From 04ff702c75ab8c41b748f8dd68f36bf1f1672b69 Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Tue, 12 Jan 2021 15:13:09 +0100
Subject: [PATCH] tests: test directory
---
tests/__init__.py | 0
tests/files/clip.bed | 8 +++++++
tests/files/exons.bed | 10 +++++++++
tests/files/genes.bed | 12 ++++++++++
tests/test.py | 51 +++++++++++++++++++++++++++++++++++++++++++
5 files changed, 81 insertions(+)
create mode 100644 tests/__init__.py
create mode 100644 tests/files/clip.bed
create mode 100644 tests/files/exons.bed
create mode 100644 tests/files/genes.bed
create mode 100644 tests/test.py
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/files/clip.bed b/tests/files/clip.bed
new file mode 100644
index 00000000..69c737df
--- /dev/null
+++ b/tests/files/clip.bed
@@ -0,0 +1,8 @@
+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
diff --git a/tests/files/exons.bed b/tests/files/exons.bed
new file mode 100644
index 00000000..a61bd39e
--- /dev/null
+++ b/tests/files/exons.bed
@@ -0,0 +1,10 @@
+#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 -
diff --git a/tests/files/genes.bed b/tests/files/genes.bed
new file mode 100644
index 00000000..5840938c
--- /dev/null
+++ b/tests/files/genes.bed
@@ -0,0 +1,12 @@
+#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 -
diff --git a/tests/test.py b/tests/test.py
new file mode 100644
index 00000000..d0892e27
--- /dev/null
+++ b/tests/test.py
@@ -0,0 +1,51 @@
+#!/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()
--
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