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-rw-r--r--tests/unit/computations/data/qtlreaper/main_output_sample.txt11
-rw-r--r--tests/unit/computations/data/qtlreaper/permu_output_sample.txt27
-rw-r--r--tests/unit/computations/test_parsers.py4
-rw-r--r--tests/unit/computations/test_qtlreaper.py135
-rw-r--r--tests/unit/db/data/genotypes/genotype_sample1.geno23
-rw-r--r--tests/unit/db/test_datasets.py42
-rw-r--r--tests/unit/db/test_genotypes.py170
-rw-r--r--tests/unit/db/test_traits.py16
-rw-r--r--tests/unit/sample_test_data.py111
-rw-r--r--tests/unit/test_heatmaps.py (renamed from tests/unit/computations/test_heatmap.py)137
10 files changed, 615 insertions, 61 deletions
diff --git a/tests/unit/computations/data/qtlreaper/main_output_sample.txt b/tests/unit/computations/data/qtlreaper/main_output_sample.txt
new file mode 100644
index 0000000..12b11b4
--- /dev/null
+++ b/tests/unit/computations/data/qtlreaper/main_output_sample.txt
@@ -0,0 +1,11 @@
+ID Locus Chr cM Mb LRS Additive pValue
+T1 rs31443144 1 1.500 3.010 0.500 -0.074 1.000
+T1 rs6269442 1 1.500 3.492 0.500 -0.074 1.000
+T1 rs32285189 1 1.630 3.511 0.500 -0.074 1.000
+T1 rs258367496 1 1.630 3.660 0.500 -0.074 1.000
+T1 rs32430919 1 1.750 3.777 0.500 -0.074 1.000
+T1 rs36251697 1 1.880 3.812 0.500 -0.074 1.000
+T1 rs30658298 1 2.010 4.431 0.500 -0.074 1.000
+T1 rs51852623 1 2.010 4.447 0.500 -0.074 1.000
+T1 rs31879829 1 2.140 4.519 0.500 -0.074 1.000
+T1 rs36742481 1 2.140 4.776 0.500 -0.074 1.000
diff --git a/tests/unit/computations/data/qtlreaper/permu_output_sample.txt b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt
new file mode 100644
index 0000000..64cff07
--- /dev/null
+++ b/tests/unit/computations/data/qtlreaper/permu_output_sample.txt
@@ -0,0 +1,27 @@
+4.44174
+5.03825
+5.08167
+5.18119
+5.18578
+5.24563
+5.24619
+5.24619
+5.27961
+5.28228
+5.43903
+5.50188
+5.51694
+5.56830
+5.63874
+5.71346
+5.71936
+5.74275
+5.76764
+5.79815
+5.81671
+5.82775
+5.89659
+5.92117
+5.93396
+5.93396
+5.94957
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/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py
new file mode 100644
index 0000000..742d106
--- /dev/null
+++ b/tests/unit/computations/test_qtlreaper.py
@@ -0,0 +1,135 @@
+"""Module contains tests for gn3.computations.qtlreaper"""
+from unittest import TestCase
+from gn3.computations.qtlreaper import (
+ parse_reaper_main_results,
+ organise_reaper_main_results,
+ parse_reaper_permutation_results)
+from tests.unit.sample_test_data import organised_trait_1
+
+class TestQTLReaper(TestCase):
+ """Class for testing qtlreaper interface functions."""
+
+ def test_parse_reaper_main_results(self):
+ """Test that the main results file is parsed correctly."""
+ self.assertEqual(
+ parse_reaper_main_results(
+ "tests/unit/computations/data/qtlreaper/main_output_sample.txt"),
+ [
+ {
+ "ID": "T1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+ "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+ "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+ "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+ "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+ "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+ "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+ "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs51852623", "Chr": 1, "cM": 2.010,
+ "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs31879829", "Chr": 1, "cM": 2.140,
+ "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "T1", "Locus": "rs36742481", "Chr": 1, "cM": 2.140,
+ "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ }
+ ])
+
+ def test_parse_reaper_permutation_results(self):
+ """Test that the permutations results file is parsed correctly."""
