Python redirect_stderr Examples

Example #1

def test_second_too_short():
    # paired-truncated.2.fastq is paired.2.fastq without the last read
    with redirect_stderr():
        cutadapt.main(
            '-a XX --paired-output out.fastq'.split() +
            [datapath('paired.1.fastq'),
             datapath('paired-truncated.2.fastq')])

Example #2

def test_missing_file():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main([
                '-a', 'XX', '--paired-output', 'out.fastq',
                datapath('paired.1.fastq')
            ])

Example #3

def test_unmatched_read_names():
    # paired-swapped.1.fastq: paired.1.fastq with reads 2 and 3 swapped
    with redirect_stderr():
        cutadapt.main(
            '-a XX --paired-output out.fastq'.split() +
            [datapath('paired-swapped.1.fastq'),
             datapath('paired.2.fastq')])

Example #4

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

Example #5

File: test_paired.py Project: stekaz/cutadapt

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()
    with redirect_stderr():
        params += ["-o", p1, "-p1", p2, "paired.1.fastq", "paired.2.fastq"]
        with pytest.raises(SystemExit):
            main(params)

Example #6

File: test_paired.py Project: marcelm/cutadapt

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()
    with redirect_stderr():
        params += ["-o", p1, "-p1", p2, "paired.1.fastq", "paired.2.fastq"]
        with pytest.raises(SystemExit):
            main(params)

Example #7

File: test_paired.py Project: wangguangya60/cutadapt

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

Example #8

def test_unmatched_read_names(cores):
    with pytest.raises(SystemExit):
        with temporary_path("swapped.1.fastq") as swapped:
            # Create a file in which reads 2 and 1 are swapped
            with open(datapath('paired.1.fastq')) as f:
                lines = f.readlines()
                lines = lines[0:4] + lines[8:12] + lines[4:8] + lines[12:]
            with open(swapped, 'w') as f:
                f.writelines(lines)
            with redirect_stderr():
                main('-a XX -o out1.fastq --paired-output out2.fastq'.split() +
                     ['--cores', str(cores)] +
                     [swapped, datapath('paired.2.fastq')])

Example #9

def test_second_too_short(cores):
    with pytest.raises(SystemExit):
        with temporary_path("truncated.2.fastq") as trunc2:
            # Create a truncated file in which the last read is missing
            with open(datapath('paired.2.fastq')) as f:
                lines = f.readlines()
                lines = lines[:-4]
            with open(trunc2, 'w') as f:
                f.writelines(lines)
            with redirect_stderr():
                main('-a XX -o /dev/null --paired-output out.fastq'.split() +
                     ['--cores', str(cores)] +
                     [datapath('paired.1.fastq'), trunc2])

Example #10

File: test_paired.py Project: stekaz/cutadapt

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

Example #11

File: test_paired.py Project: marcelm/cutadapt

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

Example #12

def test_first_too_short(tmpdir, cores):
    # Create a truncated file in which the last read is missing
    trunc1 = tmpdir.join("truncated.1.fastq")
    with open(datapath('paired.1.fastq')) as f:
        lines = f.readlines()
        lines = lines[:-4]
    trunc1.write(''.join(lines))

    with redirect_stderr():
        with pytest.raises(SystemExit):
            main([
                '-o', '/dev/null', '--paired-output',
                str(tmpdir.join('out.fastq')), '--cores',
                str(cores),
                str(trunc1),
                datapath('paired.2.fastq')
            ])

Example #13

def test_linked_anywhere():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main(['-b', 'AAA...TTT', datapath('linked.fasta')])

Example #14

File: test_paired.py Project: stekaz/cutadapt

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

Example #15

File: test_commandline.py Project: wangguangya60/cutadapt

def test_qualfile_only():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main(['file.qual'])

Example #16

def test_two_fastqs():
    with redirect_stderr():
        cutadapt.main([datapath('paired.1.fastq'), datapath('paired.2.fastq')])

Example #17

def test_paired_end_missing_file():
    with redirect_stderr():
        cutadapt.main([
            '-a', 'XX', '--paired-output', 'out.fastq',
            datapath('paired.1.fastq')
        ])

Example #18

def test_no_args():
    with redirect_stderr():
        cutadapt.main([])

Example #19

File: tests.py Project: smorfopoulou/viral_denovo_pipeline

def test_second_too_short():
	# paired-truncated.2.fastq is paired.2.fastq without the last read
	with redirect_stderr():
		cutadapt.main('-a XX --paired-output out.fastq'.split() + [datapath('paired.1.fastq'), datapath('paired-truncated.2.fastq')])

Example #20

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

Example #21

def test_two_fastqs():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main([datapath('paired.1.fastq'), datapath('paired.2.fastq')])

Example #22

File: tests.py Project: smorfopoulou/viral_denovo_pipeline

def test_qualfile_only():
	with redirect_stderr():
		cutadapt.main(['file.qual'])

Example #23

File: test_commandline.py Project: marcelm/cutadapt

def test_no_args():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main([])

Example #24

File: tests.py Project: smorfopoulou/viral_denovo_pipeline

def test_no_args():
	with redirect_stderr():
		cutadapt.main([])

Example #25

File: test_paired.py Project: marcelm/cutadapt

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

Example #26

File: tests.py Project: smorfopoulou/viral_denovo_pipeline

def test_unmatched_read_names():
	# paired-swapped.1.fastq: paired.1.fastq with reads 2 and 3 swapped
	with redirect_stderr():
		cutadapt.main('-a XX --paired-output out.fastq'.split() + [datapath('paired-swapped.1.fastq'), datapath('paired.2.fastq')])

Example #27

def test_linked_anywhere():
    with redirect_stderr():
        main(['-b', 'AAA...TTT', datapath('linked.fasta')])

Example #28

def test_non_iupac_characters():
    with redirect_stderr():
        main(['-a', 'ZACGT', datapath('small.fastq')])

Example #29

File: test_commandline.py Project: marcelm/cutadapt

def test_two_fastqs():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main([datapath('paired.1.fastq'), datapath('paired.2.fastq')])

Example #30

File: tests.py Project: smorfopoulou/viral_denovo_pipeline

def test_paired_end_missing_file():
	with redirect_stderr():
		cutadapt.main(['-a', 'XX', '--paired-output', 'out.fastq', datapath('paired.1.fastq')])

Example #31

def test_no_args():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main([])

Example #32

File: test_commandline.py Project: marcelm/cutadapt

def test_non_iupac_characters(run):
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main(['-a', 'ZACGT', datapath('small.fastq')])

Example #33

def test_non_iupac_characters():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main(['-a', 'ZACGT', datapath('small.fastq')])

Example #34

File: test_commandline.py Project: marcelm/cutadapt

def test_linked_anywhere():
    with pytest.raises(SystemExit):
        with redirect_stderr():
            main(['-b', 'AAA...TTT', datapath('linked.fasta')])

Example #35

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

Example #36

File: test_commandline.py Project: marcelm/cutadapt

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

Example #37

def test_qualfile_only():
    with redirect_stderr():
        cutadapt.main(['file.qual'])

Example #38

def test_no_args():
    with redirect_stderr():
        main([])