Refactor to use unittest and gitlab-ci (1)

.gitignore

 *.swp
 balibase/
+__pycache__/
+balibase.zip

.gitlab-ci.yml

+before_script:
+        - python3 -m pip install -r requirements.txt
+
+cache:
+        paths:
+                - balibase/
+test:
+        script:
+                - python3 -m unittest alignementseq_tests.py

alignementseq.py

@@ -38,7 +38,7 @@ def score(a, b, gap=-8, id=1, mut=-1):
 #    else:
 #        return mut
 
-def align(seq1, seq2):
+def align(seq1, seq2, score=score):
     x = seq1.seq
     y = seq2.seq
     n=len(x)
@@ -246,4 +246,3 @@ def test():
         print(s)
         print(x)
         print(y)
-test()

alignementseq_tests.py

+import unittest
+import urllib.request
+import os
+import zipfile
+
+from Bio.SeqRecord import SeqRecord
+
+class AlignmentSeqTestCase(unittest.TestCase):
+    def setUp(self):
+        balibase_zippath = "balibase.zip"
+        balibase_path = "balibase"
+        testfile_path = os.path.join(
+            balibase_path, 
+            "RV11.unaligned", "BBS11001.fasta")
+
+        if not os.path.isdir(balibase_path):
+            os.mkdir(balibase_path)
+        if not os.path.isfile(testfile_path):
+            if not os.path.isfile(balibase_zippath):
+                print("Fetching balibase archive from moodle...")
+                urllib.request.urlretrieve(
+                    "https://moodle.polytechnique.fr/mod/resource/view.php?id=38570",
+                    balibase_zippath)
+            with zipfile.ZipFile(balibase_zippath) as balibase_zip:
+                balibase_zip.extractall()
+
+    def test_simple_align(self):
+        from alignementseq import align
+        score_fn = lambda a,b : -2 if a == '' or b == '' else -1 if a != b else 1
+
+        cases = [
+                ("CHAT", "CAT", 1, "CHAT", "C-AT"),
+                ("CHAT", "CGAT", 2, "CHAT", "CGAT"),
+                ("CHAT", "AT", -2, "CHAT", "--AT")
+                ]
+        for s1, s2, exp_score, exp_r1, exp_r2 in cases:
+            score, r1, r2 = align(SeqRecord(s1), SeqRecord(s2), score_fn)
+            self.assertEqual(score, exp_score)
+            self.assertEqual(r1.seq, exp_r1)
+            self.assertEqual(r2.seq, exp_r2)
+
+if __name__ == '__main__':
+    unittest.main()
+

requirements.txt

+biopython==1.73