From 8c0e0f0629d69672375159200c57136ced644572 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Sun, 8 Nov 2020 21:51:11 +0300 Subject: Change defaultline argument in the build_line_list from None to empty string --- wqflask/wqflask/marker_regression/plink_mapping.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index fd91b6ca..8d57d556 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -154,7 +154,7 @@ def parse_plink_output(output_filename, species): # function: convert line from str to list; # output: lineList list ####################################################### -def build_line_list(line=None): +def build_line_list(line=""): line_list = line.strip().split(' ')# irregular number of whitespaces between columns line_list = [item for item in line_list if item !=''] line_list = [item.strip() for item in line_list] -- cgit v1.2.3 From 8e55eaf473d98c1d165fcaf60ab0e24abb6acd9e Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Sun, 8 Nov 2020 22:00:40 +0300 Subject: add tests for marker_regression/gemma_mapping --- .../marker_regression/test_gemma_mapping.py | 170 +++++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py new file mode 100644 index 00000000..4a88509e --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -0,0 +1,170 @@ +#test for wqflask/marker_regression/gemma_mapping.py +import unittest +import random +from unittest import mock +from wqflask.marker_regression.gemma_mapping import run_gemma +from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file +from wqflask.marker_regression.gemma_mapping import gen_covariates_file +from wqflask.marker_regression.gemma_mapping import parse_gemma_output +from wqflask.marker_regression.gemma_mapping import parse_loco_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + + +class MockDatasetGroup(AttributeSetter): + def get_samplelist(self): + return None + + +class TestGemmaMapping(unittest.TestCase): + # def test_fail(self): + # self.assertEqual(2,3) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") + def setUp(self): + pass + + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + def test_run_gemma_first_run_set_true(self, mock_gen_pheno, mock_os): + chromosomes = AttributeSetter({"chromosomes": "SA"}) + covariates = "XI:X2,X4:X3,X6:X7" + dataset_group = MockDatasetGroup({"genofile": "fileX"}) + dataset = AttributeSetter( + {"group": dataset_group, "name": "dataset1_name", "species": chromosomes}) + trait = AttributeSetter({"name": "trait1"}) + mock_gen_pheno.side_effect = None + mock_gen_pheno.return_value = None + mock_os.path.isfile.return_value = True + + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): + dataset = AttributeSetter( + {"group": AttributeSetter({"genofile": "genofile.geno"})}) + + output_files = "file1" + use_loco = False + mock_parse_loco.side_effect = None + mock_parse_loco.return_value = [] + this_trait = AttributeSetter({"name": "t1"}) + + result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ + ], covariates="", use_loco=True, first_run=False, output_files=output_files) + + expected_results = ([], "file1") + self.assertEqual(expected_results, result) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ + "x", "w", "q", "we", "R"], trait_filename="fitr.re") + + mock_open.assert_called_once_with( + '/home/user/data/gn2/fitr.re.txt', 'w') + filehandler = mock_open() + values = ["x", "w", "q", "we", "R"] + write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( + 'q\n'), mock.call('we\n'), mock.call('R\n')] + + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") + @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset") + def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): + covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" + samplelist = ["X1", "X2", "X3", "X4"] + create_dataset_side_effect = [] + create_trait_side_effect = [] + + for i in range(4): + create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) + create_trait_side_effect.append( + AttributeSetter({"data": [f'data_{i}']})) + + create_dataset.side_effect = create_trait_side_effect + create_trait.side_effect = create_trait_side_effect + + group = MockDatasetGroup({"name": "group_X", "samplelist": samplelist}) + this_dataset = AttributeSetter({"group": group}) + flat_files.return_value = "Home/Genenetwork" + + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_covariates_file(this_dataset=this_dataset, covariates=covariates, + samples=["x1", "x2", "X3"]) + # test mocked methods + + create_dataset.assert_has_calls( + [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) + mock_calls = [] + trait_names = ["X1", "Y1", "M1", "V1"] + + for i, trait in enumerate(create_trait_side_effect): + mock_calls.append( + mock.call(dataset=trait, name=trait_names[i], cellid=None)) + + create_trait.assert_has_calls(mock_calls) + + # test writing of covariates.txt + + flat_files.assert_called_once_with('mapping') + mock_open.assert_called_once_with( + 'Home/Genenetwork/group_X_covariates.txt', 'w') + filehandler = mock_open() + # expected all-9 + filehandler.write.assert_has_calls([mock.call( + '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") + def test_parse_gemma_output_obj_returned(self): + file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 +X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 +125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 +""" + with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: + results = parse_gemma_output(genofile_name="gema_file") + expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] + + mock_open.assert_called_once_with( + "/home/user/img/gema_file_output.assoc.txt") + + self.assertEqual(results, expected) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + def test_xparse_gemma_output_empty_return(self): + output_file_results = """chr\t today""" + with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: + results = parse_gemma_output(genofile_name="gema_file") + self.assertEqual(results, []) + + @mock.patch("builtins.open", mock.mock_open(read_data="chr\t")) + def test_parse_gemma_output_empty_return(self): + #duplicate + string_read = parse_gemma_output(genofile_name="hdf") + # print(string_read) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + def test_parse_loco_output_file_found(self, mock_os): + mock_os.path.isfile.return_value = False + file_to_write = """{"files":["file_1","file_2"]}""" + + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + def test_parse_loco_output_file_not_found(self, mock_os): + + mock_os.path.isfile.return_value = False + file_to_write = """{"files":["file_1","file_2"]}""" + + with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open: + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + self.assertEqual(results, []) -- cgit v1.2.3 From 5e50e19a014efdfcf0ce1397025879d4ada4d271 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Sun, 8 Nov 2020 22:04:52 +0300 Subject: add tests for marker_regression/plink_mapping.py --- .../marker_regression/test_plink_mapping.py | 83 ++++++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 wqflask/tests/wqflask/marker_regression/test_plink_mapping.py (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py new file mode 100644 index 00000000..b827fd0f --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py @@ -0,0 +1,83 @@ +# test for wqflask/marker_regression/plink_mapping.py +import unittest +from unittest import mock +from wqflask.marker_regression.plink_mapping import build_line_list +from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file +from wqflask.marker_regression.plink_mapping import flat_files +from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink +from wqflask.marker_regression.plink_mapping import parse_plink_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + + +class TestPlinkMapping(unittest.TestCase): + + def test_build_line_list(self): + line_1 = "this is line one test" + irregular_line = " this is an, irregular line " + exp_line1 = ["this", "is", "line", "one", "test"] + + results = build_line_list(irregular_line) + self.assertEqual(exp_line1, build_line_list(line_1)) + self.assertEqual([], build_line_list()) + self.assertEqual(["this", "is", "an,", "irregular", "line"], results) + + @mock.patch("wqflask.marker_regression.plink_mapping.flat_files") + def test_get_samples_from_ped_file(self, mock_flat_files): + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + file_sample = """Expected_1\tline test +Expected_2\there + Expected_3\tthree""" + mock_flat_files.return_value = "/home/user/" + with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open: + results = get_samples_from_ped_file(dataset) + mock_flat_files.assert_called_once_with("mapping") + mock_open.assert_called_once_with("/home/user/n_1.ped", "r") + self.assertEqual( + ["Expected_1", "Expected_2", "Expected_3"], results) + + @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") + def test_gen_pheno_txt_file_plink(self, mock_samples): + mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] + + trait = AttributeSetter({"name": "TX"}) + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + vals = ["value=K1", "value=K2", "value=K3"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset, + vals=vals, pheno_filename="ph_file") + mock_open.assert_called_once_with( + "/home/user/data/ph_file.txt", "wb") + filehandler = mock_open() + calls_expected = [mock.call('FID\tIID\tTX\n'), + mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')] + + filehandler.write.assert_has_calls(calls_expected) + + filehandler.close.assert_called_once() + + @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list") + def test_parse_plink_output(self, mock_line_list): + chromosomes = [0, 34, 110, 89, 123, 23, 2] + species = AttributeSetter( + {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) + + fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA""" + + mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ + "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] + # print("sdfsfdf",species.chromosomes) + with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: + parse_results = parse_plink_output( + output_filename="P1_file", species=species) + mock_open.assert_called_once_with( + "/home/user/data/P1_file.qassoc", "rb") + expected = (2, {'AACCAT': 0.89, 'AATA': 0.3}) + + self.assertEqual(parse_results, expected) -- cgit v1.2.3 From 7aaa4b87fcf405c32c11e2e2d664941c43c14430 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 13:20:53 +0300 Subject: refactor marker_regression/gemma-mapping.py run-gemma function to avoid Index Error --- wqflask/wqflask/marker_regression/gemma_mapping.py | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index 68a8d5ba..02f91a32 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -31,16 +31,11 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) this_chromosomes = this_dataset.species.chromosomes.chromosomes - chr_list_string = "" - for i in range(len(this_chromosomes)): - if i < (len(this_chromosomes) - 1): - chr_list_string += this_chromosomes[i+1].name + "," - else: - chr_list_string += this_chromosomes[i+1].name + this_chromosomes_name=[chromosome.name for chromosome in this_chromosomes] + chr_list_string=",".join(this_chromosomes_name) if covariates != "": gen_covariates_file(this_dataset, covariates, samples) - if use_loco == "True": generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'), genofile_name, -- cgit v1.2.3 From 919763173289e523d5b3c9015fc6f1117ad59581 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 13:31:42 +0300 Subject: add test for run_gemma function in marker_regression/gemma_mapping.py --- .../marker_regression/test_gemma_mapping.py | 70 +++++++++++++++++----- 1 file changed, 55 insertions(+), 15 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 4a88509e..1b09afd6 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -1,4 +1,4 @@ -#test for wqflask/marker_regression/gemma_mapping.py +# test for wqflask/marker_regression/gemma_mapping.py import unittest import random from unittest import mock @@ -24,22 +24,62 @@ class TestGemmaMapping(unittest.TestCase): # def test_fail(self): # self.assertEqual(2,3) - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def setUp(self): - pass + pass - @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") + @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") + @mock.patch("wqflask.marker_regression.gemma_mapping.string.ascii_uppercase", "R") + @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") @mock.patch("wqflask.marker_regression.gemma_mapping.os") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno, mock_os): - chromosomes = AttributeSetter({"chromosomes": "SA"}) - covariates = "XI:X2,X4:X3,X6:X7" - dataset_group = MockDatasetGroup({"genofile": "fileX"}) - dataset = AttributeSetter( - {"group": dataset_group, "name": "dataset1_name", "species": chromosomes}) + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_parse_loco): + + chromosomes = [] + for i in range(1, 5): + chromosomes.append(AttributeSetter({"name": f"CH{i}"})) + + chromo = AttributeSetter({"chromosomes": chromosomes}) + + dataset_group = MockDatasetGroup( + {"name": "GP1", "genofile": "file_geno"}) + + dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", + "species": AttributeSetter({"chromosomes": chromo})}) + trait = AttributeSetter({"name": "trait1"}) - mock_gen_pheno.side_effect = None - mock_gen_pheno.return_value = None + samples = [] + mock_gen_pheno_txt.side_effect = None + mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True + mock_os.system.return_value = None + mock_os.system.side_effect = None + mock_gen_covar.side_effect = None + mock_gen_covar.return_value = None + mock_flat_files.return_value = "/home/genotype/bimbam" + mock_parse_loco.side_effect = None + mock_parse_loco.return_value = [] + results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ + ], vals=[], covariates="", use_loco=True) + # check results + self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) + mock_gen_pheno_txt.assert_called_once() + self.assertEqual(mock_flat_files.call_count, 4) + + system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), + mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] + + mock_os.system.assert_has_calls(system_calls) + + mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt') + ) + + mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): @@ -130,7 +170,8 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 """ with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") - expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] + expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, + {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] mock_open.assert_called_once_with( "/home/user/img/gema_file_output.assoc.txt") @@ -146,7 +187,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("builtins.open", mock.mock_open(read_data="chr\t")) def test_parse_gemma_output_empty_return(self): - #duplicate + # duplicate string_read = parse_gemma_output(genofile_name="hdf") # print(string_read) @@ -156,7 +197,6 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 mock_os.path.isfile.return_value = False file_to_write = """{"files":["file_1","file_2"]}""" - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): -- cgit v1.2.3 From 74c65eb99be3f9854bd774dae15877af7c8aa4f5 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 14:03:08 +0300 Subject: mock logger in marker_regression/gemma_mapping.py --- .../marker_regression/test_gemma_mapping.py | 47 +++++++++++++--------- 1 file changed, 27 insertions(+), 20 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 1b09afd6..fd45fd65 