如何在Qiime中操作feature-classifier并理解其相关参数设置

最编程 2024-07-23 18:05:18

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Qiime feature-classifier使用参数

qiime feature-classifier classify-sklearn --help

Usage: qiime feature-classifier classify-sklearn [OPTIONS]

  Classify reads by taxon using a fitted classifier.

Inputs:
  --i-reads ARTIFACT FeatureData[Sequence]
                         The feature data to be classified.         [required]
  --i-classifier ARTIFACT
    TaxonomicClassifier  The taxonomic classifier for classifying the reads.
                                                                    [required]
Parameters:
  --p-reads-per-batch INTEGER
    Range(0, None)       Number of reads to process in each batch. If "auto",
                         this parameter is autoscaled to min( number of query
                         sequences / n-jobs, 20000).              [default: 0]
  --p-n-jobs INTEGER     The maximum number of concurrently worker processes.
                         If -1 all CPUs are used. If 1 is given, no parallel
                         computing code is used at all, which is useful for
                         debugging. For n-jobs below -1, (n_cpus + 1 + n-jobs)
                         are used. Thus for n-jobs = -2, all CPUs but one are
                         used.                                    [default: 1]
  --p-pre-dispatch TEXT  "all" or expression, as in "3*n_jobs". The number of
                         batches (of tasks) to be pre-dispatched.
                                                         [default: '2*n_jobs']
  --p-confidence VALUE Float % Range(0, 1, inclusive_end=True) | Str %
    Choices('disable')   Confidence threshold for limiting taxonomic depth.
                         Set to "disable" to disable confidence calculation,
                         or 0 to calculate confidence but not apply it to
                         limit the taxonomic depth of the assignments.
                                                                [default: 0.7]
  --p-read-orientation TEXT Choices('same', 'reverse-complement', 'auto')
                         Direction of reads with respect to reference
                         sequences. same will cause reads to be classified
                         unchanged; reverse-complement will cause reads to be
                         reversed and complemented prior to classification.
                         "auto" will autodetect orientation based on the
                         confidence estimates for the first 100 reads.
                                                             [default: 'auto']
Outputs:
  --o-classification ARTIFACT FeatureData[Taxonomy]
                                                                    [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).
  --examples             Show usage examples and exit.
  --citations            Show citations and exit.
  --help                 Show this message and exit.

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