def setUp(self):
self.tmp_root = tempfile.mkdtemp()
args = get_default_args()
provider = sll.SllProvider(self.tmp_root)
test_utils.set_pattern(provider, 'project_first')
self.proj = project.Project(args, provider)
test_utils.create_fastq_files("sll", "project_first", self.tmp_root)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
args = get_default_args()
provider = gcf.GcfProvider(self.tmp_root)
test_utils.set_pattern(provider, 'basic')
self.proj = project.Project(args, provider)
test_utils.create_fastq_files("gcf", "basic", self.tmp_root)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
first_dir = os.path.join(self.tmp_root, "1")
second_dir = os.path.join(self.tmp_root, "2")
os.makedirs(first_dir)
os.makedirs(second_dir)
test_utils.create_fastq_files("sll", "project_first", first_dir, index=1)
test_utils.create_fastq_files("sll", "project_first", second_dir, index=2)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
self.project_first_dir = os.path.join(self.tmp_root, "project_first")
self.lane_first_dir = os.path.join(self.tmp_root, "lane_first")
os.makedirs(self.project_first_dir)
os.makedirs(self.lane_first_dir)
for i in range(4):
test_utils.create_fastq_files("sll", "project_first",
self.project_first_dir, index=i+1)
test_utils.create_fastq_files("sll", "lane_first",
self.lane_first_dir, index=i+1)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
self.provider = sll.SllProvider(self.tmp_root)
test_utils.set_pattern(self.provider, 'project_first')
sample_prefix = "P1777"
sample_format = "{0}_{1}"
flowcell_dir = "150305_AHCYF2ADXX"
for i in range(1, 4):
root = os.path.join(self.tmp_root,
sample_format.format(sample_prefix, i))
fastq_root = os.path.join(root, flowcell_dir)
os.makedirs(fastq_root)
test_utils.create_fastq_files("sll", "project_first",
fastq_root, i, bad_format=True)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
for i in range(4):
test_utils.create_fastq_files("gcf", "basic", self.tmp_root,
index=i+1)
def setUp(self):
self.tmp_root = tempfile.mkdtemp()
self.bad_root = tempfile.mkdtemp()
test_utils.create_fastq_files("gcf", "basic", self.tmp_root)
