Merge pull request #484 from Alexanderlacuna/test-regression

Add tests for marker_regression

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))