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -27,18 +27,39 @@ class TestGemmaMapping(unittest.TestCase): def setUp(self): pass + + + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): + dataset = AttributeSetter( + {"group": AttributeSetter({"genofile": "genofile.geno"})}) + + output_files = "file1" + use_loco = False + mock_parse_loco.side_effect = None + mock_parse_loco.return_value = [] + this_trait = AttributeSetter({"name": "t1"}) + + result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ + ], covariates="", use_loco=True, first_run=False, output_files=output_files) + + expected_results = ([], "file1") + self.assertEqual(expected_results, result) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + @mock.patch("wqflask.marker_regression.gemma_mapping.logger") @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") @mock.patch("wqflask.marker_regression.gemma_mapping.string.ascii_uppercase", "R") @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_parse_loco): + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files,mock_logger,mock_parse_loco): chromosomes = [] for i in range(1, 5): @@ -71,32 +92,18 @@ class TestGemmaMapping(unittest.TestCase): mock_gen_pheno_txt.assert_called_once() self.assertEqual(mock_flat_files.call_count, 4) + system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] mock_os.system.assert_has_calls(system_calls) - mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt') - ) - - mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") + mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt')) - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): - dataset = AttributeSetter( - {"group": AttributeSetter({"genofile": "genofile.geno"})}) + self.assertEqual(mock_logger.debug.call_count,2) + - output_files = "file1" - use_loco = False - mock_parse_loco.side_effect = None - mock_parse_loco.return_value = [] - this_trait = AttributeSetter({"name": "t1"}) - - result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ - ], covariates="", use_loco=True, first_run=False, output_files=output_files) - - expected_results = ([], "file1") - self.assertEqual(expected_results, result) + mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): -- cgit v1.2.3 From 986b20363cc84be1822588dd7cc935fca7ef7f48 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 16:53:12 +0300 Subject: add test for get_genofile_samplelist in marker_regression/run_mapping.py --- .../wqflask/marker_regression/test_run_mapping.py | 36 ++++++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 wqflask/tests/wqflask/marker_regression/test_run_mapping.py (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py new file mode 100644 index 00000000..0a5bc565 --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -0,0 +1,36 @@ +import unittest +from unittest import mock +from wqflask.marker_regression.run_mapping import get_genofile_samplelist + + +class AttributeSetter: + def __init__(self,obj): + for k,v in obj.items(): + setattr(self,k,v) + + +class MockDataSetGroup(AttributeSetter): + + def get_genofiles(self): + return [{"location":"~/genofiles/g1_file","sample_list":["S1","S2","S3","S4"]}] +class TestRunMapping(unittest.TestCase): + def setUp(self): + self.group=MockDataSetGroup({"genofile":"~/genofiles/g1_file"}) + self.dataset=AttributeSetter({"group":self.group}) + + def tearDown(self): + self.dataset=AttributeSetter({"group":{"location":"~/genofiles/g1_file"}}) + + + def test_get_genofile_samplelist(self): + #location true and sample list true + + results_1=get_genofile_samplelist(self.dataset) + self.assertEqual(results_1,["S1","S2","S3","S4"]) + #return empty array + self.group.genofile="~/genofiles/g2_file" + result_2=get_genofile_samplelist(self.dataset) + self.assertEqual(result_2,[]) + + + -- cgit v1.2.3 From e660984015e1bc6d48e9ccee5fe59691c4acd911 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 17:22:27 +0300 Subject: add tests for geno_db_exists in marker_regression/run_mapping.py --- .../wqflask/marker_regression/test_run_mapping.py | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index 0a5bc565..61bc8a1d 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -1,7 +1,7 @@ import unittest from unittest import mock from wqflask.marker_regression.run_mapping import get_genofile_samplelist - +from wqflask.marker_regression.run_mapping import geno_db_exists class AttributeSetter: def __init__(self,obj): @@ -15,7 +15,7 @@ class MockDataSetGroup(AttributeSetter): return [{"location":"~/genofiles/g1_file","sample_list":["S1","S2","S3","S4"]}] class TestRunMapping(unittest.TestCase): def setUp(self): - self.group=MockDataSetGroup({"genofile":"~/genofiles/g1_file"}) + self.group=MockDataSetGroup({"genofile":"~/genofiles/g1_file","name":"GP1_"}) self.dataset=AttributeSetter({"group":self.group}) def tearDown(self): @@ -32,5 +32,21 @@ class TestRunMapping(unittest.TestCase): result_2=get_genofile_samplelist(self.dataset) self.assertEqual(result_2,[]) + @mock.patch("wqflask.marker_regression.run_mapping.data_set") + def test_geno_db_exists(self,mock_data_set): + # mock_data_set.create_dataset_side_effect=None + mock_data_set.create_dataset.side_effect=[AttributeSetter({}),Exception()] + results_no_error=geno_db_exists(self.dataset) + results_with_error=geno_db_exists(self.dataset) + + self.assertEqual(mock_data_set.create_dataset.call_count,2) + self.assertEqual(results_with_error,"False") + self.assertEqual(results_no_error,"True") + + + + + + -- cgit v1.2.3 From c9c06e3e2df6d9290a7b65607dd819f68290712e Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 20:10:21 +0300 Subject: remove unnecessary side_effect set to None --- .../marker_regression/test_gemma_mapping.py | 43 +++++----------------- 1 file changed, 9 insertions(+), 34 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index fd45fd65..963c131f 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -21,13 +21,6 @@ class MockDatasetGroup(AttributeSetter): class TestGemmaMapping(unittest.TestCase): - # def test_fail(self): - # self.assertEqual(2,3) - - def setUp(self): - pass - - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): @@ -36,7 +29,6 @@ class TestGemmaMapping(unittest.TestCase): output_files = "file1" use_loco = False - mock_parse_loco.side_effect = None mock_parse_loco.return_value = [] this_trait = AttributeSetter({"name": "t1"}) @@ -46,7 +38,6 @@ class TestGemmaMapping(unittest.TestCase): expected_results = ([], "file1") self.assertEqual(expected_results, result) - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") @@ -59,7 +50,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files,mock_logger,mock_parse_loco): + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): chromosomes = [] for i in range(1, 5): @@ -75,35 +66,28 @@ class TestGemmaMapping(unittest.TestCase): trait = AttributeSetter({"name": "trait1"}) samples = [] - mock_gen_pheno_txt.side_effect = None + mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True - mock_os.system.return_value = None - mock_os.system.side_effect = None - mock_gen_covar.side_effect = None mock_gen_covar.return_value = None mock_flat_files.return_value = "/home/genotype/bimbam" - mock_parse_loco.side_effect = None mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - # check results self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) mock_gen_pheno_txt.assert_called_once() self.assertEqual(mock_flat_files.call_count, 4) - - system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] mock_os.system.assert_has_calls(system_calls) - mock_os.path.isfile.assert_called_once_with(('/home/user/imgfile_output.assoc.txt')) + mock_os.path.isfile.assert_called_once_with( + ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count,2) - + self.assertEqual(mock_logger.debug.call_count, 2) - mock_parse_loco.assert_called_once_with(dataset,"GP1_GWA_RRRRRR") + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): @@ -144,7 +128,6 @@ class TestGemmaMapping(unittest.TestCase): with mock.patch("builtins.open", mock.mock_open())as mock_open: gen_covariates_file(this_dataset=this_dataset, covariates=covariates, samples=["x1", "x2", "X3"]) - # test mocked methods create_dataset.assert_has_calls( [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) @@ -157,13 +140,10 @@ class TestGemmaMapping(unittest.TestCase): create_trait.assert_has_calls(mock_calls) - # test writing of covariates.txt - flat_files.assert_called_once_with('mapping') mock_open.assert_called_once_with( 'Home/Genenetwork/group_X_covariates.txt', 'w') filehandler = mock_open() - # expected all-9 filehandler.write.assert_has_calls([mock.call( '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) @@ -186,23 +166,18 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 self.assertEqual(results, expected) @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_xparse_gemma_output_empty_return(self): + def test_parse_gemma_output_empty_return(self): output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") self.assertEqual(results, []) - @mock.patch("builtins.open", mock.mock_open(read_data="chr\t")) - def test_parse_gemma_output_empty_return(self): - # duplicate - string_read = parse_gemma_output(genofile_name="hdf") - # print(string_read) - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_found(self, mock_os): - mock_os.path.isfile.return_value = False + mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" + #incomplete @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") -- cgit v1.2.3 From bf22cc3fbb37147b5e6c3012658fe5e43b696637 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 20:26:21 +0300 Subject: remove whitespace in marker_regression --- wqflask/tests/wqflask/marker_regression/test_plink_mapping.py | 3 --- wqflask/tests/wqflask/marker_regression/test_run_mapping.py | 9 +-------- 2 files changed, 1 insertion(+), 11 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py index b827fd0f..a5fa0c04 100644 --- a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py @@ -12,8 +12,6 @@ class AttributeSetter: def __init__(self, obj): for key, val in obj.items(): setattr(self, key, val) - - class TestPlinkMapping(unittest.TestCase): def test_build_line_list(self): @@ -72,7 +70,6 @@ Expected_2\there mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] - # print("sdfsfdf",species.chromosomes) with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: parse_results = parse_plink_output( output_filename="P1_file", species=species) diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index 61bc8a1d..bba9de05 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -2,6 +2,7 @@ import unittest from unittest import mock from wqflask.marker_regression.run_mapping import get_genofile_samplelist from wqflask.marker_regression.run_mapping import geno_db_exists +from wqflask.marker_regression.run_mapping import write_input_for_browser class AttributeSetter: def __init__(self,obj): @@ -21,20 +22,16 @@ class TestRunMapping(unittest.TestCase): def tearDown(self): self.dataset=AttributeSetter({"group":{"location":"~/genofiles/g1_file"}}) - def test_get_genofile_samplelist(self): - #location true and sample list true results_1=get_genofile_samplelist(self.dataset) self.assertEqual(results_1,["S1","S2","S3","S4"]) - #return empty array self.group.genofile="~/genofiles/g2_file" result_2=get_genofile_samplelist(self.dataset) self.assertEqual(result_2,[]) @mock.patch("wqflask.marker_regression.run_mapping.data_set") def test_geno_db_exists(self,mock_data_set): - # mock_data_set.create_dataset_side_effect=None mock_data_set.create_dataset.side_effect=[AttributeSetter({}),Exception()] results_no_error=geno_db_exists(self.dataset) results_with_error=geno_db_exists(self.dataset) @@ -46,7 +43,3 @@ class TestRunMapping(unittest.TestCase): - - - - -- cgit v1.2.3 From 3ccc964fc466467c1c65f000fa7b43a38e10987a Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 21:15:24 +0300 Subject: refactor test_run_gemma function --- wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 963c131f..bc0cb4e0 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -46,11 +46,10 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.logger") @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") - @mock.patch("wqflask.marker_regression.gemma_mapping.string.ascii_uppercase", "R") - @mock.patch("wqflask.marker_regression.gemma_mapping.string.digits", "R") + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os,mock_choice,mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): chromosomes = [] for i in range(1, 5): @@ -70,6 +69,7 @@ class TestGemmaMapping(unittest.TestCase): mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True mock_gen_covar.return_value = None + mock_choice.return_value="R" mock_flat_files.return_value = "/home/genotype/bimbam" mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ @@ -177,7 +177,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 def test_parse_loco_output_file_found(self, mock_os): mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" - #incomplete + # incomplete @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") -- cgit v1.2.3 From ba065fa885841dc39681d0e420ac06df1ea846ae Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Mon, 9 Nov 2020 21:27:54 +0300 Subject: correct typo and variable naming --- .../marker_regression/test_gemma_mapping.py | 30 +++++----------------- 1 file changed, 7 insertions(+), 23 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index bc0cb4e0..06ce55d8 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -49,52 +49,41 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os,mock_choice,mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): - + def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): chromosomes = [] for i in range(1, 5): chromosomes.append(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": chromosomes}) - dataset_group = MockDatasetGroup( {"name": "GP1", "genofile": "file_geno"}) - dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", "species": AttributeSetter({"chromosomes": chromo})}) - trait = AttributeSetter({"name": "trait1"}) samples = [] - mock_gen_pheno_txt.return_value = None mock_os.path.isfile.return_value = True mock_gen_covar.return_value = None - mock_choice.return_value="R" + mock_choice.return_value = "R" mock_flat_files.return_value = "/home/genotype/bimbam" mock_parse_loco.return_value = [] results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ ], vals=[], covariates="", use_loco=True) - self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) - mock_gen_pheno_txt.assert_called_once() - self.assertEqual(mock_flat_files.call_count, 4) system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] - mock_os.system.assert_has_calls(system_calls) - + mock_gen_pheno_txt.assert_called_once() + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") mock_os.path.isfile.assert_called_once_with( ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count, 2) - - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") + self.assertEqual(mock_flat_files.call_count, 4) + self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): with mock.patch("builtins.open", mock.mock_open())as mock_open: gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ "x", "w", "q", "we", "R"], trait_filename="fitr.re") - mock_open.assert_called_once_with( '/home/user/data/gn2/fitr.re.txt', 'w') filehandler = mock_open() @@ -159,26 +148,21 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 results = parse_gemma_output(genofile_name="gema_file") expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] - mock_open.assert_called_once_with( "/home/user/img/gema_file_output.assoc.txt") - self.assertEqual(results, expected) - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") def