Mercurial > repos > rhpvorderman > shm_csr

comparison tests/test_shm_csr.py @ 3:dced6d52d218 draft

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"planemo upload commit bdfa4424496371fbea3edd3de07d8be9d0bad432"
author rhpvorderman
date Mon, 15 Nov 2021 11:35:18 +0000
parents 64d74ba01a7c
children 495a521cf9f2
comparison
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2:72d68e2e1fd3 3:dced6d52d218
34 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz" 34 CONTROL_NWK377_PB_IGHC_MID1_40nt_2 = TEST_DATA_DIR / "CONTROL_NWK377_PB_IGHC_MID1_40nt_2.txz"
35 35
36 36
37 @pytest.fixture(scope="module") 37 @pytest.fixture(scope="module")
38 def shm_csr_result(): 38 def shm_csr_result():
39 temp_dir = tempfile.mktemp() 39 temp_dir = Path(tempfile.mkdtemp())
40 shutil.copytree(GIT_ROOT, temp_dir) 40 tool_dir = temp_dir / "shm_csr"
41 shutil.copytree(GIT_ROOT, tool_dir)
42 working_dir = temp_dir / "working"
43 working_dir.mkdir(parents=True)
44 output_dir = temp_dir / "outputs"
45 output_dir.mkdir(parents=True)
46 wrapper = str(tool_dir / "wrapper.sh")
41 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2) 47 input = str(CONTROL_NWK377_PB_IGHC_MID1_40nt_2)
42 out_files_path = os.path.join(temp_dir, "results") 48 out_files_path = output_dir / "results"
43 out_file = os.path.join(out_files_path, "result.html") 49 out_file = out_files_path / "result.html"
44 infile_name = "input_data" 50 infile_name = "input_data"
45 functionality = "productive" 51 functionality = "productive"
46 unique = "Sequence.ID" 52 unique = "Sequence.ID"
47 naive_output = "no" 53 naive_output = "no"
48 naive_output_ca = "None" 54 naive_output_ca = "None"
55 class_filter = '70_70' 61 class_filter = '70_70'
56 empty_region_filter = 'FR1' 62 empty_region_filter = 'FR1'
57 fast = 'no' 63 fast = 'no'
58 cmd = [ 64 cmd = [
59 "bash", 65 "bash",
60 "wrapper.sh", 66 wrapper,
61 input, 67 input,
62 "custom", 68 "custom",
63 out_file, 69 str(out_file),
64 out_files_path, 70 str(out_files_path),
65 infile_name, 71 infile_name,
66 "-", 72 "-",
67 functionality, 73 functionality,
68 unique, 74 unique,
69 naive_output, 75 naive_output,
76 filter_unique_count, 82 filter_unique_count,
77 class_filter, 83 class_filter,
78 empty_region_filter, 84 empty_region_filter,
79 fast 85 fast
80 ] 86 ]
81 subprocess.run(cmd, cwd=temp_dir, stdout=sys.stdout, stderr=sys.stderr, 87 with open(temp_dir / "stderr", "wt") as stderr_file:
82 check=True) 88 with open(temp_dir / "stdout", "wt") as stdout_file:
89 subprocess.run(cmd, cwd=working_dir, stdout=stdout_file,
90 stderr=stderr_file, check=True)
83 yield Path(out_files_path) 91 yield Path(out_files_path)
84 #shutil.rmtree(temp_dir) 92 #shutil.rmtree(temp_dir)
85 93
86 94
87 def test_check_output(shm_csr_result): 95 def test_check_output(shm_csr_result):