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-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py205
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py85
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py21
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py48
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py284
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py9
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py22
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py46
8 files changed, 684 insertions, 36 deletions
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..5eec93f1
--- /dev/null
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -0,0 +1,85 @@
+# 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):
+ """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"]
+
+ 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..c585f1df
--- /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"""
+ 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(query_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/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,
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index fd91b6ca..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()
@@ -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]
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))