cogent3.core.alphabet.make_qual_converter

make_qual_converter(scoring_scheme: PhredEncoding | str = PhredEncoding.PHRED_33) → bytes_to_array

make a converter from fastq quality ASCII bytes to numpy uint8 scores.

Parameters:

scoring_scheme

the fastq quality encoding scheme. Either a PhredEncoding member or one of the string values "phred+33" or "phred+64" (case insensitive).

Raises:

NotImplementedError

if scoring_scheme is not a supported scheme.

Notes

The returned converter maps the ASCII range valid for the encoding onto consecutive numpy.uint8 quality scores starting at zero. Pass it as the qual_converter argument to cogent3.parse.fastq.iter_fastq_records to obtain quality scores as numpy arrays while iterating fastq records.