INNER CODE UNIT · Python

filter_reads

Gabaldonlab/redundans · redundans.py:304

def filter_reads(outdir, fq1, fq2, minlen, maxlen, limit, minqual=10):
    """Filter FastQ files and return output fnames."""
    fastq = (fq1, fq2)
    # generate output files
    fn1 = os.path.join(outdir, "_reads.%s" % (os.path.basename(fq1.name.rstrip(".gz"))))
    fn2 = os.path.join(outdir, "_reads.%s" % (os.path.basename(fq2.name.rstrip(".gz"))))
    # skip if fq files already generated
    if os.path.isfile(fn1) and os.path.isfile(fn2):
        # notify about empty trimmed libs
        if not os.path.getsize(fn1) or not os.path.getsize(fn2):
            return fn1, fn2, 0
        return fn1, fn2, 1
    # open output files
    out1 = open(fn1, "w")
    out2 = open(fn2, "w")
    outfiles = (out1, out2, 0, 0)
    # run filtering
    i, filtered, orphans = filter_paired(

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