diff options
Diffstat (limited to 'tests/unit')
| -rw-r--r-- | tests/unit/computations/test_parsers.py | 4 | ||||
| -rw-r--r-- | tests/unit/test_heatmaps.py | 70 |
2 files changed, 37 insertions, 37 deletions
diff --git a/tests/unit/computations/test_parsers.py b/tests/unit/computations/test_parsers.py index 19c3067..b51b0bf 100644 --- a/tests/unit/computations/test_parsers.py +++ b/tests/unit/computations/test_parsers.py @@ -15,7 +15,7 @@ class TestParsers(unittest.TestCase): def test_parse_genofile_with_existing_file(self): """Test that a genotype file is parsed correctly""" - strains = ["bxd1", "bxd2"] + samples = ["bxd1", "bxd2"] genotypes = [ {"chr": "1", "locus": "rs31443144", "cm": "1.50", "mb": "3.010274", @@ -51,4 +51,4 @@ class TestParsers(unittest.TestCase): "../test_data/genotype.txt" )) self.assertEqual(parse_genofile( - test_genotype_file), (strains, genotypes)) + test_genotype_file), (samples, genotypes)) diff --git a/tests/unit/test_heatmaps.py b/tests/unit/test_heatmaps.py index fd91cf9..b54e2f3 100644 --- a/tests/unit/test_heatmaps.py +++ b/tests/unit/test_heatmaps.py @@ -5,41 +5,41 @@ from gn3.heatmaps import ( get_lrs_from_chr, export_trait_data, compute_traits_order, - retrieve_strains_and_values, + retrieve_samples_and_values, process_traits_data_for_heatmap) from tests.unit.sample_test_data import organised_trait_1, organised_trait_2 -strainlist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] +samplelist = ["B6cC3-1", "BXD1", "BXD12", "BXD16", "BXD19", "BXD2"] trait_data = { "mysqlid": 36688172, "data": { - "B6cC3-1": {"strain_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None}, - "BXD1": {"strain_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None}, - "BXD12": {"strain_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None}, - "BXD16": {"strain_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None}, - "BXD19": {"strain_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None}, - "BXD2": {"strain_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None}, - "BXD21": {"strain_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None}, - "BXD24": {"strain_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None}, - "BXD27": {"strain_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None}, - "BXD28": {"strain_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None}, - "BXD32": {"strain_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None}, - "BXD39": {"strain_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None}, - "BXD40": {"strain_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None}, - "BXD42": {"strain_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None}, - "BXD6": {"strain_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None}, - "BXH14": {"strain_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None}, - "BXH19": {"strain_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None}, - "BXH2": {"strain_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None}, - "BXH22": {"strain_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None}, - "BXH4": {"strain_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None}, - "BXH6": {"strain_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None}, - "BXH7": {"strain_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None}, - "BXH8": {"strain_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None}, - "BXH9": {"strain_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None}, - "C3H/HeJ": {"strain_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None}, - "C57BL/6J": {"strain_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None}, - "DBA/2J": {"strain_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}} + "B6cC3-1": {"sample_name": "B6cC3-1", "value": 