Pre-fitted sklearn-based taxonomy classifier

Parameters

reads : FeatureData[Sequence]

The feature data to be classified.

classifier : TaxonomicClassifier

The taxonomic classifier for classifying the reads.

reads_per_batch : Int % Range(0, None), optional

Number of reads to process in each batch. If 0, this parameter is autoscaled to min( number of query sequences / n_jobs, 20000).

pre_dispatch : Str, optional

"all" or expression, as in "3*n_jobs". The number of batches (of tasks) to be pre-dispatched.

confidence : Float, optional

Confidence threshold for limiting taxonomic depth. Provide -1 to disable confidence calculation, or 0 to calculate confidence but not apply it to limit the taxonomic depth of the assignments.

read_orientation : Str % Choices('same', 'reverse-complement'), optional

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. Default is to autodetect based on the confidence estimates for the first 100 reads.

Returns

classification : FeatureData[Taxonomy]