test_parse_gemma_output_empty_return(self): output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") self.assertEqual(results, []) - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_found(self, mock_os): mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" - # incomplete - + pass @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): -- cgit v1.2.3 From 137dff191dd8b78e8207e6c5adc4e1c421a75ff0 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Tue, 10 Nov 2020 13:57:24 +0300 Subject: add tests for export_mapping_results in marker_regression/run_mapping.py --- .../wqflask/marker_regression/test_run_mapping.py | 192 ++++++++++++++++++--- 1 file changed, 167 insertions(+), 25 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index bba9de05..e925ad28 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -1,45 +1,187 @@ import unittest +import datetime from unittest import mock + from wqflask.marker_regression.run_mapping import get_genofile_samplelist from wqflask.marker_regression.run_mapping import geno_db_exists from wqflask.marker_regression.run_mapping import write_input_for_browser +from wqflask.marker_regression.run_mapping import export_mapping_results +from wqflask.marker_regression.run_mapping import trim_markers_for_figure + class AttributeSetter: - def __init__(self,obj): - for k,v in obj.items(): - setattr(self,k,v) + def __init__(self, obj): + for k, v in obj.items(): + setattr(self, k, v) class MockDataSetGroup(AttributeSetter): - - def get_genofiles(self): - return [{"location":"~/genofiles/g1_file","sample_list":["S1","S2","S3","S4"]}] + + def get_genofiles(self): + return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] + + class TestRunMapping(unittest.TestCase): - def setUp(self): - self.group=MockDataSetGroup({"genofile":"~/genofiles/g1_file","name":"GP1_"}) - self.dataset=AttributeSetter({"group":self.group}) + def setUp(self): + self.group = MockDataSetGroup( + {"genofile": "~/genofiles/g1_file", "name": "GP1_","species":"Human"}) + self.dataset = AttributeSetter({"fullname":"dataser_1","group": self.group,"type":"ProbeSet"}) + self.trait=AttributeSetter({"symbol":"IGFI","chr":"X1","mb":123313}) + + def tearDown(self): + self.dataset = AttributeSetter( + {"group": {"location": "~/genofiles/g1_file"}}) + + def test_get_genofile_samplelist(self): + + results_1 = get_genofile_samplelist(self.dataset) + self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) + self.group.genofile = "~/genofiles/g2_file" + result_2 = get_genofile_samplelist(self.dataset) + self.assertEqual(result_2, []) + + @mock.patch("wqflask.marker_regression.run_mapping.data_set") + def test_geno_db_exists(self, mock_data_set): + mock_data_set.create_dataset.side_effect = [ + AttributeSetter({}), Exception()] + results_no_error = geno_db_exists(self.dataset) + results_with_error = geno_db_exists(self.dataset) + + self.assertEqual(mock_data_set.create_dataset.call_count, 2) + self.assertEqual(results_with_error, "False") + self.assertEqual(results_no_error, "True") + + + def test_trim_markers_for_figure(self): - def tearDown(self): - self.dataset=AttributeSetter({"group":{"location":"~/genofiles/g1_file"}}) - def test_get_genofile_samplelist(self): + markers=[{ + "name":"MK1", + "chr":"C1", + "cM":"1", + "Mb":"12000", + "genotypes":[], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name":"MK2", + "chr":"C2", + "cM":"15", + "Mb":"10000", + "genotypes":[], + "lod_score":0.7 + }, + { + "name":"MK1", + "chr":"C3", + "cM":"45", + "Mb":"1", + "genotypes":[], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + }] - results_1=get_genofile_samplelist(self.dataset) - self.assertEqual(results_1,["S1","S2","S3","S4"]) - self.group.genofile="~/genofiles/g2_file" - result_2=get_genofile_samplelist(self.dataset) - self.assertEqual(result_2,[]) + marker_2=[{ + "name":"MK1", + "chr":"C1", + "cM":"1", + "Mb":"12000", + "genotypes":[], + "dominance":"TT", + "additive":"VA", + "p_wald":4.6 + }] + results=trim_markers_for_figure(markers) + result_2=trim_markers_for_figure(marker_2) + expected=[ + { + "name":"MK1", + "chr":"C1", + "cM":"1", + "Mb":"12000", + "genotypes":[], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name":"MK1", + "chr":"C3", + "cM":"45", + "Mb":"1", + "genotypes":[], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + } - @mock.patch("wqflask.marker_regression.run_mapping.data_set") - def test_geno_db_exists(self,mock_data_set): - mock_data_set.create_dataset.side_effect=[AttributeSetter({}),Exception()] - results_no_error=geno_db_exists(self.dataset) - results_with_error=geno_db_exists(self.dataset) + ] + self.assertEqual(results,expected) + self.assertEqual(result_2,marker_2) - self.assertEqual(mock_data_set.create_dataset.call_count,2) - self.assertEqual(results_with_error,"False") - self.assertEqual(results_no_error,"True") + def test_export_mapping_results(self): + datetime_mock=mock.Mock(wraps=datetime.datetime) + datetime_mock.now.return_value=datetime.datetime(2019,9,1,10,12,12) + markers=[{ + "name":"MK1", + "chr":"C1", + "cM":"1", + "Mb":"12000", + "genotypes":[], + "dominance":"TT", + "additive":"VA", + "lod_score":3 + }, + { + "name":"MK2", + "chr":"C2", + "cM":"15", + "Mb":"10000", + "genotypes":[], + "lod_score":7 + }, + { + "name":"MK1", + "chr":"C3", + "cM":"45", + "Mb":"1", + "genotypes":[], + "dominance":"Tt", + "additive":"VE", + "lod_score":7 + }] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + + # mock_open.assert_called_once_with("~/results","w+") + # filehandler=mock_open() + with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime",new=datetime_mock): + export_mapping_results(dataset=self.dataset,trait=self.trait,markers=markers,results_path="~/results",mapping_scale="physic",score_type="-log(p)") + + write_calls=[ + mock.call('Time/Date: 09/01/19 / 10:12:12\n'), + mock.call('Population: Human GP1_\n'),mock.call('Data Set: dataser_1\n'), + mock.call('Gene Symbol: IGFI\n'), mock.call('Location: X1 @ 123313 Mb\n'), + mock.call('\n'), mock.call('Name,Chr,'), + mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call(',Additive'),mock.call(',Dominance'), + mock.call('\n'),mock.call('MK1,C1,'), + mock.call('12000,'), mock.call('1,'), + mock.call('3'), mock.call(',VA'), + mock.call(',TT'),mock.call('\n'), + mock.call('MK2,C2,'),mock.call('10000,'), + mock.call('15,'), mock.call('7'), + mock.call('\n'), mock.call('MK1,C3,'), + mock.call('1,'),mock.call('45,'), + mock.call('7'), mock.call(',VE'), + mock.call(',Tt') + ] + mock_open.assert_called_once_with("~/results","w+") + filehandler=mock_open() + filehandler.write.assert_has_calls(write_calls) \ No newline at end of file -- cgit v1.2.3 From 96dd0a10f0bfe66afab9701dd028f169d63cdae5 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Tue, 10 Nov 2020 19:56:07 +0300 Subject: add tests for write input for browser in marker_regression/run_mapping.py --- .../wqflask/marker_regression/test_run_mapping.py | 277 +++++++++++---------- 1 file changed, 144 insertions(+), 133 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index e925ad28..6521c41d 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -24,9 +24,11 @@ class MockDataSetGroup(AttributeSetter): class TestRunMapping(unittest.TestCase): def setUp(self): self.group = MockDataSetGroup( - {"genofile": "~/genofiles/g1_file", "name": "GP1_","species":"Human"}) - self.dataset = AttributeSetter({"fullname":"dataser_1","group": self.group,"type":"ProbeSet"}) - self.trait=AttributeSetter({"symbol":"IGFI","chr":"X1","mb":123313}) + {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) + self.dataset = AttributeSetter( + {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + self.trait = AttributeSetter( + {"symbol": "IGFI", "chr": "X1", "mb": 123313}) def tearDown(self): self.dataset = AttributeSetter( @@ -51,137 +53,146 @@ class TestRunMapping(unittest.TestCase): self.assertEqual(results_with_error, "False") self.assertEqual(results_no_error, "True") - def test_trim_markers_for_figure(self): - - markers=[{ - "name":"MK1", - "chr":"C1", - "cM":"1", - "Mb":"12000", - "genotypes":[], - "dominance":"TT", - "additive":"VA", - "lod_score":0.5 - }, - { - "name":"MK2", - "chr":"C2", - "cM":"15", - "Mb":"10000", - "genotypes":[], - "lod_score":0.7 - }, - { - "name":"MK1", - "chr":"C3", - "cM":"45", - "Mb":"1", - "genotypes":[], - "dominance":"Tt", - "additive":"VE", - "lod_score":1 - }] - - marker_2=[{ - "name":"MK1", - "chr":"C1", - "cM":"1", - "Mb":"12000", - "genotypes":[], - "dominance":"TT", - "additive":"VA", - "p_wald":4.6 - }] - results=trim_markers_for_figure(markers) - result_2=trim_markers_for_figure(marker_2) - expected=[ - { - "name":"MK1", - "chr":"C1", - "cM":"1", - "Mb":"12000", - "genotypes":[], - "dominance":"TT", - "additive":"VA", - "lod_score":0.5 - }, - { - "name":"MK1", - "chr":"C3", - "cM":"45", - "Mb":"1", - "genotypes":[], - "dominance":"Tt", - "additive":"VE", - "lod_score":1 - } - - ] - self.assertEqual(results,expected) - self.assertEqual(result_2,marker_2) + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":0.7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + }] + + marker_2 = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "p_wald":4.6 + }] + results = trim_markers_for_figure(markers) + result_2 = trim_markers_for_figure(marker_2) + expected = [ + { + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + } + + ] + self.assertEqual(results, expected) + self.assertEqual(result_2, marker_2) def test_export_mapping_results(self): - datetime_mock=mock.Mock(wraps=datetime.datetime) - datetime_mock.now.return_value=datetime.datetime(2019,9,1,10,12,12) - - markers=[{ - "name":"MK1", - "chr":"C1", - "cM":"1", - "Mb":"12000", - "genotypes":[], - "dominance":"TT", - "additive":"VA", - "lod_score":3 - }, - { - "name":"MK2", - "chr":"C2", - "cM":"15", - "Mb":"10000", - "genotypes":[], - "lod_score":7 - }, - { - "name":"MK1", - "chr":"C3", - "cM":"45", - "Mb":"1", - "genotypes":[], - "dominance":"Tt", - "additive":"VE", - "lod_score":7 - }] - - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - - # mock_open.assert_called_once_with("~/results","w+") - # filehandler=mock_open() - with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime",new=datetime_mock): - export_mapping_results(dataset=self.dataset,trait=self.trait,markers=markers,results_path="~/results",mapping_scale="physic",score_type="-log(p)") - - - write_calls=[ - mock.call('Time/Date: 09/01/19 / 10:12:12\n'), - mock.call('Population: Human GP1_\n'),mock.call('Data Set: dataser_1\n'), - mock.call('Gene Symbol: IGFI\n'), mock.call('Location: X1 @ 123313 Mb\n'), - mock.call('\n'), mock.call('Name,Chr,'), - mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), - mock.call(',Additive'),mock.call(',Dominance'), - mock.call('\n'),mock.call('MK1,C1,'), - mock.call('12000,'), mock.call('1,'), - mock.call('3'), mock.call(',VA'), - mock.call(',TT'),mock.call('\n'), - mock.call('MK2,C2,'),mock.call('10000,'), - mock.call('15,'), mock.call('7'), - mock.call('\n'), mock.call('MK1,C3,'), - mock.call('1,'),mock.call('45,'), - mock.call('7'), mock.call(',VE'), - mock.call(',Tt') - - ] - mock_open.assert_called_once_with("~/results","w+") - filehandler=mock_open() - filehandler.write.assert_has_calls(write_calls) \ No newline at end of file + datetime_mock = mock.Mock(wraps=datetime.datetime) + datetime_mock.now.return_value = datetime.datetime( + 2019, 9, 1, 10, 12, 12) + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":3 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":7 + }] + + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + + with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): + export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, + results_path="~/results", mapping_scale="physic", score_type="-log(p)") + + write_calls = [ + mock.call('Time/Date: 09/01/19 / 10:12:12\n'), + mock.call('Population: Human GP1_\n'), mock.call( + 'Data Set: dataser_1\n'), + mock.call('Gene Symbol: IGFI\n'), mock.call( + 'Location: X1 @ 123313 Mb\n'), + mock.call('\n'), mock.call('Name,Chr,'), + mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call(',Additive'), mock.call(',Dominance'), + mock.call('\n'), mock.call('MK1,C1,'), + mock.call('12000,'), mock.call('1,'), + mock.call('3'), mock.call(',VA'), + mock.call(',TT'), mock.call('\n'), + mock.call('MK2,C2,'), mock.call('10000,'), + mock.call('15,'), mock.call('7'), + mock.call('\n'), mock.call('MK1,C3,'), + mock.call('1,'), mock.call('45,'), + mock.call('7'), mock.call(',VE'), + mock.call(',Tt') + + ] + mock_open.assert_called_once_with("~/results", "w+") + filehandler = mock_open() + filehandler.write.assert_has_calls(write_calls) + + + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") + def test_write_input_for_browser(self,mock_choice): + mock_choice.side_effect=["F","i","l","e","s","x"] + with mock.patch("builtins.open",mock.mock_open()) as mock_open: + expected=['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] + + results=write_input_for_browser(this_dataset=self.dataset,gwas_results={},annotations={}) + self.assertEqual(results,expected) -- cgit v1.2.3 From 424f44c0656da8f99dce0fa0a00bd5e6ba9bace3 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 11 Nov 2020 23:05:17 +0300 Subject: add tests for marker_regression/gemma_mapping.py --- wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index 06ce55d8..ed72cb33 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -151,18 +151,21 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 mock_open.assert_called_once_with( "/home/user/img/gema_file_output.assoc.txt") self.assertEqual(results, expected) + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") def test_parse_gemma_output_empty_return(self): output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") self.assertEqual(results, []) + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_found(self, mock_os): mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" pass + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): -- cgit v1.2.3 From 3396e1f008f3605439b38837f7a50407588d1f9b Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 11 Nov 2020 23:06:27 +0300 Subject: add tests for marker_regression/run_mapping.py --- .../wqflask/marker_regression/test_run_mapping.py | 85 ++++++++++++++++++++++ 1 file changed, 85 insertions(+) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index 6521c41d..be6e6e48 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -7,6 +7,8 @@ from wqflask.marker_regression.run_mapping import geno_db_exists from wqflask.marker_regression.run_mapping import write_input_for_browser from wqflask.marker_regression.run_mapping import export_mapping_results from wqflask.marker_regression.run_mapping import trim_markers_for_figure +from wqflask.marker_regression.run_mapping import get_perm_strata +from wqflask.marker_regression.run_mapping import get_chr_lengths class AttributeSetter: @@ -23,10 +25,27 @@ class MockDataSetGroup(AttributeSetter): class TestRunMapping(unittest.TestCase): def setUp(self): + self.group = MockDataSetGroup( {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) + chromosomes={ + "3":AttributeSetter({ + "name":"C1", + "length":"0.04" + }), + "4":AttributeSetter({ + "name":"C2", + "length":"0.03" + }), + "5":AttributeSetter({ + "name":"C4", + "length":"0.01" + }) + } self.dataset = AttributeSetter( {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + + self.chromosomes=AttributeSetter({"chromosomes":chromosomes}) self.trait = AttributeSetter( {"symbol": "IGFI", "chr": "X1", "mb": 123313}) @@ -196,3 +215,69 @@ class TestRunMapping(unittest.TestCase): results=write_input_for_browser(this_dataset=self.dataset,gwas_results={},annotations={}) self.assertEqual(results,expected) + + + def test_get_perm_strata(self): + categorical_vars=["C1","C2","W1"] + used_samples=["S1","S2"] + sample_list=AttributeSetter({"sample_attribute_values":{ + "S1":{ + "C1":"c1_value", + "C2":"c2_value", + "W1":"w1_value" + + }, + "S2":{ + "W1":"w2_value", + "W2":"w2_value" + + }, + "S3":{ + + "C1":"c1_value", + "C2":"c2_value" + + }, + + }}) + + results=get_perm_strata(this_trait={},sample_list=sample_list,categorical_vars=categorical_vars,used_samples=used_samples) + self.assertEqual(results,[2,1]) + + + def test_get_chr_length(self): + chromosomes=AttributeSetter({"chromosomes":self.chromosomes}) + dataset=AttributeSetter({"species":chromosomes}) + results=get_chr_lengths(mapping_scale="physic",mapping_method="reaper",dataset=dataset,qtl_results=[]) + chr_lengths=[] + for key,chromo in self.chromosomes.chromosomes.items(): + chr_lengths.append({"chr":chromo.name,"size":chromo.length}) + + self.assertEqual(chr_lengths,results) + + qtl_results=[{ + "chr":"16", + "cM":"0.2" + }, + { + "chr":"12", + "cM":"0.5" + }, + { + "chr":"18", + "cM":"0.1" + }, + { + "chr":"22", + "cM":"0.4" + }, + ] + + + + result_with_other_mapping_scale=get_chr_lengths(mapping_scale="other",mapping_method="reaper",dataset=dataset,qtl_results=qtl_results) + expected_value= [{'chr': '1', 'size': '0'}, {'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] + + self.assertEqual(result_with_other_mapping_scale,expected_value) + + -- cgit v1.2.3 From 8f85c96b2094a9ce722b93a0e375ec3de90c959a Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 11 Nov 2020 23:08:14 +0300 Subject: add tests for marker_regression/qtlreaper_mapping.py --- .../marker_regression/test_qtlreaper_mapping.