+ self.assertEqual(
+ parse_reaper_permutation_results(
+ "tests/unit/computations/data/qtlreaper/permu_output_sample.txt"),
+ [4.44174, 5.03825, 5.08167, 5.18119, 5.18578, 5.24563, 5.24619,
+ 5.24619, 5.27961, 5.28228, 5.43903, 5.50188, 5.51694, 5.56830,
+ 5.63874, 5.71346, 5.71936, 5.74275, 5.76764, 5.79815, 5.81671,
+ 5.82775, 5.89659, 5.92117, 5.93396, 5.93396, 5.94957])
+
+ def test_organise_reaper_main_results(self):
+ """Check that results are organised correctly."""
+ self.assertEqual(
+ organise_reaper_main_results([
+ {
+ "ID": "1", "Locus": "rs31443144", "Chr": 1, "cM": 1.500,
+ "Mb": 3.010, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs6269442", "Chr": 1, "cM": 1.500,
+ "Mb": 3.492, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs32285189", "Chr": 1, "cM": 1.630,
+ "Mb": 3.511, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs258367496", "Chr": 1, "cM": 1.630,
+ "Mb": 3.660, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs32430919", "Chr": 1, "cM": 1.750,
+ "Mb": 3.777, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs36251697", "Chr": 1, "cM": 1.880,
+ "Mb": 3.812, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs30658298", "Chr": 1, "cM": 2.010,
+ "Mb": 4.431, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs51852623", "Chr": 2, "cM": 2.010,
+ "Mb": 4.447, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs31879829", "Chr": 2, "cM": 2.140,
+ "Mb": 4.519, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ },
+ {
+ "ID": "1", "Locus": "rs36742481", "Chr": 2, "cM": 2.140,
+ "Mb": 4.776, "LRS": 0.500, "Additive": -0.074,
+ "pValue": 1.000
+ }
+ ]),
+ organised_trait_1)
diff --git a/tests/unit/db/data/genotypes/genotype_sample1.geno b/tests/unit/db/data/genotypes/genotype_sample1.geno
new file mode 100644
index 0000000..2a55964
--- /dev/null
+++ b/tests/unit/db/data/genotypes/genotype_sample1.geno
@@ -0,0 +1,23 @@
+# File name: genotype_sample for testing
+
+# Metadata: Please retain this header information with file.
+
+
+@name: BXD
+@type: riset
+@mat: B
+@pat: D
+@het:H
+@unk: U
+
+
+
+
+
+
+Chr Locus cM Mb BXD1 BXD2 BXD5 BXD6 BXD8 BXD9
+1 rs31443144 1.50 3.010274 B B D D D B
+1 rs6269442 1.50 3.492195 B B D D H Y
+1 rs32285189 1.63 3.511204 B U D D D B
+2 rs31443144 1.50 3.010274 B B D D D B
+2 rs6269442 1.50 3.492195 B B D D H Y \ No newline at end of file
diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py
index 38de0e2..39f4af9 100644
--- a/tests/unit/db/test_datasets.py
+++ b/tests/unit/db/test_datasets.py
@@ -3,10 +3,10 @@
from unittest import mock, TestCase
from gn3.db.datasets import (
retrieve_dataset_name,
- retrieve_riset_fields,
- retrieve_geno_riset_fields,
- retrieve_publish_riset_fields,
- retrieve_probeset_riset_fields)
+ retrieve_group_fields,
+ retrieve_geno_group_fields,
+ retrieve_publish_group_fields,
+ retrieve_probeset_group_fields)
class TestDatasetsDBFunctions(TestCase):
"""Test cases for datasets functions."""
@@ -40,9 +40,9 @@ class TestDatasetsDBFunctions(TestCase):
table=table, cols=columns),
{"threshold": thresh, "name": dataset_name})
- def test_retrieve_probeset_riset_fields(self):
+ def test_retrieve_probeset_group_fields(self):
"""
- Test that the `riset` and `riset_id` fields are retrieved appropriately
+ Test that the `group` and `group_id` fields are retrieved appropriately
for the 'ProbeSet' trait type.
"""
for trait_name, expected in [
@@ -52,7 +52,7 @@ class TestDatasetsDBFunctions(TestCase):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
- retrieve_probeset_riset_fields(trait_name, db_mock),
+ retrieve_probeset_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
@@ -63,34 +63,34 @@ class TestDatasetsDBFunctions(TestCase):
" AND ProbeSetFreeze.Name = %(name)s"),
{"name": trait_name})
- def test_retrieve_riset_fields(self):
+ def test_retrieve_group_fields(self):
"""
- Test that the riset fields are set up correctly for the different trait
+ Test that the group fields are set up correctly for the different trait
types.
