From 8c2b856ead25b5423d104b94cc05c40265573590 Mon Sep 17 00:00:00 2001
From: Melvin Alappat <melvin.alappat@unibas.ch>
Date: Mon, 20 Dec 2021 21:06:08 +0100
Subject: [PATCH] added: tests for priming_prob.py and CLI
---
tests/test_cli_priming_prob.py | 39 ++++++++++++++++++++++++++++++++++
tests/test_priming_prob.py | 35 ++++++++++++++++++++++++++++++
2 files changed, 74 insertions(+)
create mode 100644 tests/test_cli_priming_prob.py
create mode 100644 tests/test_priming_prob.py
diff --git a/tests/test_cli_priming_prob.py b/tests/test_cli_priming_prob.py
new file mode 100644
index 0000000..76e561a
--- /dev/null
+++ b/tests/test_cli_priming_prob.py
@@ -0,0 +1,39 @@
+"""Unit tests for module ``CLI_PrimingProb.py``."""
+import pytest
+from pathlib import Path
+from src.primingprob import cli_priming_prob as CPb
+from unittest.mock import patch, MagicMock
+
+PACKAGE_DIR = Path(__file__).resolve().parents[1]
+TEST_FILE = "./tests/resources/Energies_test.txt"
+
+
+class TestParseArgs:
+ """Test ``parse_args()`` function."""
+
+ def test_no_positional_args(self):
+ """Call without positional args."""
+ with pytest.raises(SystemExit) as exc:
+ CPb.parse_args()
+ assert exc.value.code != 0
+
+
+class TestMain:
+ """Test ``main()`` function."""
+
+ def test_without_args(self):
+ """Call without args."""
+ with pytest.raises(SystemExit) as exc:
+ CPb.main()
+ assert exc.value.code != 0
+
+ def test_last_line(self):
+ """Test name equals main."""
+ # Arrange
+ with patch.object(CPb, "main", MagicMock()) as mock_main:
+ with patch.object(CPb, "__name__", "__main__"):
+ # Act
+ CPb.init()
+
+ # Assert
+ mock_main.assert_called_once()
diff --git a/tests/test_priming_prob.py b/tests/test_priming_prob.py
new file mode 100644
index 0000000..ad351ad
--- /dev/null
+++ b/tests/test_priming_prob.py
@@ -0,0 +1,35 @@
+"""Unit tests for module ``PrimingProb_CI``."""
+import os
+from src.primingprob.priming_prob import Probability as Pbt
+
+Energy_file = "./tests/resources/Energies_test.txt"
+Fasta_file = "./tests/resources/transcript.fasta"
+Output_file = "./tests/resources/Potential_Priming_Sites.txt"
+
+
+def test_inter_para():
+ """Tests InterPara function."""
+ testdata = Pbt.inter_para(Energy_file)
+ assert len(testdata) == 3 # Number of interactions
+ assert type(testdata) is list
+ for i in range(0, len(testdata)):
+ assert testdata[i][0].isdigit()
+
+ return testdata
+
+
+testdata2 = test_inter_para()
+
+
+def test_inter_prob():
+ """Tests InterProb function."""
+ Pbt.inter_prob(testdata2, Fasta_file, Output_file)
+ assert os.path.exists(Output_file) is True # Check whether file exists
+
+ mytestfile = open(Output_file, "r") # Test whether gff file start with transcript ID
+ for mylinecounter in mytestfile:
+ assert mylinecounter.startswith("NW_005196756.1:c68260-66684")
+
+ with open(Output_file, "r") as tt: # Check whether number of interactions is right
+ x = len(tt.readlines())
+ assert x == 3
--
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