diff options
| -rw-r--r-- | gn3/computations/__init__.py | 0 | ||||
| -rw-r--r-- | gn3/computations/gemma.py | 14 | ||||
| -rw-r--r-- | tests/unit/computations/__init__.py | 0 | ||||
| -rw-r--r-- | tests/unit/computations/test_gemma.py | 24 |
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")]) |