How to use the cutadapt.__main__.main function in cutadapt

def _run(params, inpath1, inpath2=None, expected1=None, expected2=None, cores=1):
        assert not (inpath1 and inpath2 and expected1 and expected2)
        assert not (expected2 and not expected1)
        assert not (inpath2 and not inpath1)
        if type(params) is str:
            params = params.split()
        params += ["--interleaved", "--cores", str(cores), "--buffer-size=512"]
        tmp1 = str(tmpdir.join("out1-" + expected1))
        params += ["-o", tmp1]
        paths = [datapath(inpath1)]
        if inpath2:
            paths += [datapath(inpath2)]
        if expected2:
            tmp2 = str(tmpdir.join("out2-" + expected2))
            params += ["-p", tmp2]
            assert main(params + paths) is None
            assert_files_equal(cutpath(expected2), tmp2)
        else:
            assert main(params + paths) is None
        assert_files_equal(cutpath(expected1), tmp1)

def test_interleaved_neither_nor(tmpdir):
    """Option --interleaved used, but pairs of files given for input and output"""
    p1 = str(tmpdir.join("temp-paired.1.fastq"))
    p2 = str(tmpdir.join("temp-paired.2.fastq"))
    params = "-a XX --interleaved".split()
    params += ["-o", p1, "-p1", p2, "paired.1.fastq", "paired.2.fastq"]
    with pytest.raises(SystemExit):
        main(params)

def test_anywhere_anchored_3p():
    with pytest.raises(SystemExit):
        main(['-b', 'TTT$', datapath('small.fastq')])

("A", "T", True),
        ("C", "G", True),
        ("C", "T", True),
    ]
    if discarduntrimmed:
        combinations += [
            ("unknown", "G", False),
            ("A", "unknown", False),
        ]
        params += ["--discard-untrimmed"]
    else:
        combinations += [
            ("unknown", "G", True),
            ("A", "unknown", True),
        ]
    assert main(params) is None
    for (name1, name2, should_exist) in combinations:
        for i in (1, 2):
            name = "combinatorial.{name1}_{name2}.{i}.fasta".format(name1=name1, name2=name2, i=i)
            path = cutpath(os.path.join("combinatorial", name))
            if should_exist:
                assert tmpdir.join(name).check(), "Output file missing"
                assert_files_equal(path, str(tmpdir.join(name)))
            else:
                assert not tmpdir.join(name).check(), "Output file should not exist"

def test_missing_file(tmpdir):
    with pytest.raises(SystemExit):
        main(["--paired-output", str(tmpdir.join("out.fastq")), datapath("paired.1.fastq")])

def test_second_too_short(tmpdir, cores):
    # Create a truncated file in which the last read is missing
    trunc2 = tmpdir.join("truncated.2.fastq")
    with open(datapath("paired.2.fastq")) as f:
        lines = f.readlines()
        lines = lines[:-4]
    trunc2.write("".join(lines))

    with pytest.raises(SystemExit):
        main([
            "-o", "/dev/null",
            "--paired-output", str(tmpdir.join("out.fastq")),
            "--cores", str(cores),
            datapath("paired.1.fastq"), str(trunc2)
        ])

record = ">r{}:{}\n{}\n".format(l1, l2, "A" * l1)
    record += ">r{}:{}\n{}".format(l1, l2, "A" * l2)
    with open(inpath, "w") as f:
        print(record, file=f)
    with open(expected, "w") as f:
        if (m1 is None or func(l1, m1)) and (m2 is None or func(l2, m2)):
            print(record, file=f)

    assert os.path.exists(inpath)
    assert os.path.exists(expected)
    if m1 is None:
        m1 = ""
    if m2 is None:
        m2 = ""

    main(["--interleaved", "-o", outpath, "-" + name, "{}:{}".format(m1, m2), inpath])
    assert_files_equal(expected, outpath)

def test_help():
    with pytest.raises(SystemExit) as e:
        main(["--help"])
    assert e.value.args[0] == 0

def test_unconditional_cut_invalid_number():
    with pytest.raises(SystemExit):
        main(["-u", "a,b", datapath("small.fastq")])

def test_demultiplex():
    tempdir = tempfile.mkdtemp(prefix='cutadapt-tests.')
    multiout = os.path.join(tempdir, 'tmp-demulti.{name}.fasta')
    params = ['-a', 'first=AATTTCAGGAATT', '-a', 'second=GTTCTCTAGTTCT', '-o', multiout, datapath('twoadapters.fasta')]
    assert main(params) is None
    assert_files_equal(cutpath('twoadapters.first.fasta'), multiout.format(name='first'))
    assert_files_equal(cutpath('twoadapters.second.fasta'), multiout.format(name='second'))
    assert_files_equal(cutpath('twoadapters.unknown.fasta'), multiout.format(name='unknown'))
    shutil.rmtree(tempdir)