コード例 #1
0
 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)
コード例 #2
0
 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)
コード例 #3
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 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)
コード例 #4
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 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)
コード例 #5
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 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)
コード例 #6
0
 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)
コード例 #7
0
 def setUp(self):
     self.tmp_root = tempfile.mkdtemp()
     self.bad_root = tempfile.mkdtemp()
     test_utils.create_fastq_files("gcf", "basic", self.tmp_root)