INNER CODE UNIT · Python

read_write_fq

nf-core/eager · bin/extract_map_reads.py:92

def read_write_fq(fq_in, fq_out, mapped_reads, mode, write_mode, proc):
    """
    Read and write fastq file with mapped reads removed
    Args:
        fq_in(str): path to input fastq file
        fq_out(str): path to output fastq file
        mapped_reads(set): set of mapped reads name (str)
        mode(str): read removal mode (remove or replace)
        write_mode(str): write mode (w or wb)
        proc(int): number of parallel processes
        merged(bool): True if bam file was created from merged fastq files
    """
    if write_mode == "w":
        cm = open(fq_out, write_mode)
    elif write_mode == "wb":
        cm = xopen(fq_out, mode=write_mode, threads=proc)
    with pysam.FastxFile(fq_in) as fh:
        with cm as fh_out:

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