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py new file mode 100644 index 00000000..7ece663a --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -0,0 +1,22 @@ +import unittest +from unittest import mock +from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file +from wqflask.marker_regression.qtlreaper_mapping import natural_sort + +#issues some methods in genofile object are not defined +#modify samples should equal to vals +class TestQtlReaperMapping(unittest.TestCase): + @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + vals=["V1","x","V4","V3","x"] + samples=["S1","S2","S3","S4","S5"] + trait_filename="trait_file" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") + filehandler=mock_open() + write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] + + filehandler.write.assert_has_calls(write_calls) + + -- cgit v1.2.3 From e63e85868ed7b63bbe784368b3c1babf0d1f2088 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 11 Nov 2020 23:09:01 +0300 Subject: add tests for marker_regression/rqtl_mapping.py --- .../wqflask/marker_regression/test_rqtl_mapping.py | 55 ++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py new file mode 100644 index 00000000..641644cc --- /dev/null +++ b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py @@ -0,0 +1,55 @@ +import unittest +from unittest import mock +from wqflask import app +from wqflask.marker_regression.rqtl_mapping import get_trait_data_type +from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype +from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names + +class TestRqtlMapping(unittest.TestCase): + + def setUp(self): + self.app_context=app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + + @mock.patch("wqflask.marker_regression.rqtl_mapping.g") + @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") + def test_get_trait_data_type_found(self,mock_logger,mock_db): + caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results=get_trait_data_type("traid_id") + mock_db.db.execute.assert_called_with(caller_value) + self.assertEqual(results,"fer434f") + + + @mock.patch("wqflask.marker_regression.rqtl_mapping.g") + @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") + def test_get_trait_data_type_not_found(self,mock_logger,mock_db): + caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results=get_trait_data_type("other") + mock_db.db.execute.assert_called_with(caller_value) + self.assertEqual(results,"numeric") + + def test_sanitize_rqtl_phenotype(self): + vals=['f',"x","r","x","x"] + results=sanitize_rqtl_phenotype(vals) + expected_phenotype_string='c(f,NA,r,NA,NA)' + + self.assertEqual(results,expected_phenotype_string) + + def test_sanitize_rqtl_names(self): + vals=['f',"x","r","x","x"] + expected_sanitized_name="c('f',NA,'r',NA,NA)" + results=sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name,results) + + + + + + + -- cgit v1.2.3 From f4dbdc51102d942079c7159ac48071282ec995ea Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Thu, 12 Nov 2020 00:45:03 +0300 Subject: modify tests for marker regression --- .../marker_regression/test_gemma_mapping.py | 8 ++ .../marker_regression/test_plink_mapping.py | 4 + .../marker_regression/test_qtlreaper_mapping.py | 3 +- .../wqflask/marker_regression/test_rqtl_mapping.py | 13 +- .../wqflask/marker_regression/test_run_mapping.py | 153 +++++++++++---------- 5 files changed, 93 insertions(+), 88 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index ed72cb33..e47c8335 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -24,6 +24,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): + """add tests for gemma function where first run is set to false""" dataset = AttributeSetter( {"group": AttributeSetter({"genofile": "genofile.geno"})}) @@ -50,6 +51,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + """add tests for run_gemma where first run is set to true""" chromosomes = [] for i in range(1, 5): chromosomes.append(AttributeSetter({"name": f"CH{i}"})) @@ -81,6 +83,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") def test_gen_pheno_txt_file(self): + """add tests for generating pheno txt file""" with mock.patch("builtins.open", mock.mock_open())as mock_open: gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ "x", "w", "q", "we", "R"], trait_filename="fitr.re") @@ -97,6 +100,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset") def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): + """add tests for generating covariates files""" covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" samplelist = ["X1", "X2", "X3", "X4"] create_dataset_side_effect = [] @@ -138,6 +142,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") def test_parse_gemma_output_obj_returned(self): + """add test for generating gemma output with obj returned""" file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 @@ -154,6 +159,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") def test_parse_gemma_output_empty_return(self): + """add tests for parse gemma output where nothing returned""" output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: results = parse_gemma_output(genofile_name="gema_file") @@ -162,6 +168,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_found(self, mock_os): + """add tests for parse loco output file found""" mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" pass @@ -169,6 +176,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") def test_parse_loco_output_file_not_found(self, mock_os): + """add tests for parse loco output file not found""" mock_os.path.isfile.return_value = False file_to_write = """{"files":["file_1","file_2"]}""" diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py index a5fa0c04..428f45b9 100644 --- a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py @@ -15,6 +15,7 @@ class AttributeSetter: class TestPlinkMapping(unittest.TestCase): def test_build_line_list(self): + """testing for building line list""" line_1 = "this is line one test" irregular_line = " this is an, irregular line " exp_line1 = ["this", "is", "line", "one", "test"] @@ -26,6 +27,7 @@ class TestPlinkMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.plink_mapping.flat_files") def test_get_samples_from_ped_file(self, mock_flat_files): + """test for getting samples from ped file""" dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) file_sample = """Expected_1\tline test Expected_2\there @@ -41,6 +43,7 @@ Expected_2\there @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") def test_gen_pheno_txt_file_plink(self, mock_samples): + """test for getting gen_pheno txt file""" mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] trait = AttributeSetter({"name": "TX"}) @@ -62,6 +65,7 @@ Expected_2\there @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list") def test_parse_plink_output(self, mock_line_list): + """test for parsing plink output""" chromosomes = [0, 34, 110, 89, 123, 23, 2] species = AttributeSetter( {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) diff --git a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py index 7ece663a..b47f877a 100644 --- a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -1,13 +1,12 @@ import unittest from unittest import mock from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file -from wqflask.marker_regression.qtlreaper_mapping import natural_sort #issues some methods in genofile object are not defined #modify samples should equal to vals class TestQtlReaperMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): + def test_gen_pheno_txt_file(self): vals=["V1","x","V4","V3","x"] samples=["S1","S2","S3","S4","S5"] trait_filename="trait_file" diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py index 641644cc..9fd32a30 100644 --- a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py @@ -18,23 +18,15 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") def test_get_trait_data_type_found(self,mock_logger,mock_db): + """test for getting trait data_type return True""" caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results=get_trait_data_type("traid_id") mock_db.db.execute.assert_called_with(caller_value) self.assertEqual(results,"fer434f") - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data_type_not_found(self,mock_logger,mock_db): - caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("other") - mock_db.db.execute.assert_called_with(caller_value) - self.assertEqual(results,"numeric") - def test_sanitize_rqtl_phenotype(self): + """test for sanitizing rqtl phenotype""" vals=['f',"x","r","x","x"] results=sanitize_rqtl_phenotype(vals) expected_phenotype_string='c(f,NA,r,NA,NA)' @@ -42,6 +34,7 @@ class TestRqtlMapping(unittest.TestCase): self.assertEqual(results,expected_phenotype_string) def test_sanitize_rqtl_names(self): + """test for sanitzing rqtl names""" vals=['f',"x","r","x","x"] expected_sanitized_name="c('f',NA,'r',NA,NA)" results=sanitize_rqtl_names(vals) diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index be6e6e48..2af4c3e3 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -28,24 +28,24 @@ class TestRunMapping(unittest.TestCase): self.group = MockDataSetGroup( {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) - chromosomes={ - "3":AttributeSetter({ - "name":"C1", - "length":"0.04" - }), - "4":AttributeSetter({ - "name":"C2", - "length":"0.03" - }), - "5":AttributeSetter({ - "name":"C4", - "length":"0.01" - }) - } + chromosomes = { + "3": AttributeSetter({ + "name": "C1", + "length": "0.04" + }), + "4": AttributeSetter({ + "name": "C2", + "length": "0.03" + }), + "5": AttributeSetter({ + "name": "C4", + "length": "0.01" + }) + } self.dataset = AttributeSetter( {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) - self.chromosomes=AttributeSetter({"chromosomes":chromosomes}) + self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) self.trait = AttributeSetter( {"symbol": "IGFI", "chr": "X1", "mb": 123313}) @@ -142,6 +142,7 @@ class TestRunMapping(unittest.TestCase): self.assertEqual(result_2, marker_2) def test_export_mapping_results(self): + """test for exporting mapping results""" datetime_mock = mock.Mock(wraps=datetime.datetime) datetime_mock.now.return_value = datetime.datetime( 2019, 9, 1, 10, 12, 12) @@ -206,78 +207,78 @@ class TestRunMapping(unittest.TestCase): filehandler = mock_open() filehandler.write.assert_has_calls(write_calls) - @mock.patch("wqflask.marker_regression.run_mapping.random.choice") - def test_write_input_for_browser(self,mock_choice): - mock_choice.side_effect=["F","i","l","e","s","x"] - with mock.patch("builtins.open",mock.mock_open()) as mock_open: - expected=['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] - - results=write_input_for_browser(this_dataset=self.dataset,gwas_results={},annotations={}) - self.assertEqual(results,expected) + def test_write_input_for_browser(self, mock_choice): + """test for writing input for browser""" + mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] + results = write_input_for_browser( + this_dataset=self.dataset, gwas_results={}, annotations={}) + self.assertEqual(results, expected) def test_get_perm_strata(self): - categorical_vars=["C1","C2","W1"] - used_samples=["S1","S2"] - sample_list=AttributeSetter({"sample_attribute_values":{ - "S1":{ - "C1":"c1_value", - "C2":"c2_value", - "W1":"w1_value" + categorical_vars = ["C1", "C2", "W1"] + used_samples = ["S1", "S2"] + sample_list = AttributeSetter({"sample_attribute_values": { + "S1": { + "C1": "c1_value", + "C2": "c2_value", + "W1": "w1_value" - }, - "S2":{ - "W1":"w2_value", - "W2":"w2_value" + }, + "S2": { + "W1": "w2_value", + "W2": "w2_value" - }, - "S3":{ + }, + "S3": { - "C1":"c1_value", - "C2":"c2_value" + "C1": "c1_value", + "C2": "c2_value" - }, - - }}) + }, - results=get_perm_strata(this_trait={},sample_list=sample_list,categorical_vars=categorical_vars,used_samples=used_samples) - self.assertEqual(results,[2,1]) + }}) + results = get_perm_strata(this_trait={}, sample_list=sample_list, + categorical_vars=categorical_vars, used_samples=used_samples) + self.assertEqual(results, [2, 1]) def test_get_chr_length(self): - chromosomes=AttributeSetter({"chromosomes":self.chromosomes}) - dataset=AttributeSetter({"species":chromosomes}) - results=get_chr_lengths(mapping_scale="physic",mapping_method="reaper",dataset=dataset,qtl_results=[]) - chr_lengths=[] - for key,chromo in self.chromosomes.chromosomes.items(): - chr_lengths.append({"chr":chromo.name,"size":chromo.length}) - - self.assertEqual(chr_lengths,results) - - qtl_results=[{ - "chr":"16", - "cM":"0.2" - }, - { - "chr":"12", - "cM":"0.5" - }, - { - "chr":"18", - "cM":"0.1" - }, - { - "chr":"22", - "cM":"0.4" - }, - ] - - - - result_with_other_mapping_scale=get_chr_lengths(mapping_scale="other",mapping_method="reaper",dataset=dataset,qtl_results=qtl_results) - expected_value= [{'chr': '1', 'size': '0'}, {'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] - - self.assertEqual(result_with_other_mapping_scale,expected_value) + """test for getting chromosome length""" + chromosomes = AttributeSetter({"chromosomes": self.chromosomes}) + dataset = AttributeSetter({"species": chromosomes}) + results = get_chr_lengths( + mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[]) + chr_lengths = [] + for key, chromo in self.chromosomes.chromosomes.items(): + chr_lengths.append({"chr": chromo.name, "size": chromo.length}) + + self.assertEqual(chr_lengths, results) + + qtl_results = [{ + "chr": "16", + "cM": "0.2" + }, + { + "chr": "12", + "cM": "0.5" + }, + { + "chr": "18", + "cM": "0.1" + }, + { + "chr": "22", + "cM": "0.4" + }, + ] + result_with_other_mapping_scale = get_chr_lengths( + mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results) + expected_value = [{'chr': '1', 'size': '0'}, { + 