ProcessPool-fastq-metrics.py

import concurrent.futures as cfutures
import nanomath
from Bio import SeqIO

def stream_fastq_full(fastq, threads):
    '''
    Extract from a fastq file:
    -readname
    -average and median quality
    -read_lenght
    '''
    with cfutures.ProcessPoolExecutor(max_workers=threads) as executor:
        for results in executor.map(extract_all_from_fastq, SeqIO.parse(fastq, "fastq")):
            yield results

def extract_all_from_fastq(rec):
    '''
    Worker function for extraction of metrics from a fastq record Seq object
    If length 0, nanomath.aveQual will throw a ZeroDivisionError
    Skipping the read is okay then.
    '''
    try:
        return (rec.id,
                len(rec),
                nanomath.ave_qual(rec.letter_annotations["phred_quality"]),
                nanomath.median_qual(rec.letter_annotations["phred_quality"]))
    except ZeroDivisionError:
        pass