Docstring:
Usage: qiime rescript evaluate-seqs [OPTIONS]
Compute summary statistics on sequence artifact(s) and visualize. Summary
statistics include the number of unique sequences, sequence entropy, kmer
entropy, and sequence length distributions. This action is useful for both
reference taxonomies and classification results.
Inputs:
--i-sequences ARTIFACTS... List[FeatureData[Sequence]]
One or more sets of sequences to evaluate. [required]
Parameters:
--p-labels TEXT... List of labels to use for labeling evaluation results
List[Str] in the resulting visualization. Inputs are labeled with
labels in the order that each is input. If there are
fewer labels than inputs (or no labels), unnamed inputs
are labeled numerically in sequential order. Extra
labels are ignored. [optional]
--p-kmer-lengths INTEGERS...
Range(1, None) Sequence kmer lengths to optionally use for entropy
calculation. Warning: kmer entropy calculations may be
time-consuming for large sequence sets. [optional]
--p-subsample-kmers PROPORTION Range(0, 1, inclusive_start=False,
inclusive_end=True)
Optionally subsample sequences prior to kmer entropy
measurement. A fraction of the input sequences will be
randomly subsampled at the specified value.
[default: 1.0]
--p-palette TEXT Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2',
'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c',
'viridis', 'plasma', 'inferno', 'magma', 'cividis', 'terrain', 'rainbow',
'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', 'RdYlBu', 'RdYlGn',
'Spectral', 'coolwarm', 'bwr', 'seismic')
Color palette to use for plotting evaluation results.
[default: 'viridis']
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.
--help Show this message and exit.
Import:
from qiime2.plugins.rescript.visualizers import evaluate_seqs
Docstring:
Compute summary statistics on sequence artifact(s).
Compute summary statistics on sequence artifact(s) and visualize. Summary
statistics include the number of unique sequences, sequence entropy, kmer
entropy, and sequence length distributions. This action is useful for both
reference taxonomies and classification results.
Parameters
----------
sequences : List[FeatureData[Sequence]]
One or more sets of sequences to evaluate.
labels : List[Str], optional
List of labels to use for labeling evaluation results in the resulting
visualization. Inputs are labeled with labels in the order that each is
input. If there are fewer labels than inputs (or no labels), unnamed
inputs are labeled numerically in sequential order. Extra labels are
ignored.
kmer_lengths : List[Int % Range(1, None)], optional
Sequence kmer lengths to optionally use for entropy calculation.
Warning: kmer entropy calculations may be time-consuming for large
sequence sets.
subsample_kmers : Float % Range(0, 1, inclusive_start=False, inclusive_end=True), optional
Optionally subsample sequences prior to kmer entropy measurement. A
fraction of the input sequences will be randomly subsampled at the
specified value.
palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'cividis', 'terrain', 'rainbow', 'PiYG', 'PRGn', 'BrBG', 'PuOr', 'RdGy', 'RdBu', 'RdYlBu', 'RdYlGn', 'Spectral', 'coolwarm', 'bwr', 'seismic'), optional
Color palette to use for plotting evaluation results.
Returns
-------
visualization : Visualization