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] + self.assertEqual(result_with_other_mapping_scale, expected_value) -- cgit v1.2.3 From a48e8d5e652551eb2d57953304ea0ec3587217ce Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Thu, 12 Nov 2020 21:11:28 +0300 Subject: add test for parse gemma output in marker_regression/gemma_mapping.py --- .../marker_regression/test_gemma_mapping.py | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index e47c8335..bcc5dab9 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -167,11 +167,29 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") - def test_parse_loco_output_file_found(self, mock_os): + @mock.patch("wqflask.marker_regression.gemma_mapping.json") + def test_parse_loco_output_file_found(self,mock_json,mock_os): """add tests for parse loco output file found""" + mock_json.load.return_value={ + "files":[["file_name","user","~/file1"], + ["file_name","user","~/file2"]] + } + return_file_1="""X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" + return_file_2="""chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" - pass + with mock.patch("builtins.open") as mock_open: + + handles=(mock.mock_open(read_data="gwas").return_value,mock.mock_open(read_data=return_file_1).return_value,mock.mock_open(read_data=return_file_2).return_value) + mock_open.side_effect=handles + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + expected_results= [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + + self.assertEqual(expected_results,results) + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") -- cgit v1.2.3 From da794df7cf9094fc81edbcf007149db86bf68d01 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Thu, 12 Nov 2020 21:12:48 +0300 Subject: add pep8 fixes in marker_regression/gemma_mapping.py --- .../marker_regression/test_gemma_mapping.py | 23 +++++++++++----------- 1 file changed, 12 insertions(+), 11 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index bcc5dab9..a44ccb00 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -168,28 +168,29 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.json") - def test_parse_loco_output_file_found(self,mock_json,mock_os): + def test_parse_loco_output_file_found(self, mock_json, mock_os): """add tests for parse loco output file found""" - mock_json.load.return_value={ - "files":[["file_name","user","~/file1"], - ["file_name","user","~/file2"]] + mock_json.load.return_value = { + "files": [["file_name", "user", "~/file1"], + ["file_name", "user", "~/file2"]] } - return_file_1="""X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 + return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" - return_file_2="""chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" + return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" mock_os.path.isfile.return_value = True file_to_write = """{"files":["file_1","file_2"]}""" with mock.patch("builtins.open") as mock_open: - handles=(mock.mock_open(read_data="gwas").return_value,mock.mock_open(read_data=return_file_1).return_value,mock.mock_open(read_data=return_file_2).return_value) - mock_open.side_effect=handles + handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( + read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) + mock_open.side_effect = handles results = parse_loco_output( this_dataset={}, gwa_output_filename=".xw/") - expected_results= [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] - - self.assertEqual(expected_results,results) + expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { + 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + self.assertEqual(expected_results, results) @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") -- cgit v1.2.3 From d4b3e8f43c4f4b10fb9614d80cb9d4e2a723c879 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Thu, 12 Nov 2020 21:40:49 +0300 Subject: refactor code --- wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index a44ccb00..af20c1b8 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -28,13 +28,12 @@ class TestGemmaMapping(unittest.TestCase): dataset = AttributeSetter( {"group": AttributeSetter({"genofile": "genofile.geno"})}) - output_files = "file1" - use_loco = False + output_file = "file1" mock_parse_loco.return_value = [] this_trait = AttributeSetter({"name": "t1"}) result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ - ], covariates="", use_loco=True, first_run=False, output_files=output_files) + ], covariates="", use_loco=True, first_run=False, output_files=output_file) expected_results = ([], "file1") self.assertEqual(expected_results, result) -- cgit v1.2.3 From ceeae6fd087d91637c5007e0433ce347048fa96d Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Tue, 17 Nov 2020 22:31:10 +0300 Subject: use better function names --- .../tests/wqflask/marker_regression/test_gemma_mapping.py | 14 +++++++------- .../tests/wqflask/marker_regression/test_rqtl_mapping.py | 2 +- .../tests/wqflask/marker_regression/test_run_mapping.py | 2 +- 3 files changed, 9 insertions(+), 9 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py index af20c1b8..4fafd95a 100644 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py @@ -23,7 +23,7 @@ class MockDatasetGroup(AttributeSetter): class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - def test_run_gemma_first_run_loco_set_false(self, mock_parse_loco): + def test_run_gemma_firstrun_set_false(self, mock_parse_loco): """add tests for gemma function where first run is set to false""" dataset = AttributeSetter( {"group": AttributeSetter({"genofile": "genofile.geno"})}) @@ -49,7 +49,7 @@ class TestGemmaMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.run_mapping.random.choice") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_first_run_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): """add tests for run_gemma where first run is set to true""" chromosomes = [] for i in range(1, 5): @@ -140,7 +140,7 @@ class TestGemmaMapping(unittest.TestCase): '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") - def test_parse_gemma_output_obj_returned(self): + def test_parse_gemma_output(self): """add test for generating gemma output with obj returned""" file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 @@ -157,7 +157,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 self.assertEqual(results, expected) @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_parse_gemma_output_empty_return(self): + def test_parse_gemma_output_with_empty_return(self): """add tests for parse gemma output where nothing returned""" output_file_results = """chr\t today""" with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: @@ -167,7 +167,7 @@ X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") @mock.patch("wqflask.marker_regression.gemma_mapping.json") - def test_parse_loco_output_file_found(self, mock_json, mock_os): + def test_parse_loco_outputfile_found(self, mock_json, mock_os): """add tests for parse loco output file found""" mock_json.load.return_value = { "files": [["file_name", "user", "~/file1"], @@ -193,8 +193,8 @@ chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") @mock.patch("wqflask.marker_regression.gemma_mapping.os") - def test_parse_loco_output_file_not_found(self, mock_os): - """add tests for parse loco output file not found""" + def test_parse_loco_outputfile_not_found(self, mock_os): + """add tests for parse loco output where output file not found""" mock_os.path.isfile.return_value = False file_to_write = """{"files":["file_1","file_2"]}""" diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py index 9fd32a30..69f53721 100644 --- a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py @@ -17,7 +17,7 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.g") @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data_type_found(self,mock_logger,mock_db): + def test_get_trait_data(self,mock_logger,mock_db): """test for getting trait data_type return True""" caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py index 2af4c3e3..a134f551 100644 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py @@ -62,7 +62,7 @@ class TestRunMapping(unittest.TestCase): self.assertEqual(result_2, []) @mock.patch("wqflask.marker_regression.run_mapping.data_set") - def test_geno_db_exists(self, mock_data_set): + def test_if_geno_db_exists(self, mock_data_set): mock_data_set.create_dataset.side_effect = [ AttributeSetter({}), Exception()] results_no_error = geno_db_exists(self.dataset) -- cgit v1.2.3 From 9d3493f2e8ee2d2185854b95d2b13a5d2b4e38e1 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 18 Nov 2020 02:18:45 +0300 Subject: use f strings in marker_regression/plink_mapping --- wqflask/wqflask/marker_regression/plink_mapping.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py index 8d57d556..5d675c38 100644 --- a/wqflask/wqflask/marker_regression/plink_mapping.py +++ b/wqflask/wqflask/marker_regression/plink_mapping.py @@ -9,11 +9,11 @@ import utility.logger logger = utility.logger.getLogger(__name__ ) def run_plink(this_trait, dataset, species, vals, maf): - plink_output_filename = webqtlUtil.genRandStr("%s_%s_"%(dataset.group.name, this_trait.name)) + plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_") gen_pheno_txt_file(dataset, vals) - plink_command = PLINK_COMMAND + ' --noweb --bfile %s/%s --no-pheno --no-fid --no-parents --no-sex --maf %s --out %s%s --assoc ' % ( - flat_files('mapping'), dataset.group.name, maf, TMPDIR, plink_output_filename) + + plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc " logger.debug("plink_command:", plink_command) os.system(plink_command) @@ -29,12 +29,12 @@ def gen_pheno_txt_file(this_dataset, vals): """Generates phenotype file for GEMMA/PLINK""" current_file_data = [] - with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "r") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam", "r") as outfile: for i, line in enumerate(outfile): split_line = line.split() current_file_data.append(split_line) - with open("{}/{}.fam".format(flat_files('mapping'), this_dataset.group.name), "w") as outfile: + with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam","w") as outfile: for i, line in enumerate(current_file_data): if vals[i] == "x": this_val = -9 @@ -44,8 +44,8 @@ def gen_pheno_txt_file(this_dataset, vals): def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): ped_sample_list = get_samples_from_ped_file(dataset) - output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb") - header = 'FID\tIID\t%s\n' % this_trait.name + output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb") + header = f"FID\tIID\t{this_trait.name}\n" output_file.write(header) new_value_list = [] @@ -65,7 +65,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): for i, sample in enumerate(ped_sample_list): j = i+1 value = new_value_list[i] - new_line += '%s\t%s\t%s\n'%(sample, sample, value) + new_line += f"{sample}\t{sample}\t{value}\n" if j%1000 == 0: output_file.write(newLine) @@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''): # get strain name from ped file in order def get_samples_from_ped_file(dataset): - ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r") + ped_file= open(f"{flat_files('mapping')}{dataset.group.name}.ped","r") line = ped_file.readline() sample_list=[] @@ -98,7 +98,7 @@ def parse_plink_output(output_filename, species): threshold_p_value = 1 - result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb") + result_fp = open(f"{TMPDIR}{output_filename}.qassoc","rb") line = result_fp.readline() -- cgit v1.2.3 From 77dff447c83a4b0824fe6626d16484cfd826ca77 Mon Sep 17 00:00:00 2001 From: Alexanderlacuna Date: Wed, 18 Nov 2020 03:06:27 +0300 Subject: use f strings in marker_regression/qtlreaper_mapping.py --- .../wqflask/marker_regression/qtlreaper_mapping.py | 46 +++++++++++++--------- 1 file changed, 28 insertions(+), 18 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py index 78b1f7b0..505ae295 100644 --- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py +++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py @@ -17,22 +17,29 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo else: genofile_name = this_dataset.group.name - trait_filename = str(this_trait.name) + "_" + str(this_dataset.name) + "_pheno" + trait_filename =f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno" gen_pheno_txt_file(samples, vals, trait_filename) - output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + output_filename = (f"{this_dataset.group.name}_GWA_"+ + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ) bootstrap_filename = None permu_filename = None opt_list = [] if boot_check and num_bootstrap > 0: - bootstrap_filename = this_dataset.group.name + "_BOOTSTRAP_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" + + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + ) opt_list.append("-b") - opt_list.append("--n_bootstrap " + str(num_bootstrap)) - opt_list.append("--bootstrap_output " + webqtlConfig.GENERATED_IMAGE_DIR + bootstrap_filename + ".txt") + opt_list.append(f"--n_bootstrap{str(num_bootstrap)}") + opt_list.append(f"--bootstrap_output{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") if num_perm > 0: - permu_filename = this_dataset.group.name + "_PERM_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6)) + permu_filename =("{this_dataset.group.name}_PERM_" + + ''.join(random.choice(string.ascii_uppercase + + string.digits) for _ in range(6)) + ) opt_list.append("-n " + str(num_perm)) opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt") if control_marker != "" and do_control == "true": @@ -40,13 +47,15 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo if manhattan_plot != True: opt_list.append("--interval 1") - reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), - genofile_name, - TEMPDIR, - trait_filename, - " ".join(opt_list), - webqtlConfig.GENERATED_IMAGE_DIR, - output_filename) + reaper_command = (REAPER_COMMAND + + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'), + + genofile_name, + TEMPDIR, + trait_filename, + " ".join(opt_list), + webqtlConfig.GENERATED_IMAGE_DIR, + output_filename)) logger.debug("reaper_command:" + reaper_command) os.system(reaper_command) @@ -61,12 +70,13 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo suggestive = permu_vals[int(num_perm*0.37-1)] significant = permu_vals[int(num_perm*0.95-1)] - return marker_obs, permu_vals, suggestive, significant, bootstrap_vals, [output_filename, permu_filename, bootstrap_filename] + return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, + [output_filename, permu_filename, bootstrap_filename]) def gen_pheno_txt_file(samples, vals, trait_filename): """Generates phenotype file for GEMMA""" - with open("{}/gn2/{}.txt".format(TEMPDIR, trait_filename), "w") as outfile: + with open(f"{TEMPDIR}/gn2/{trait_filename}.txt","w") as outfile: outfile.write("Trait\t") filtered_sample_list = [] @@ -90,7 +100,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): only_cm = False only_mb = False - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, gwa_filename)) as output_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{gwa_filename}.txt") as output_file: for line in output_file: if line.startswith("ID\t"): if len(line.split("\t")) < 8: @@ -137,13 +147,13 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename): permu_vals = [] if permu_filename: - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, permu_filename)) as permu_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{permu_filename}.txt") as permu_file: for line in permu_file: permu_vals.append(float(line)) bootstrap_vals = [] if bootstrap_filename: - with open("{}{}.