7.51879, "variance": None, "ndata": None}, + "BXD1": {"sample_name": "BXD1", "value": 7.77141, "variance": None, "ndata": None}, + "BXD12": {"sample_name": "BXD12", "value": 8.39265, "variance": None, "ndata": None}, + "BXD16": {"sample_name": "BXD16", "value": 8.17443, "variance": None, "ndata": None}, + "BXD19": {"sample_name": "BXD19", "value": 8.30401, "variance": None, "ndata": None}, + "BXD2": {"sample_name": "BXD2", "value": 7.80944, "variance": None, "ndata": None}, + "BXD21": {"sample_name": "BXD21", "value": 8.93809, "variance": None, "ndata": None}, + "BXD24": {"sample_name": "BXD24", "value": 7.99415, "variance": None, "ndata": None}, + "BXD27": {"sample_name": "BXD27", "value": 8.12177, "variance": None, "ndata": None}, + "BXD28": {"sample_name": "BXD28", "value": 7.67688, "variance": None, "ndata": None}, + "BXD32": {"sample_name": "BXD32", "value": 7.79062, "variance": None, "ndata": None}, + "BXD39": {"sample_name": "BXD39", "value": 8.27641, "variance": None, "ndata": None}, + "BXD40": {"sample_name": "BXD40", "value": 8.18012, "variance": None, "ndata": None}, + "BXD42": {"sample_name": "BXD42", "value": 7.82433, "variance": None, "ndata": None}, + "BXD6": {"sample_name": "BXD6", "value": 8.09718, "variance": None, "ndata": None}, + "BXH14": {"sample_name": "BXH14", "value": 7.97475, "variance": None, "ndata": None}, + "BXH19": {"sample_name": "BXH19", "value": 7.67223, "variance": None, "ndata": None}, + "BXH2": {"sample_name": "BXH2", "value": 7.93622, "variance": None, "ndata": None}, + "BXH22": {"sample_name": "BXH22", "value": 7.43692, "variance": None, "ndata": None}, + "BXH4": {"sample_name": "BXH4", "value": 7.96336, "variance": None, "ndata": None}, + "BXH6": {"sample_name": "BXH6", "value": 7.75132, "variance": None, "ndata": None}, + "BXH7": {"sample_name": "BXH7", "value": 8.12927, "variance": None, "ndata": None}, + "BXH8": {"sample_name": "BXH8", "value": 6.77338, "variance": None, "ndata": None}, + "BXH9": {"sample_name": "BXH9", "value": 8.03836, "variance": None, "ndata": None}, + "C3H/HeJ": {"sample_name": "C3H/HeJ", "value": 7.42795, "variance": None, "ndata": None}, + "C57BL/6J": {"sample_name": "C57BL/6J", "value": 7.50606, "variance": None, "ndata": None}, + "DBA/2J": {"sample_name": "DBA/2J", "value": 7.72588, "variance": None, "ndata": None}}} slinked = ( (((0, 2, 0.16381088984330505), @@ -66,7 +66,7 @@ class TestHeatmap(TestCase): ["all", (7.51879, 7.77141, 8.39265, 8.17443, 8.30401, 7.80944)]]: with self.subTest(dtype=dtype): self.assertEqual( - export_trait_data(trait_data, strainlist, dtype=dtype), + export_trait_data(trait_data, samplelist, dtype=dtype), expected) def test_export_trait_data_dtype_all_flags(self): @@ -106,7 +106,7 @@ class TestHeatmap(TestCase): with self.subTest(dtype=dtype, vflag=vflag, nflag=nflag): self.assertEqual( export_trait_data( - trait_data, strainlist, dtype=dtype, var_exists=vflag, + trait_data, samplelist, dtype=dtype, var_exists=vflag, n_exists=nflag), expected) @@ -164,8 +164,8 @@ class TestHeatmap(TestCase): self.assertEqual( compute_traits_order(slinked), (0, 2, 1, 7, 5, 9, 3, 6, 8, 4)) - def test_retrieve_strains_and_values(self): - """Test retrieval of strains and values.""" + def test_retrieve_samples_and_values(self): + """Test retrieval of samples and values.""" for orders, slist, tdata, expected in [ [ [2], @@ -185,9 +185,9 @@ class TestHeatmap(TestCase): [6, None, None, 4, None]], [[3, ["s1", "s4"], [6, 4]]] ]]: - with self.subTest(strainlist=slist, traitdata=tdata): + with self.subTest(samplelist=slist, traitdata=tdata): self.assertEqual( - retrieve_strains_and_values(orders, slist, tdata), expected) + retrieve_samples_and_values(orders, slist, tdata), expected) def test_get_lrs_from_chr(self): """Check that function gets correct LRS values""" |