Merge branch 'main' of https://github.com/genenetwork/genenetwork3 into bug/fix_rqtl_covariates

1 files changed, 111 insertions, 0 deletions

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
+                    }]}}}}