example command

example.py

def can_pipe(command, fastq_file):
    '''
    bwa-mem handles longer (> 70bp) reads with improved piping.
    Randomly samples 5000 reads from the first two million.
    Default to no piping if more than 75% of the sampled reads are small.
    '''
    min_size = 70
    thresh = 0.75
    head_count = 8000000
    tocheck = 5000
    cat_cmd = 'cat {fastq_file}'
    cmd = (cat_cmd + " | head -n {head_count} | "
           "{command} sample -s42 - {tocheck} | "
           "awk '{{if(NR%4==2) print length($1)}}' | sort | uniq -c")
    count_out = subprocess.check_output(cmd.format(**locals()), shell=True,
                                        executable="/bin/bash", stderr=open("/dev/null", "w"))
    if not count_out.strip():
        raise IOError("Failed to check fastq file sizes with: %s" % cmd.format(**locals()))

    shorter = 0
    for count, size in (l.strip().split() for l in count_out.strip().split("\n")):
        if int(size) < min_size:
            shorter += int(count)
    return (float(shorter) / float(tocheck)) <= thresh