"""
for trait_type, trait_name, dataset_info, expected in [
["Publish", "pubTraitName01", {"dataset_name": "pubDBName01"},
- {"dataset_name": "pubDBName01", "riset": ""}],
+ {"dataset_name": "pubDBName01", "group": ""}],
["ProbeSet", "prbTraitName01", {"dataset_name": "prbDBName01"},
- {"dataset_name": "prbDBName01", "riset": ""}],
+ {"dataset_name": "prbDBName01", "group": ""}],
["Geno", "genoTraitName01", {"dataset_name": "genoDBName01"},
- {"dataset_name": "genoDBName01", "riset": ""}],
- ["Temp", "tempTraitName01", {}, {"riset": ""}],
+ {"dataset_name": "genoDBName01", "group": ""}],
+ ["Temp", "tempTraitName01", {}, {"group": ""}],
]:
db_mock = mock.MagicMock()
with self.subTest(
trait_type=trait_type, trait_name=trait_name,
dataset_info=dataset_info):
with db_mock.cursor() as cursor:
- cursor.execute.return_value = ("riset_name", 0)
+ cursor.execute.return_value = ("group_name", 0)
self.assertEqual(
- retrieve_riset_fields(
+ retrieve_group_fields(
trait_type, trait_name, dataset_info, db_mock),
expected)
- def test_retrieve_publish_riset_fields(self):
+ def test_retrieve_publish_group_fields(self):
"""
- Test that the `riset` and `riset_id` fields are retrieved appropriately
+ Test that the `group` and `group_id` fields are retrieved appropriately
for the 'Publish' trait type.
"""
for trait_name, expected in [
@@ -100,7 +100,7 @@ class TestDatasetsDBFunctions(TestCase):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
- retrieve_publish_riset_fields(trait_name, db_mock),
+ retrieve_publish_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
@@ -110,9 +110,9 @@ class TestDatasetsDBFunctions(TestCase):
" AND PublishFreeze.Name = %(name)s"),
{"name": trait_name})
- def test_retrieve_geno_riset_fields(self):
+ def test_retrieve_geno_group_fields(self):
"""
- Test that the `riset` and `riset_id` fields are retrieved appropriately
+ Test that the `group` and `group_id` fields are retrieved appropriately
for the 'Geno' trait type.
"""
for trait_name, expected in [
@@ -122,7 +122,7 @@ class TestDatasetsDBFunctions(TestCase):
with db_mock.cursor() as cursor:
cursor.execute.return_value = ()
self.assertEqual(
- retrieve_geno_riset_fields(trait_name, db_mock),
+ retrieve_geno_group_fields(trait_name, db_mock),
expected)
cursor.execute.assert_called_once_with(
(
diff --git a/tests/unit/db/test_genotypes.py b/tests/unit/db/test_genotypes.py
new file mode 100644
index 0000000..c125224
--- /dev/null
+++ b/tests/unit/db/test_genotypes.py
@@ -0,0 +1,170 @@
+"""Tests gn3.db.genotypes"""
+from unittest import TestCase
+from gn3.db.genotypes import (
+ parse_genotype_file,
+ parse_genotype_labels,
+ parse_genotype_header,
+ parse_genotype_marker,
+ build_genotype_chromosomes)
+
+class TestGenotypes(TestCase):
+ """Tests for functions in `gn3.db.genotypes`."""
+
+ def test_parse_genotype_labels(self):
+ """Test that the genotype labels are parsed correctly."""
+ self.assertEqual(
+ parse_genotype_labels([
+ "@name: test_group\t", "@filler: test_filler ",
+ "@type:test_type", "@mat:test_mat \t", "@pat:test_pat ",
+ "@het: test_het ", "@unk: test_unk", "@other: test_other",
+ "@brrr: test_brrr "]),
+ (("group", "test_group"), ("filler", "test_filler"),
+ ("type", "test_type"), ("mat", "test_mat"), ("pat", "test_pat"),
+ ("het", "test_het"), ("unk", "test_unk")))
+
+ def test_parse_genotype_header(self):
+ """Test that the genotype header is parsed correctly."""