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, bootstrap_filename)) as bootstrap_file: + with open(f"{webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt") as bootstrap_file: for line in bootstrap_file: bootstrap_vals.append(int(line)) -- cgit v1.2.3 From 7f35213b64707e7c61affb6fa376f561200ac1d6 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Fri, 27 Nov 2020 19:59:17 +0300 Subject: move tests to unit folder --- .../marker_regression/test_gemma_mapping.py | 205 +++++++++++++++ .../marker_regression/test_plink_mapping.py | 84 ++++++ .../marker_regression/test_qtlreaper_mapping.py | 21 ++ .../wqflask/marker_regression/test_rqtl_mapping.py | 48 ++++ .../wqflask/marker_regression/test_run_mapping.py | 284 +++++++++++++++++++++ .../marker_regression/test_gemma_mapping.py | 205 --------------- .../marker_regression/test_plink_mapping.py | 84 ------ .../marker_regression/test_qtlreaper_mapping.py | 21 -- .../wqflask/marker_regression/test_rqtl_mapping.py | 48 ---- .../wqflask/marker_regression/test_run_mapping.py | 284 --------------------- 10 files changed, 642 insertions(+), 642 deletions(-) create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py create mode 100644 wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_plink_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py delete mode 100644 wqflask/tests/wqflask/marker_regression/test_run_mapping.py (limited to 'wqflask') diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py new file mode 100644 index 00000000..5b621264 --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py @@ -0,0 +1,205 @@ +# test for wqflask/marker_regression/gemma_mapping.py +import unittest +import random +from unittest import mock +from wqflask.marker_regression.gemma_mapping import run_gemma +from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file +from wqflask.marker_regression.gemma_mapping import gen_covariates_file +from wqflask.marker_regression.gemma_mapping import parse_gemma_output +from wqflask.marker_regression.gemma_mapping import parse_loco_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) + + +class MockGroup(AttributeSetter): + def get_samplelist(self): + return None + + +class TestGemmaMapping(unittest.TestCase): + + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + def test_run_gemma_firstrun_set_false(self, mock_parse_loco): + """add tests for gemma function where first run is set to false""" + dataset = AttributeSetter( + {"group": AttributeSetter({"genofile": "genofile.geno"})}) + + output_file = "file1" + mock_parse_loco.return_value = [] + this_trait = AttributeSetter({"name": "t1"}) + + result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ + ], covariates="", use_loco=True, first_run=False, output_files=output_file) + + expected_results = ([], "file1") + self.assertEqual(expected_results, result) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") + @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") + @mock.patch("wqflask.marker_regression.gemma_mapping.logger") + @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") + def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): + """add tests for run_gemma where first run is set to true""" + chromosomes = [] + for i in range(1, 5): + chromosomes.append(AttributeSetter({"name": f"CH{i}"})) + chromo = AttributeSetter({"chromosomes": chromosomes}) + dataset_group = MockGroup( + {"name": "GP1", "genofile": "file_geno"}) + dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", + "species": AttributeSetter({"chromosomes": chromo})}) + trait = AttributeSetter({"name": "trait1"}) + samples = [] + mock_gen_pheno_txt.return_value = None + mock_os.path.isfile.return_value = True + mock_gen_covar.return_value = None + mock_choice.return_value = "R" + mock_flat_files.return_value = "/home/genotype/bimbam" + mock_parse_loco.return_value = [] + results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ + ], vals=[], covariates="", use_loco=True) + system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), + mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] + mock_os.system.assert_has_calls(system_calls) + mock_gen_pheno_txt.assert_called_once() + mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") + mock_os.path.isfile.assert_called_once_with( + ('/home/user/imgfile_output.assoc.txt')) + self.assertEqual(mock_logger.debug.call_count, 2) + self.assertEqual(mock_flat_files.call_count, 4) + self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + """add tests for generating pheno txt file""" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ + "x", "w", "q", "we", "R"], trait_filename="fitr.re") + mock_open.assert_called_once_with( + '/home/user/data/gn2/fitr.re.txt', 'w') + filehandler = mock_open() + values = ["x", "w", "q", "we", "R"] + write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( + 'q\n'), mock.call('we\n'), mock.call('R\n')] + + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") + @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") + @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset") + def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): + """add tests for generating covariates files""" + covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" + samplelist = ["X1", "X2", "X3", "X4"] + create_dataset_side_effect = [] + create_trait_side_effect = [] + + for i in range(4): + create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) + create_trait_side_effect.append( + AttributeSetter({"data": [f'data_{i}']})) + + create_dataset.side_effect = create_trait_side_effect + create_trait.side_effect = create_trait_side_effect + + group = MockGroup({"name": "group_X", "samplelist": samplelist}) + this_dataset = AttributeSetter({"group": group}) + flat_files.return_value = "Home/Genenetwork" + + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_covariates_file(this_dataset=this_dataset, covariates=covariates, + samples=["x1", "x2", "X3"]) + + create_dataset.assert_has_calls( + [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) + mock_calls = [] + trait_names = ["X1", "Y1", "M1", "V1"] + + for i, trait in enumerate(create_trait_side_effect): + mock_calls.append( + mock.call(dataset=trait, name=trait_names[i], cellid=None)) + + create_trait.assert_has_calls(mock_calls) + + flat_files.assert_called_once_with('mapping') + mock_open.assert_called_once_with( + 'Home/Genenetwork/group_X_covariates.txt', 'w') + filehandler = mock_open() + filehandler.write.assert_has_calls([mock.call( + '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") + def test_parse_gemma_output(self): + """add test for generating gemma output with obj returned""" + file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 +X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 +125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 +""" + with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: + results = parse_gemma_output(genofile_name="gema_file") + expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, + {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] + mock_open.assert_called_once_with( + "/home/user/img/gema_file_output.assoc.txt") + self.assertEqual(results, expected) + + @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") + def test_parse_gemma_output_with_empty_return(self): + """add tests for parse gemma output where nothing returned""" + output_file_results = """chr\t today""" + with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: + results = parse_gemma_output(genofile_name="gema_file") + self.assertEqual(results, []) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + @mock.patch("wqflask.marker_regression.gemma_mapping.json") + def test_parse_loco_outputfile_found(self, mock_json, mock_os): + """add tests for parse loco output file found""" + mock_json.load.return_value = { + "files": [["file_name", "user", "~/file1"], + ["file_name", "user", "~/file2"]] + } + return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 +chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" + return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" + mock_os.path.isfile.return_value = True + file_to_write = """{"files":["file_1","file_2"]}""" + with mock.patch("builtins.open") as mock_open: + + handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( + read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) + mock_open.side_effect = handles + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { + 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] + + self.assertEqual(expected_results, results) + + @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") + @mock.patch("wqflask.marker_regression.gemma_mapping.os") + def test_parse_loco_outputfile_not_found(self, mock_os): + """add tests for parse loco output where output file not found""" + + mock_os.path.isfile.return_value = False + file_to_write = """{"files":["file_1","file_2"]}""" + + with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open: + results = parse_loco_output( + this_dataset={}, gwa_output_filename=".xw/") + self.assertEqual(results, []) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py new file mode 100644 index 00000000..428f45b9 --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -0,0 +1,84 @@ +# test for wqflask/marker_regression/plink_mapping.py +import unittest +from unittest import mock +from wqflask.marker_regression.plink_mapping import build_line_list +from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file +from wqflask.marker_regression.plink_mapping import flat_files +from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink +from wqflask.marker_regression.plink_mapping import parse_plink_output + + +class AttributeSetter: + def __init__(self, obj): + for key, val in obj.items(): + setattr(self, key, val) +class TestPlinkMapping(unittest.TestCase): + + def test_build_line_list(self): + """testing for building line list""" + line_1 = "this is line one test" + irregular_line = " this is an, irregular line " + exp_line1 = ["this", "is", "line", "one", "test"] + + results = build_line_list(irregular_line) + self.assertEqual(exp_line1, build_line_list(line_1)) + self.assertEqual([], build_line_list()) + self.assertEqual(["this", "is", "an,", "irregular", "line"], results) + + @mock.patch("wqflask.marker_regression.plink_mapping.flat_files") + def test_get_samples_from_ped_file(self, mock_flat_files): + """test for getting samples from ped file""" + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + file_sample = """Expected_1\tline test +Expected_2\there + Expected_3\tthree""" + mock_flat_files.return_value = "/home/user/" + with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open: + results = get_samples_from_ped_file(dataset) + mock_flat_files.assert_called_once_with("mapping") + mock_open.assert_called_once_with("/home/user/n_1.ped", "r") + self.assertEqual( + ["Expected_1", "Expected_2", "Expected_3"], results) + + @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") + def test_gen_pheno_txt_file_plink(self, mock_samples): + """test for getting gen_pheno txt file""" + mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] + + trait = AttributeSetter({"name": "TX"}) + dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) + vals = ["value=K1", "value=K2", "value=K3"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset, + vals=vals, pheno_filename="ph_file") + mock_open.assert_called_once_with( + "/home/user/data/ph_file.txt", "wb") + filehandler = mock_open() + calls_expected = [mock.call('FID\tIID\tTX\n'), + mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')] + + filehandler.write.assert_has_calls(calls_expected) + + filehandler.close.assert_called_once() + + @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") + @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list") + def test_parse_plink_output(self, mock_line_list): + """test for parsing plink output""" + chromosomes = [0, 34, 110, 89, 123, 23, 2] + species = AttributeSetter( + {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) + + fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA""" + + mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ + "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] + with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: + parse_results = parse_plink_output( + output_filename="P1_file", species=species) + mock_open.assert_called_once_with( + "/home/user/data/P1_file.qassoc", "rb") + expected = (2, {'AACCAT': 0.89, 'AATA': 0.3}) + + self.assertEqual(parse_results, expected) diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py new file mode 100644 index 00000000..b47f877a --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py @@ -0,0 +1,21 @@ +import unittest +from unittest import mock +from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file + +#issues some methods in genofile object are not defined +#modify samples should equal to vals +class TestQtlReaperMapping(unittest.TestCase): + @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") + def test_gen_pheno_txt_file(self): + vals=["V1","x","V4","V3","x"] + samples=["S1","S2","S3","S4","S5"] + trait_filename="trait_file" + with mock.patch("builtins.open", mock.mock_open())as mock_open: + gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) + mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") + filehandler=mock_open() + write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] + + filehandler.write.assert_has_calls(write_calls) + + diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py new file mode 100644 index 00000000..69f53721 --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -0,0 +1,48 @@ +import unittest +from unittest import mock +from wqflask import app +from wqflask.marker_regression.rqtl_mapping import get_trait_data_type +from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype +from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names + +class TestRqtlMapping(unittest.TestCase): + + def setUp(self): + self.app_context=app.app_context() + self.app_context.push() + + def tearDown(self): + self.app_context.pop() + + + @mock.patch("wqflask.marker_regression.rqtl_mapping.g") + @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") + def test_get_trait_data(self,mock_logger,mock_db): + """test for getting trait data_type return True""" + caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] + results=get_trait_data_type("traid_id") + mock_db.db.execute.assert_called_with(caller_value) + self.assertEqual(results,"fer434f") + + def test_sanitize_rqtl_phenotype(self): + """test for sanitizing rqtl phenotype""" + vals=['f',"x","r","x","x"] + results=sanitize_rqtl_phenotype(vals) + expected_phenotype_string='c(f,NA,r,NA,NA)' + + self.assertEqual(results,expected_phenotype_string) + + def test_sanitize_rqtl_names(self): + """test for sanitzing rqtl names""" + vals=['f',"x","r","x","x"] + expected_sanitized_name="c('f',NA,'r',NA,NA)" + results=sanitize_rqtl_names(vals) + self.assertEqual(expected_sanitized_name,results) + + + + + + + diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py new file mode 100644 index 00000000..4129cc0c --- /dev/null +++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py @@ -0,0 +1,284 @@ +import unittest +import datetime +from unittest import mock + +from wqflask.marker_regression.run_mapping import get_genofile_samplelist +from wqflask.marker_regression.run_mapping import geno_db_exists +from wqflask.marker_regression.run_mapping import write_input_for_browser +from wqflask.marker_regression.run_mapping import export_mapping_results +from wqflask.marker_regression.run_mapping