tests: test directory

tests/files/clip.bed

+18	28645943	28646043	1	clip1	-
+18	28646043	28646070	1	clip2	-
+18	28709190	28709200	2	clip3	-
+18	28898040	28898060	3	clip4	+
+18	28898060	28898080	3	clip5	+
+18	28898080	28898100	3	clip6	+
+18	51062273	51062283	8	clip7	+
+18	49866521	49866541	8	clip8	+
\ No newline at end of file

tests/files/exons.bed

+#ref	start	end	id	score	strand
+18	28681865	28682388	1_1	0	-
+18	28681183	28681432	1_2	0	-
+18	28673521	28673606	1_3	0	-
+18	28672063	28672263	1_4	0	-
+18	28671489	28671530	1_5	0	-
+18	28670990	28671110	1_6	0	-
+18	28669401	28669557	1_7	0	-
+18	28667631	28667776	1_8	0	-
+18	28666538	28666705	1_9	0	-

tests/files/genes.bed

+#ref	start	end	id	score	strand
+18	28645943	28682388	1	DSC2	-
+18	28709190	28742819	2	DSC1	-
+18	28898050	28937394	3	DSG1	+
+18	28956739	28994869	4	DSG4	+
+13	45766989	45775176	5	KCTD4	-
+13	45911001	45915347	6	TPT1	-
+18	48918411	49088839	7	AC011260.1	+
+18	49866541	51062273	8	DCC	+
+13	45967450	45992516	9	SLC25A30	-
+20	238376	241735	415	DEFB132	+
+X	102962271	102983552	10123	GLRA4	-

tests/test.py

+#!/usr/bin/env python3
+
+# -*- coding: UTF-8 -*-
+
+"""
+Description:
+"""
+
+import doctest
+from pathlib import Path
+from typing import List
+import unittest
+import sys
+
+sys.path.insert(0, str(Path(__file__).parents[1].resolve()))
+
+
+# recover ignored files
+def get_ignored_files() -> List[str]:
+    """
+    Recover ignored python files in gitignore
+    """
+    gitignore = Path(__file__).parents[1] / '.gitignore'
+    if not gitignore.is_file():
+        return []
+    with gitignore.open('r') as f:
+        files = f.read().splitlines()
+    return [cfile.replace('.py', '').replace('/', '.')
+            for cfile in files if cfile.endswith('.py')] + \
+           ["src.db_utils.interactions.features_interactions"]
+
+
+# Loading every python file in this folder
+list_mod = [str(mfile.relative_to(Path(__file__).resolve().parents[1]))
+            for mfile in
+            list((Path(__file__).resolve().parents[1] / "src").rglob('*.py'))]
+list_mod2 = [m.replace('.py', '').replace('/', '.') for m in list_mod
+             if '__init__' not in m
+             and '__main__' not in m
+             and 'test' not in m]
+final_mod = [mod for mod in list_mod2 if mod not in get_ignored_files()]
+
+
+def load_tests(loader, tests, ignore):
+    for cmod in final_mod:
+        tests.addTest(doctest.DocTestSuite(cmod))
+    return tests
+
+
+if __name__ == "__main__":
+    unittest.main()