+ for header, expected in [
+ [("Chr\tLocus\tcM\tMb\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\t"
+ "BXD11\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18\tBXD19"),
+ (("Mbmap", True), ("cm_column", 2), ("mb_column", 3),
+ ("prgy",
+ ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11",
+ "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18",
+ "BXD19")),
+ ("nprgy", 14))],
+ [("Chr\tLocus\tcM\tBXD1\tBXD2\tBXD5\tBXD6\tBXD8\tBXD9\tBXD11"
+ "\tBXD12\tBXD13\tBXD14\tBXD15\tBXD16\tBXD18"),
+ (("Mbmap", False), ("cm_column", 2), ("mb_column", None),
+ ("prgy",
+ ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9", "BXD11",
+ "BXD12", "BXD13", "BXD14", "BXD15", "BXD16", "BXD18")),
+ ("nprgy", 13))]]:
+ with self.subTest(header=header):
+ self.assertEqual(parse_genotype_header(header), expected)
+
+ def test_parse_genotype_data_line(self):
+ """Test parsing of data lines."""
+ for line, geno_obj, parlist, expected in [
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB",
+ {"mat": "test_mat", "pat": "test_pat", "het": "test_het",
+ "unk": "test_unk", "cm_column": 2, "Mbmap": True,
+ "mb_column": 3},
+ tuple(),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype",
+ ("U", "U", "U", "U", "U", "U", "U", "U", "U", "U")))],
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tD\tD\tB\tB\tD\tB\tB",
+ {"mat": "test_mat", "pat": "test_pat", "het": "test_het",
+ "unk": "test_unk", "cm_column": 2, "Mbmap": True,
+ "mb_column": 3},
+ ("some", "parlist", "content"),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype",
+ (-1, 1, "U", "U", "U", "U", "U", "U", "U", "U")))],
+ ["1\trs31443144\t1.50\t3.010274\tB\tB\tD\tH\tD\tB\tU\tD\tB\tB",
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": True, "mb_column": 3},
+ tuple(),
+ (("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))]]:
+ with self.subTest(line=line):
+ self.assertEqual(
+ parse_genotype_marker(line, geno_obj, parlist),
+ expected)
+
+ def test_build_genotype_chromosomes(self):
+ """
+ Given `markers` and `geno_obj`, test that `build_genotype_chromosomes`
+ builds a sequence of chromosomes with the given markers ordered
+ according to the `chr` value."""
+ for markers, geno_obj, expected in [
+ [[(("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1))),
+ (("chr", "2"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", 3.0),
+ ("genotype", (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)))],
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": True, "mb_column": 3},
+ ((("name", "1"), ("mb_exists", True), ("cm_column", 2),
+ ("mb_column", 3),
+ ("loci",
+ ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": 3.0,
+ "genotype": (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)},))),
+ (("name", "2"), ("mb_exists", True), ("cm_column", 2),
+ ("mb_column", 3),
+ ("loci",
+ ({"chr": "2", "name": "rs31443144", "cM": 2.0, "Mb": 3.0,
+ "genotype": (-1, -1, 1, 0, 1, -1, "U", 1, -1, -1)},))))],
+ [[(("chr", "1"), ("name", "rs31443144"), ("cM", 2.0),
+ ("Mb", None),
+ ("genotype", (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)))],
+ {"mat": "B", "pat": "D", "het": "H", "unk": "U",
+ "cm_column": 2, "Mbmap": False, "mb_column": None},
