Python run Exemples

Exemple #1

Fichier : test_assembler_benchmark.py Projet : bioboxes/command-line-interface

def test_assembly_benchmark_with_no_refs():
    path = os.path.join(tempfile.mkdtemp(), "quast")
    args = create_args(path)
    del args[4] # Delete the reference from the input arg list
    biobox.run(args)
    expected = os.path.join(path, "biobox.yaml")
    assert os.path.isfile(expected)

Exemple #2

Fichier : test_assembler_benchmark.py Projet : michaelbarton/command-line-interface

def test_assembly_benchmark_with_no_refs():
    path = os.path.join(tempfile.mkdtemp(), "quast")
    args = create_args(path)
    del args[4]  # Delete the reference from the input arg list
    biobox.run(args)
    expected = os.path.join(path, "biobox.yaml")
    assert os.path.isfile(expected)

Exemple #3

Fichier : test_short_read_assembly.py Projet : bioboxes/command-line-interface

def test_short_read_assembler():
    path = tempfile.mkdtemp()
    biobox.run(create_args(path))
    expected = os.path.join(path, "contigs.fa")
    assert os.path.isfile(expected)

Exemple #4

def test_short_read_assembler():
    path = tempfile.mkdtemp()
    biobox.run(create_args(path))
    expected = os.path.join(path, "contigs.fa")
    assert os.path.isfile(expected)

Exemple #5

Fichier : test_assembler_benchmark.py Projet : bioboxes/command-line-interface

def test_assembly_benchmark_with_refs_and_non_existing_output():
    path = os.path.join(tempfile.mkdtemp(), "quast")
    biobox.run(create_args(path))
    expected = os.path.join(path, "biobox.yaml")
    assert os.path.isfile(expected)

Exemple #6

Fichier : test_container.py Projet : michaelbarton/command-line-interface

def test_short_read_assembler():
    # Will run the remove() function
    # Difficult to check this has worked though
    biobox.run(create_args(tempfile.mkdtemp()))

Exemple #7

Fichier : test_assembler_benchmark.py Projet : michaelbarton/command-line-interface

def test_assembly_benchmark_with_refs_and_non_existing_output():
    path = os.path.join(tempfile.mkdtemp(), "quast")
    biobox.run(create_args(path))
    expected = os.path.join(path, "biobox.yaml")
    assert os.path.isfile(expected)