import trim_markers_for_figure +from wqflask.marker_regression.run_mapping import get_perm_strata +from wqflask.marker_regression.run_mapping import get_chr_lengths + + +class AttributeSetter: + def __init__(self, obj): + for k, v in obj.items(): + setattr(self, k, v) + + +class MockGroup(AttributeSetter): + + def get_genofiles(self): + return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] + + +class TestRunMapping(unittest.TestCase): + def setUp(self): + + self.group = MockGroup( + {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) + chromosomes = { + "3": AttributeSetter({ + "name": "C1", + "length": "0.04" + }), + "4": AttributeSetter({ + "name": "C2", + "length": "0.03" + }), + "5": AttributeSetter({ + "name": "C4", + "length": "0.01" + }) + } + self.dataset = AttributeSetter( + {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) + + self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) + self.trait = AttributeSetter( + {"symbol": "IGFI", "chr": "X1", "mb": 123313}) + + def tearDown(self): + self.dataset = AttributeSetter( + {"group": {"location": "~/genofiles/g1_file"}}) + + def test_get_genofile_samplelist(self): + + results_1 = get_genofile_samplelist(self.dataset) + self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) + self.group.genofile = "~/genofiles/g2_file" + result_2 = get_genofile_samplelist(self.dataset) + self.assertEqual(result_2, []) + + @mock.patch("wqflask.marker_regression.run_mapping.data_set") + def test_if_geno_db_exists(self, mock_data_set): + mock_data_set.create_dataset.side_effect = [ + AttributeSetter({}), Exception()] + results_no_error = geno_db_exists(self.dataset) + results_with_error = geno_db_exists(self.dataset) + + self.assertEqual(mock_data_set.create_dataset.call_count, 2) + self.assertEqual(results_with_error, "False") + self.assertEqual(results_no_error, "True") + + def test_trim_markers_for_figure(self): + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":0.7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + }] + + marker_2 = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "p_wald":4.6 + }] + results = trim_markers_for_figure(markers) + result_2 = trim_markers_for_figure(marker_2) + expected = [ + { + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":0.5 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":1 + } + + ] + self.assertEqual(results, expected) + self.assertEqual(result_2, marker_2) + + def test_export_mapping_results(self): + """test for exporting mapping results""" + datetime_mock = mock.Mock(wraps=datetime.datetime) + datetime_mock.now.return_value = datetime.datetime( + 2019, 9, 1, 10, 12, 12) + + markers = [{ + "name": "MK1", + "chr": "C1", + "cM": "1", + "Mb": "12000", + "genotypes": [], + "dominance":"TT", + "additive":"VA", + "lod_score":3 + }, + { + "name": "MK2", + "chr": "C2", + "cM": "15", + "Mb": "10000", + "genotypes": [], + "lod_score":7 + }, + { + "name": "MK1", + "chr": "C3", + "cM": "45", + "Mb": "1", + "genotypes": [], + "dominance":"Tt", + "additive":"VE", + "lod_score":7 + }] + + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + + with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): + export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, + results_path="~/results", mapping_scale="physic", score_type="-log(p)") + + write_calls = [ + mock.call('Time/Date: 09/01/19 / 10:12:12\n'), + mock.call('Population: Human GP1_\n'), mock.call( + 'Data Set: dataser_1\n'), + mock.call('Gene Symbol: IGFI\n'), mock.call( + 'Location: X1 @ 123313 Mb\n'), + mock.call('\n'), mock.call('Name,Chr,'), + mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), + mock.call(',Additive'), mock.call(',Dominance'), + mock.call('\n'), mock.call('MK1,C1,'), + mock.call('12000,'), mock.call('1,'), + mock.call('3'), mock.call(',VA'), + mock.call(',TT'), mock.call('\n'), + mock.call('MK2,C2,'), mock.call('10000,'), + mock.call('15,'), mock.call('7'), + mock.call('\n'), mock.call('MK1,C3,'), + mock.call('1,'), mock.call('45,'), + mock.call('7'), mock.call(',VE'), + mock.call(',Tt') + + ] + mock_open.assert_called_once_with("~/results", "w+") + filehandler = mock_open() + filehandler.write.assert_has_calls(write_calls) + + @mock.patch("wqflask.marker_regression.run_mapping.random.choice") + def test_write_input_for_browser(self, mock_choice): + """test for writing input for browser""" + mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"] + with mock.patch("builtins.open", mock.mock_open()) as mock_open: + expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] + + results = write_input_for_browser( + this_dataset=self.dataset, gwas_results={}, annotations={}) + self.assertEqual(results, expected) + + def test_get_perm_strata(self): + categorical_vars = ["C1", "C2", "W1"] + used_samples = ["S1", "S2"] + sample_list = AttributeSetter({"sample_attribute_values": { + "S1": { + "C1": "c1_value", + "C2": "c2_value", + "W1": "w1_value" + + }, + "S2": { + "W1": "w2_value", + "W2": "w2_value" + + }, + "S3": { + + "C1": "c1_value", + "C2": "c2_value" + + }, + + }}) + + results = get_perm_strata(this_trait={}, sample_list=sample_list, + categorical_vars=categorical_vars, used_samples=used_samples) + self.assertEqual(results, [2, 1]) + + def test_get_chr_length(self): + """test for getting chromosome length""" + chromosomes = AttributeSetter({"chromosomes": self.chromosomes}) + dataset = AttributeSetter({"species": chromosomes}) + results = get_chr_lengths( + mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[]) + chr_lengths = [] + for key, chromo in self.chromosomes.chromosomes.items(): + chr_lengths.append({"chr": chromo.name, "size": chromo.length}) + + self.assertEqual(chr_lengths, results) + + qtl_results = [{ + "chr": "16", + "cM": "0.2" + }, + { + "chr": "12", + "cM": "0.5" + }, + { + "chr": "18", + "cM": "0.1" + }, + { + "chr": "22", + "cM": "0.4" + }, + ] + + result_with_other_mapping_scale = get_chr_lengths( + mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results) + expected_value = [{'chr': '1', 'size': '0'}, { + 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] + + self.assertEqual(result_with_other_mapping_scale, expected_value) diff --git a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py deleted file mode 100644 index 4fafd95a..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_gemma_mapping.py +++ /dev/null @@ -1,205 +0,0 @@ -# test for wqflask/marker_regression/gemma_mapping.py -import unittest -import random -from unittest import mock -from wqflask.marker_regression.gemma_mapping import run_gemma -from wqflask.marker_regression.gemma_mapping import gen_pheno_txt_file -from wqflask.marker_regression.gemma_mapping import gen_covariates_file -from wqflask.marker_regression.gemma_mapping import parse_gemma_output -from wqflask.marker_regression.gemma_mapping import parse_loco_output - - -class AttributeSetter: - def __init__(self, obj): - for key, val in obj.items(): - setattr(self, key, val) - - -class MockDatasetGroup(AttributeSetter): - def get_samplelist(self): - return None - - -class TestGemmaMapping(unittest.TestCase): - - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - def test_run_gemma_firstrun_set_false(self, mock_parse_loco): - """add tests for gemma function where first run is set to false""" - dataset = AttributeSetter( - {"group": AttributeSetter({"genofile": "genofile.geno"})}) - - output_file = "file1" - mock_parse_loco.return_value = [] - this_trait = AttributeSetter({"name": "t1"}) - - result = run_gemma(this_trait=this_trait, this_dataset=dataset, samples=[], vals=[ - ], covariates="", use_loco=True, first_run=False, output_files=output_file) - - expected_results = ([], "file1") - self.assertEqual(expected_results, result) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMAOPTS", "-debug") - @mock.patch("wqflask.marker_regression.gemma_mapping.GEMMA_WRAPPER_COMMAND", "ghc") - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data/") - @mock.patch("wqflask.marker_regression.gemma_mapping.parse_loco_output") - @mock.patch("wqflask.marker_regression.gemma_mapping.logger") - @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") - @mock.patch("wqflask.marker_regression.gemma_mapping.gen_covariates_file") - @mock.patch("wqflask.marker_regression.run_mapping.random.choice") - @mock.patch("wqflask.marker_regression.gemma_mapping.os") - @mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file") - def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_logger, mock_parse_loco): - """add tests for run_gemma where first run is set to true""" - chromosomes = [] - for i in range(1, 5): - chromosomes.append(AttributeSetter({"name": f"CH{i}"})) - chromo = AttributeSetter({"chromosomes": chromosomes}) - dataset_group = MockDatasetGroup( - {"name": "GP1", "genofile": "file_geno"}) - dataset = AttributeSetter({"group": dataset_group, "name": "dataset1_name", - "species": AttributeSetter({"chromosomes": chromo})}) - trait = AttributeSetter({"name": "trait1"}) - samples = [] - mock_gen_pheno_txt.return_value = None - mock_os.path.isfile.return_value = True - mock_gen_covar.return_value = None - mock_choice.return_value = "R" - mock_flat_files.return_value = "/home/genotype/bimbam" - mock_parse_loco.return_value = [] - results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[ - ], vals=[], covariates="", use_loco=True) - system_calls = [mock.call('ghc --json -- -debug -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt -a /home/genotype/bimbam/file_snps.txt -gk > /home/user/data//gn2/GP1_K_RRRRRR.json'), - mock.call('ghc --json --input /home/user/data//gn2/GP1_K_RRRRRR.json -- -debug -a /home/genotype/bimbam/file_snps.txt -lmm 2 -g /home/genotype/bimbam/file_geno.txt -p /home/user/data//gn2/trait1_dataset1_name_pheno.txt > /home/user/data//gn2/GP1_GWA_RRRRRR.json')] - mock_os.system.assert_has_calls(system_calls) - mock_gen_pheno_txt.assert_called_once() - mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR") - mock_os.path.isfile.assert_called_once_with( - ('/home/user/imgfile_output.assoc.txt')) - self.assertEqual(mock_logger.debug.call_count, 2) - self.assertEqual(mock_flat_files.call_count, 4) - self.assertEqual(results, ([], "GP1_GWA_RRRRRR")) - - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - """add tests for generating pheno txt file""" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(this_dataset={}, genofile_name="", vals=[ - "x", "w", "q", "we", "R"], trait_filename="fitr.re") - mock_open.assert_called_once_with( - '/home/user/data/gn2/fitr.re.txt', 'w') - filehandler = mock_open() - values = ["x", "w", "q", "we", "R"] - write_calls = [mock.call('NA\n'), mock.call('w\n'), mock.call( - 'q\n'), mock.call('we\n'), mock.call('R\n')] - - filehandler.write.assert_has_calls(write_calls) - - @mock.patch("wqflask.marker_regression.gemma_mapping.flat_files") - @mock.patch("wqflask.marker_regression.gemma_mapping.create_trait") - @mock.patch("wqflask.marker_regression.gemma_mapping.create_dataset") - def test_gen_covariates_file(self, create_dataset, create_trait, flat_files): - """add tests for generating covariates files""" - covariates = "X1:X2,Y1:Y2,M1:M3,V1:V2" - samplelist = ["X1", "X2", "X3", "X4"] - create_dataset_side_effect = [] - create_trait_side_effect = [] - - for i in range(4): - create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'})) - create_trait_side_effect.append( - AttributeSetter({"data": [f'data_{i}']})) - - create_dataset.side_effect = create_trait_side_effect - create_trait.side_effect = create_trait_side_effect - - group = MockDatasetGroup({"name": "group_X", "samplelist": samplelist}) - this_dataset = AttributeSetter({"group": group}) - flat_files.return_value = "Home/Genenetwork" - - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_covariates_file(this_dataset=this_dataset, covariates=covariates, - samples=["x1", "x2", "X3"]) - - create_dataset.assert_has_calls( - [mock.call('X2'), mock.call('Y2'), mock.call('M3'), mock.call('V2')]) - mock_calls = [] - trait_names = ["X1", "Y1", "M1", "V1"] - - for i, trait in enumerate(create_trait_side_effect): - mock_calls.append( - mock.call(dataset=trait, name=trait_names[i], cellid=None)) - - create_trait.assert_has_calls(mock_calls) - - flat_files.assert_called_once_with('mapping') - mock_open.assert_called_once_with( - 'Home/Genenetwork/group_X_covariates.txt', 'w') - filehandler = mock_open() - filehandler.write.assert_has_calls([mock.call( - '-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('-9\t'), mock.call('\n')]) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img/") - def test_parse_gemma_output(self): - """add test for generating gemma output with obj returned""" - file = """X/Y\t gn2\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tgn2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tgn1\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7 -X\tgn7\t2324424\tQ\tE\tA\tP\tMMB\tCDE\t0.4 -125\tgn9\t433575\tQ\tE\tA\tP\tMMB\tCDE\t0.67 -""" - with mock.patch("builtins.open", mock.mock_open(read_data=file)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - expected = [{'name': ' gn2', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {'name': 'gn2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, - {'name': 'gn7', 'chr': 'X', 'Mb': 2.324424, 'p_value': 0.4, 'lod_score': 0.3979400086720376}, {'name': 'gn9', 'chr': 125, 'Mb': 0.433575, 'p_value': 0.67, 'lod_score': 0.17392519729917352}] - mock_open.assert_called_once_with( - "/home/user/img/gema_file_output.assoc.txt") - self.assertEqual(results, expected) - - @mock.patch("wqflask.marker_regression.gemma_mapping.webqtlConfig.GENERATED_IMAGE_DIR", "/home/user/img") - def test_parse_gemma_output_with_empty_return(self): - """add tests for parse gemma output where nothing returned""" - output_file_results = """chr\t today""" - with mock.patch("builtins.open", mock.mock_open(read_data=output_file_results)) as mock_open: - results = parse_gemma_output(genofile_name="gema_file") - self.assertEqual(results, []) - - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") - @mock.patch("wqflask.marker_regression.gemma_mapping.os") - @mock.patch("wqflask.marker_regression.gemma_mapping.json") - def test_parse_loco_outputfile_found(self, mock_json, mock_os): - """add tests for parse loco output file found""" - mock_json.load.return_value = { - "files": [["file_name", "user", "~/file1"], - ["file_name", "user", "~/file2"]] - } - return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5 -chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7""" - return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5""" - mock_os.path.isfile.return_value = True - file_to_write = """{"files":["file_1","file_2"]}""" - with mock.patch("builtins.open") as mock_open: - - handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open( - read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value) - mock_open.side_effect = handles - results = parse_loco_output( - this_dataset={}, gwa_output_filename=".xw/") - expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, { - 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}] - - self.assertEqual(expected_results, results) - - @mock.patch("wqflask.marker_regression.gemma_mapping.TEMPDIR", "/home/tmp") - @mock.patch("wqflask.marker_regression.gemma_mapping.os") - def test_parse_loco_outputfile_not_found(self, mock_os): - """add tests for parse loco output where output file not found""" - - mock_os.path.isfile.return_value = False - file_to_write = """{"files":["file_1","file_2"]}""" - - with mock.patch("builtins.open", mock.mock_open(read_data=file_to_write)) as mock_open: - results = parse_loco_output( - this_dataset={}, gwa_output_filename=".xw/") - self.assertEqual(results, []) diff --git a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py deleted file mode 100644 index 428f45b9..