+ ((("name", "1"), ("mb_exists", False), ("cm_column", 2),
+ ("mb_column", None),
+ ("loci",
+ ({"chr": "1", "name": "rs31443144", "cM": 2.0, "Mb": None,
+ "genotype": (-1, 1, 1, 0, 1, -1, "U", 1, -1, -1)},))),)]]:
+ with self.subTest(markers=markers):
+ self.assertEqual(
+ build_genotype_chromosomes(geno_obj, markers),
+ expected)
+
+ def test_parse_genotype_file(self):
+ """Test the parsing of genotype files. """
+ self.assertEqual(
+ parse_genotype_file(
+ "tests/unit/db/data/genotypes/genotype_sample1.geno"),
+ {"group": "BXD",
+ "type": "riset",
+ "mat": "B",
+ "pat": "D",
+ "het": "H",
+ "unk": "U",
+ "Mbmap": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "prgy": ("BXD1", "BXD2", "BXD5", "BXD6", "BXD8", "BXD9"),
+ "nprgy": 6,
+ "chromosomes": (
+ {"name": "1",
+ "mb_exists": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "loci": (
+ {"chr": "1",
+ "name": "rs31443144",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 1, -1)
+ },
+ {"chr": "1",
+ "name": "rs6269442",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 0, "U")},
+ {"chr": "1",
+ "name": "rs32285189",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, "U", 1, 1, 1, -1)})},
+ {"name": "2",
+ "mb_exists": True,
+ "cm_column": 2,
+ "mb_column": 3,
+ "loci": (
+ {"chr": "2",
+ "name": "rs31443144",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 1, -1)},
+ {"chr": "2",
+ "name": "rs6269442",
+ "cM": 2.0,
+ "Mb": 3.0,
+ "genotype": (-1, -1, 1, 1, 0, "U")})})})
diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py
index ee98893..8af8e82 100644
--- a/tests/unit/db/test_traits.py
+++ b/tests/unit/db/test_traits.py
@@ -166,15 +166,19 @@ class TestTraitsDBFunctions(TestCase):
the right calls.
"""
+ # pylint: disable=C0103
db_mock = mock.MagicMock()
STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s"
- PUBLISH_DATA_SQL: str = ("UPDATE PublishData SET value = %s "
- "WHERE StrainId = %s AND Id = %s")
- PUBLISH_SE_SQL: str = ("UPDATE PublishSE SET error = %s "
- "WHERE StrainId = %s AND DataId = %s")
- N_STRAIN_SQL: str = ("UPDATE NStrain SET count = %s "
- "WHERE StrainId = %s AND DataId = %s")
+ PUBLISH_DATA_SQL: str = (
+ "UPDATE PublishData SET value = %s "
+ "WHERE StrainId = %s AND Id = %s")
+ PUBLISH_SE_SQL: str = (
+ "UPDATE PublishSE SET error = %s "
+ "WHERE StrainId = %s AND DataId = %s")
+ N_STRAIN_SQL: str = (
+ "UPDATE NStrain SET count = %s "
+ "WHERE StrainId = %s AND DataId = %s")
with db_mock.cursor() as cursor:
type(cursor).rowcount = 1
diff --git a/tests/unit/sample_test_data.py b/tests/unit/sample_test_data.py
new file mode 100644
index 0000000..407d074
--- /dev/null
+++ b/tests/unit/sample_test_data.py
@@ -0,0 +1,111 @@
+"""
+This module holds a collection of sample data variables, used in more than one
+ test.
+
+This is mostly to avoid the `duplicate-code` pylint error that gets raised if
+the same data is defined in more than one file. It has been found that adding
+the `# pylint: disable=R0801` or `# pylint: disable=duplicate-code` to the top
+of the file seems to not work as expected.
+
+Adding these same declarations to .pylintrc is not an option, since that,
+seemingly, would deactivate the warnings for all code in the project: We do not
+want that.
