:
--p-n INTEGER The number of sequences that should be selected at
random for quality score plots. The quality plots
will present the average positional qualities across
all of the sequences selected. If input sequences are
paired end, plots will be generated for both forward
and reverse reads for the same `n` sequences.
[default: 10000]
Outputs:
--o-visualization VISUALIZATION
[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: demux
qiime demux summarize \
--i-data demux.qza \
--o-visualization visualization.qzv
Import:
from qiime2.plugins.demux.visualizers import summarize
Docstring:
Summarize counts per sample.
Summarize counts per sample for all samples, and generate interactive
positional quality plots based on `n` randomly selected sequences.
Parameters
----------
data : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
The demultiplexed sequences to be summarized.
n : Int, optional
The number of sequences that should be selected at random for quality
score plots. The quality plots will present the average positional
qualities across all of the sequences selected. If input sequences are
paired end, plots will be generated for both forward and reverse reads
for the same `n` sequences.
Returns
-------
visualization : Visualization