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_plink_mapping.py +++ /dev/null @@ -1,84 +0,0 @@ -# test for wqflask/marker_regression/plink_mapping.py -import unittest -from unittest import mock -from wqflask.marker_regression.plink_mapping import build_line_list -from wqflask.marker_regression.plink_mapping import get_samples_from_ped_file -from wqflask.marker_regression.plink_mapping import flat_files -from wqflask.marker_regression.plink_mapping import gen_pheno_txt_file_plink -from wqflask.marker_regression.plink_mapping import parse_plink_output - - -class AttributeSetter: - def __init__(self, obj): - for key, val in obj.items(): - setattr(self, key, val) -class TestPlinkMapping(unittest.TestCase): - - def test_build_line_list(self): - """testing for building line list""" - line_1 = "this is line one test" - irregular_line = " this is an, irregular line " - exp_line1 = ["this", "is", "line", "one", "test"] - - results = build_line_list(irregular_line) - self.assertEqual(exp_line1, build_line_list(line_1)) - self.assertEqual([], build_line_list()) - self.assertEqual(["this", "is", "an,", "irregular", "line"], results) - - @mock.patch("wqflask.marker_regression.plink_mapping.flat_files") - def test_get_samples_from_ped_file(self, mock_flat_files): - """test for getting samples from ped file""" - dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) - file_sample = """Expected_1\tline test -Expected_2\there - Expected_3\tthree""" - mock_flat_files.return_value = "/home/user/" - with mock.patch("builtins.open", mock.mock_open(read_data=file_sample)) as mock_open: - results = get_samples_from_ped_file(dataset) - mock_flat_files.assert_called_once_with("mapping") - mock_open.assert_called_once_with("/home/user/n_1.ped", "r") - self.assertEqual( - ["Expected_1", "Expected_2", "Expected_3"], results) - - @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") - @mock.patch("wqflask.marker_regression.plink_mapping.get_samples_from_ped_file") - def test_gen_pheno_txt_file_plink(self, mock_samples): - """test for getting gen_pheno txt file""" - mock_samples.return_value = ["Expected_1", "Expected_2", "Expected_3"] - - trait = AttributeSetter({"name": "TX"}) - dataset = AttributeSetter({"group": AttributeSetter({"name": "n_1"})}) - vals = ["value=K1", "value=K2", "value=K3"] - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - results = gen_pheno_txt_file_plink(this_trait=trait, dataset=dataset, - vals=vals, pheno_filename="ph_file") - mock_open.assert_called_once_with( - "/home/user/data/ph_file.txt", "wb") - filehandler = mock_open() - calls_expected = [mock.call('FID\tIID\tTX\n'), - mock.call('Expected_1\tExpected_1\tK1\nExpected_2\tExpected_2\tK2\nExpected_3\tExpected_3\tK3\n')] - - filehandler.write.assert_has_calls(calls_expected) - - filehandler.close.assert_called_once() - - @mock.patch("wqflask.marker_regression.plink_mapping.TMPDIR", "/home/user/data/") - @mock.patch("wqflask.marker_regression.plink_mapping.build_line_list") - def test_parse_plink_output(self, mock_line_list): - """test for parsing plink output""" - chromosomes = [0, 34, 110, 89, 123, 23, 2] - species = AttributeSetter( - {"name": "S1", "chromosomes": AttributeSetter({"chromosomes": chromosomes})}) - - fake_file = """0 AACCAT T98.6 0.89\n2 AATA B45 0.3\n121 ACG B56.4 NA""" - - mock_line_list.side_effect = [["0", "AACCAT", "T98.6", "0.89"], [ - "2", "AATA", "B45", "0.3"], ["121", "ACG", "B56.4", "NA"]] - with mock.patch("builtins.open", mock.mock_open(read_data=fake_file)) as mock_open: - parse_results = parse_plink_output( - output_filename="P1_file", species=species) - mock_open.assert_called_once_with( - "/home/user/data/P1_file.qassoc", "rb") - expected = (2, {'AACCAT': 0.89, 'AATA': 0.3}) - - self.assertEqual(parse_results, expected) diff --git a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py deleted file mode 100644 index b47f877a..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_qtlreaper_mapping.py +++ /dev/null @@ -1,21 +0,0 @@ -import unittest -from unittest import mock -from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file - -#issues some methods in genofile object are not defined -#modify samples should equal to vals -class TestQtlReaperMapping(unittest.TestCase): - @mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data") - def test_gen_pheno_txt_file(self): - vals=["V1","x","V4","V3","x"] - samples=["S1","S2","S3","S4","S5"] - trait_filename="trait_file" - with mock.patch("builtins.open", mock.mock_open())as mock_open: - gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename) - mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w") - filehandler=mock_open() - write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')] - - filehandler.write.assert_has_calls(write_calls) - - diff --git a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py deleted file mode 100644 index 69f53721..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_rqtl_mapping.py +++ /dev/null @@ -1,48 +0,0 @@ -import unittest -from unittest import mock -from wqflask import app -from wqflask.marker_regression.rqtl_mapping import get_trait_data_type -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype -from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names - -class TestRqtlMapping(unittest.TestCase): - - def setUp(self): - self.app_context=app.app_context() - self.app_context.push() - - def tearDown(self): - self.app_context.pop() - - - @mock.patch("wqflask.marker_regression.rqtl_mapping.g") - @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") - def test_get_trait_data(self,mock_logger,mock_db): - """test for getting trait data_type return True""" - caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" - mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] - results=get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(caller_value) - self.assertEqual(results,"fer434f") - - def test_sanitize_rqtl_phenotype(self): - """test for sanitizing rqtl phenotype""" - vals=['f',"x","r","x","x"] - results=sanitize_rqtl_phenotype(vals) - expected_phenotype_string='c(f,NA,r,NA,NA)' - - self.assertEqual(results,expected_phenotype_string) - - def test_sanitize_rqtl_names(self): - """test for sanitzing rqtl names""" - vals=['f',"x","r","x","x"] - expected_sanitized_name="c('f',NA,'r',NA,NA)" - results=sanitize_rqtl_names(vals) - self.assertEqual(expected_sanitized_name,results) - - - - - - - diff --git a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/wqflask/marker_regression/test_run_mapping.py deleted file mode 100644 index a134f551..00000000 --- a/wqflask/tests/wqflask/marker_regression/test_run_mapping.py +++ /dev/null @@ -1,284 +0,0 @@ -import unittest -import datetime -from unittest import mock - -from wqflask.marker_regression.run_mapping import get_genofile_samplelist -from wqflask.marker_regression.run_mapping import geno_db_exists -from wqflask.marker_regression.run_mapping import write_input_for_browser -from wqflask.marker_regression.run_mapping import export_mapping_results -from wqflask.marker_regression.run_mapping import trim_markers_for_figure -from wqflask.marker_regression.run_mapping import get_perm_strata -from wqflask.marker_regression.run_mapping import get_chr_lengths - - -class AttributeSetter: - def __init__(self, obj): - for k, v in obj.items(): - setattr(self, k, v) - - -class MockDataSetGroup(AttributeSetter): - - def get_genofiles(self): - return [{"location": "~/genofiles/g1_file", "sample_list": ["S1", "S2", "S3", "S4"]}] - - -class TestRunMapping(unittest.TestCase): - def setUp(self): - - self.group = MockDataSetGroup( - {"genofile": "~/genofiles/g1_file", "name": "GP1_", "species": "Human"}) - chromosomes = { - "3": AttributeSetter({ - "name": "C1", - "length": "0.04" - }), - "4": AttributeSetter({ - "name": "C2", - "length": "0.03" - }), - "5": AttributeSetter({ - "name": "C4", - "length": "0.01" - }) - } - self.dataset = AttributeSetter( - {"fullname": "dataser_1", "group": self.group, "type": "ProbeSet"}) - - self.chromosomes = AttributeSetter({"chromosomes": chromosomes}) - self.trait = AttributeSetter( - {"symbol": "IGFI", "chr": "X1", "mb": 123313}) - - def tearDown(self): - self.dataset = AttributeSetter( - {"group": {"location": "~/genofiles/g1_file"}}) - - def test_get_genofile_samplelist(self): - - results_1 = get_genofile_samplelist(self.dataset) - self.assertEqual(results_1, ["S1", "S2", "S3", "S4"]) - self.group.genofile = "~/genofiles/g2_file" - result_2 = get_genofile_samplelist(self.dataset) - self.assertEqual(result_2, []) - - @mock.patch("wqflask.marker_regression.run_mapping.data_set") - def test_if_geno_db_exists(self, mock_data_set): - mock_data_set.create_dataset.side_effect = [ - AttributeSetter({}), Exception()] - results_no_error = geno_db_exists(self.dataset) - results_with_error = geno_db_exists(self.dataset) - - self.assertEqual(mock_data_set.create_dataset.call_count, 2) - self.assertEqual(results_with_error, "False") - self.assertEqual(results_no_error, "True") - - def test_trim_markers_for_figure(self): - - markers = [{ - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "lod_score":0.5 - }, - { - "name": "MK2", - "chr": "C2", - "cM": "15", - "Mb": "10000", - "genotypes": [], - "lod_score":0.7 - }, - { - "name": "MK1", - "chr": "C3", - "cM": "45", - "Mb": "1", - "genotypes": [], - "dominance":"Tt", - "additive":"VE", - "lod_score":1 - }] - - marker_2 = [{ - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "p_wald":4.6 - }] - results = trim_markers_for_figure(markers) - result_2 = trim_markers_for_figure(marker_2) - expected = [ - { - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "lod_score":0.5 - }, - { - "name": "MK1", - "chr": "C3", - "cM": "45", - "Mb": "1", - "genotypes": [], - "dominance":"Tt", - "additive":"VE", - "lod_score":1 - } - - ] - self.assertEqual(results, expected) - self.assertEqual(result_2, marker_2) - - def test_export_mapping_results(self): - """test for exporting mapping results""" - datetime_mock = mock.Mock(wraps=datetime.datetime) - datetime_mock.now.return_value = datetime.datetime( - 2019, 9, 1, 10, 12, 12) - - markers = [{ - "name": "MK1", - "chr": "C1", - "cM": "1", - "Mb": "12000", - "genotypes": [], - "dominance":"TT", - "additive":"VA", - "lod_score":3 - }, - { - "name": "MK2", - "chr": "C2", - "cM": "15", - "Mb": "10000", - "genotypes": [], - "lod_score":7 - }, - { - "name": "MK1", - "chr": "C3", - "cM": "45", - "Mb": "1", - "genotypes": [], - "dominance":"Tt", - "additive":"VE", - "lod_score":7 - }] - - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - - with mock.patch("wqflask.marker_regression.run_mapping.datetime.datetime", new=datetime_mock): - export_mapping_results(dataset=self.dataset, trait=self.trait, markers=markers, - results_path="~/results", mapping_scale="physic", score_type="-log(p)") - - write_calls = [ - mock.call('Time/Date: 09/01/19 / 10:12:12\n'), - mock.call('Population: Human GP1_\n'), mock.call( - 'Data Set: dataser_1\n'), - mock.call('Gene Symbol: IGFI\n'), mock.call( - 'Location: X1 @ 123313 Mb\n'), - mock.call('\n'), mock.call('Name,Chr,'), - mock.call('Mb,-log(p)'), mock.call('Cm,-log(p)'), - mock.call(',Additive'), mock.call(',Dominance'), - mock.call('\n'), mock.call('MK1,C1,'), - mock.call('12000,'), mock.call('1,'), - mock.call('3'), mock.call(',VA'), - mock.call(',TT'), mock.call('\n'), - mock.call('MK2,C2,'), mock.call('10000,'), - mock.call('15,'), mock.call('7'), - mock.call('\n'), mock.call('MK1,C3,'), - mock.call('1,'), mock.call('45,'), - mock.call('7'), mock.call(',VE'), - mock.call(',Tt') - - ] - mock_open.assert_called_once_with("~/results", "w+") - filehandler = mock_open() - filehandler.write.assert_has_calls(write_calls) - - @mock.patch("wqflask.marker_regression.run_mapping.random.choice") - def test_write_input_for_browser(self, mock_choice): - """test for writing input for browser""" - mock_choice.side_effect = ["F", "i", "l", "e", "s", "x"] - with mock.patch("builtins.open", mock.mock_open()) as mock_open: - expected = ['GP1__Filesx_GWAS', 'GP1__Filesx_ANNOT'] - - results = write_input_for_browser( - this_dataset=self.dataset, gwas_results={}, annotations={}) - self.assertEqual(results, expected) - - def test_get_perm_strata(self): - categorical_vars = ["C1", "C2", "W1"] - used_samples = ["S1", "S2"] - sample_list = AttributeSetter({"sample_attribute_values": { - "S1": { - "C1": "c1_value", - "C2": "c2_value", - "W1": "w1_value" - - }, - "S2": { - "W1": "w2_value", - "W2": "w2_value" - - }, - "S3": { - - "C1": "c1_value", - "C2": "c2_value" - - }, - - }}) - - results = get_perm_strata(this_trait={}, sample_list=sample_list, - categorical_vars=categorical_vars, used_samples=used_samples) - self.assertEqual(results, [2, 1]) - - def test_get_chr_length(self): - """test for getting chromosome length""" - chromosomes = AttributeSetter({"chromosomes": self.chromosomes}) - dataset = AttributeSetter({"species": chromosomes}) - results = get_chr_lengths( - mapping_scale="physic", mapping_method="reaper", dataset=dataset, qtl_results=[]) - chr_lengths = [] - for key, chromo in self.chromosomes.chromosomes.items(): - chr_lengths.append({"chr": chromo.name, "size": chromo.length}) - - self.assertEqual(chr_lengths, results) - - qtl_results = [{ - "chr": "16", - "cM": "0.2" - }, - { - "chr": "12", - "cM": "0.5" - }, - { - "chr": "18", - "cM": "0.1" - }, - { - "chr": "22", - "cM": "0.4" - }, - ] - - result_with_other_mapping_scale = get_chr_lengths( - mapping_scale="other", mapping_method="reaper", dataset=dataset, qtl_results=qtl_results) - expected_value = [{'chr': '1', 'size': '0'}, { - 'chr': '16', 'size': '500000.0'}, {'chr': '18', 'size': '400000.0'}] - - self.assertEqual(result_with_other_mapping_scale, expected_value) -- cgit v1.2.3 From c96c1db5660367f1f86cfa76309c87866e79bf79 Mon Sep 17 00:00:00 2001 From: Alexander Kabui Date: Sat, 28 Nov 2020 16:23:53 +0300 Subject: modify test for plink mapping and rqtl_mapping --- wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py | 3 ++- wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) (limited to 'wqflask') diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py index 428f45b9..5eec93f1 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py @@ -14,8 +14,9 @@ class AttributeSetter: setattr(self, key, val) class TestPlinkMapping(unittest.TestCase): + def test_build_line_list(self): - """testing for building line list""" + """test for building line list""" line_1 = "this is line one test" irregular_line = " this is an, irregular line " exp_line1 = ["this", "is", "line", "one", "test"] diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py index 69f53721..c585f1df 100644 --- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py +++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py @@ -19,10 +19,10 @@ class TestRqtlMapping(unittest.TestCase): @mock.patch("wqflask.marker_regression.rqtl_mapping.logger") def test_get_trait_data(self,mock_logger,mock_db): """test for getting trait data_type return True""" - caller_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" + query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'""" mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""] results=get_trait_data_type("traid_id") - mock_db.db.execute.assert_called_with(caller_value) + mock_db.db.execute.assert_called_with(query_value) self.assertEqual(results,"fer434f") def test_sanitize_rqtl_phenotype(self): -- cgit v1.2.3