Create a new method for generating a valid phenotype file on the fly

4 files changed, 38 insertions, 0 deletions

diff --git a/gn3/computations/__init__.py b/gn3/computations/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/gn3/computations/__init__.py
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
new file mode 100644
index 0000000..9a972ba
--- /dev/null
+++ b/gn3/computations/gemma.py
@@ -0,0 +1,14 @@
+"""Procedures related gemma computations"""
+
+
+def generate_pheno_txt_file(trait_filename: str,
+                            values: str,
+                            tmpdir: str = "/tmp") -> str:
+    """Given VALUES, and TMPDIR, generate a valide traits file"""
+    with open(f"{tmpdir}/gn2/{trait_filename}", "w") as _file:
+        for value in values:
+            if value == "x":
+                _file.write("NA\n")
+            else:
+                _file.write(f"{value}\n")
+    return f"{tmpdir}/gn2/{trait_filename}"
diff --git a/tests/unit/computations/__init__.py b/tests/unit/computations/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/tests/unit/computations/__init__.py
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
new file mode 100644
index 0000000..89c8d00
--- /dev/null
+++ b/tests/unit/computations/test_gemma.py
@@ -0,0 +1,24 @@
+"""Test cases for procedures defined in computations.gemma"""
+import unittest
+
+from unittest import mock
+from gn3.computations.gemma import generate_pheno_txt_file
+
+
+class TestGemma(unittest.TestCase):
+    """Test cases for computations.gemma module"""
+
+    def test_generate_pheno_txt_file(self):
+        """Test that the pheno text file is generated correctly"""
+        open_mock = mock.mock_open()
+        with mock.patch("gn3.computations.gemma.open",
+                        open_mock, create=True):
+            _file = generate_pheno_txt_file(tmpdir="/tmp",
+                                            trait_filename="phenotype.txt",
+                                            values=["x", "x", "BXD07 438.700"])
+            self.assertEqual(_file, "/tmp/gn2/phenotype.txt")
+        open_mock.assert_called_with("/tmp/gn2/phenotype.txt", "w")
+        open_mock.return_value.write.assert_has_calls([
+            mock.call("NA\n"),
+            mock.call("NA\n"),
+            mock.call("BXD07 438.700\n")])