+"""
+
+organised_trait_1 = {
+ "1": {
+ "ID": "1",
+ "chromosomes": {
+ 1: {"Chr": 1,
+ "loci": [
+ {
+ "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ }]},
+ 2: {"Chr": 2,
+ "loci": [
+ {
+ "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ }]}}}}
+
+organised_trait_2 = {
+ "2": {
+ "ID": "2",
+ "chromosomes": {
+ 1: {"Chr": 1,
+ "loci": [
+ {
+ "Locus": "rs31443144", "cM": 1.500, "Mb": 3.010,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs6269442", "cM": 1.500, "Mb": 3.492,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs32285189", "cM": 1.630, "Mb": 3.511,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs258367496", "cM": 1.630, "Mb": 3.660,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs32430919", "cM": 1.750, "Mb": 3.777,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs36251697", "cM": 1.880, "Mb": 3.812,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs30658298", "cM": 2.010, "Mb": 4.431,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ }]},
+ 2: {"Chr": 2,
+ "loci": [
+ {
+ "Locus": "rs51852623", "cM": 2.010, "Mb": 4.447,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs31879829", "cM": 2.140, "Mb": 4.519,
+ "LRS": 0.500, "Additive": -0.074, "pValue": 1.000
+ },
+ {
+ "Locus": "rs36742481", "cM": 2.140, "Mb": 4.776,
+ "LRS": 0.579, "Additive": -0.074, "pValue": 1.000
+ }]}}}}
diff --git a/tests/unit/computations/test_heatmap.py b/tests/unit/test_heatmaps.py
index 650cb45..b54e2f3 100644
--- a/tests/unit/computations/test_heatmap.py
+++ b/tests/unit/test_heatmaps.py
@@ -1,38 +1,55 @@
-"""Module contains tests for gn3.computations.heatmap"""
+"""Module contains tests for gn3.heatmaps.heatmaps"""
from unittest import TestCase
-from gn3.computations.heatmap import cluster_traits, export_trait_data
+from gn3.heatmaps import (
+ cluster_traits,
+ get_lrs_from_chr,
+ export_trait_data,
+ compute_traits_order,
+ 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),
+ ((1, 7, 0.06024619831474998), 5, 0.19179284676938602),
+ 0.20337048635536847),
+ 9,
+ 0.23451785425383564),
+ ((3, (6, 8, 0.2140799896286565), 0.25879514152086425),
+ 4, 0.8968250491499363),
+ 0.9313185954797953)
class TestHeatmap(TestCase):
"""Class for testing heatmap computation functions"""
@@ -49,7 +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):
@@ -89,7 +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)
@@ -141,3 +158,59 @@ class TestHeatmap(TestCase):
0.9313185954797953, 1.1683723389247052, 0.23451785425383564,
1.7413442197913358, 0.33370067057028485, 1.3256191648260216,
0.0)))
+
+ def test_compute_heatmap_order(self):
+ """Test the orders."""
+ self.assertEqual(
+ compute_traits_order(slinked), (0, 2, 1, 7, 5, 9, 3, 6, 8, 4))
+
+ def test_retrieve_samples_and_values(self):
+ """Test retrieval of samples and values."""
+ for orders, slist, tdata, expected in [
+ [
+ [2],
+ ["s1", "s2", "s3", "s4"],
+ [[2, 9, 6, None, 4],
+ [7, 5, None, None, 4],
+ [9, None, 5, 4, 7],
+ [6, None, None, 4, None]],
+ [[2, ["s1", "s3", "s4"], [9, 5, 4]]]
+ ],
+ [
+ [3],
+ ["s1", "s2", "s3", "s4", "s5"],
+ [[2, 9, 6, None, 4],
+ [7, 5, None, None, 4],
+ [9, None, 5, 4, 7],
+ [6, None, None, 4, None]],
+ [[3, ["s1", "s4"], [6, 4]]]
+ ]]:
+ with self.subTest(samplelist=slist, traitdata=tdata):
+ self.assertEqual(
+ retrieve_samples_and_values(orders, slist, tdata), expected)
+
+ def test_get_lrs_from_chr(self):
+ """Check that function gets correct LRS values"""
+ for trait, chromosome, expected in [
+ [{"chromosomes": {}}, 3, [None]],
+ [{"chromosomes": {3: {"loci": [
+ {"Locus": "b", "LRS": 1.9},
+ {"Locus": "a", "LRS": 13.2},
+ {"Locus": "d", "LRS": 53.21},
+ {"Locus": "c", "LRS": 2.22}]}}},
+ 3,
+ [13.2, 1.9, 2.22, 53.21]]]:
+ with self.subTest(trait=trait, chromosome=chromosome):
+ self.assertEqual(get_lrs_from_chr(trait, chromosome), expected)
+
+ def test_process_traits_data_for_heatmap(self):
+ """Check for correct processing of data for heatmap generation."""
+ self.assertEqual(
+ process_traits_data_for_heatmap(
+ {**organised_trait_1, **organised_trait_2},
+ ["2", "1"],
+ [1, 2]),
+ [[[0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
+ [0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]],
+ [[0.5, 0.579, 0.5],
+ [0.5, 0.5, 0.5]]])
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 00:27:31 +0000