Fixed a couple of typos in comments. PEP8 formatting

biopython · Jan 28, 2013 · 6a31cb3 · 6a31cb3
1 parent 708d3ee
commit 6a31cb3
Showing 1 changed file with 26 additions and 16 deletions.
diff --git a/Tests/test_pairwise2.py b/Tests/test_pairwise2.py
@@ -379,22 +379,24 @@ def test_align_one_char3(self):
 
 
 class TestPersiteGapPenalties(unittest.TestCase):
-    """
+    """Check gap penalty callbacks use correct gap opening position.
-    This tests that the gap penalty callbacks are really being used with the correct gap opening position.
-    The second test forces a bad alignment by having a very expsive gap penalty where one would noremally expect a gap, and a cheap gap pentaly in another place.
-    """
 
+    This tests that the gap penalty callbacks are really being used
+    with the correct gap opening position.
+    """
 
     def test_gap_here_only_1(self):
         seq1 = "AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA"
         seq2 = "AABBBAAAACCCCAAAABBBAA"
-        breaks = [0,11,len(seq2)]
+        breaks = [0, 11, len(seq2)]
-        nogaps = lambda x,y: -2000 -y#Very expensive to open a gap in seq1
+        # Very expensive to open a gap in seq1:
-        specificgaps = lambda x,y: (-2 -y) if x in breaks else (-2000 -y)#Very expensive to open a gap in seq2 unless it is in one of the allowed positions
+        nogaps = lambda x, y: -2000 - y
-        alignments = pairwise2.align.globalmc(seq1,seq2,1,-1,nogaps,specificgaps)
+        # Very expensive to open a gap in seq2 unless it is in one of the allowed positions
-        self.assertEqual(len(alignments),1)
+        specificgaps = lambda x, y: (-2 -y) if x in breaks else (-2000 - y)
+        alignments = pairwise2.align.globalmc(seq1, seq2, 1, -1, nogaps, specificgaps)
+        self.assertEqual(len(alignments), 1)
         formatted = pairwise2.format_alignment(*alignments[0])
-        self.assertEqual(formatted,"""\
+        self.assertEqual(formatted, """\
 AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA
 ||||||||||||||||||||||||||||||||||||
 --AABBBAAAACC----------CCAAAABBBAA--
@@ -403,15 +405,23 @@ def test_gap_here_only_1(self):
 
 
     def test_gap_here_only_2(self):
+        """Force a bad alignment.
+
+        Forces a bad alignment by having a very expensive gap penalty
+        where one would normally expect a gap, and a cheap gap penalty
+        in another place.
+        """
         seq1 = "AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA"
         seq2 = "AABBBAAAACCCCAAAABBBAA"
-        breaks = [0,3,len(seq2)]
+        breaks = [0, 3, len(seq2)]
-        nogaps = lambda x,y: -2000 -y#Very expensive to open a gap in seq1
+        #Very expensive to open a gap in seq1:
-        specificgaps = lambda x,y: (-2 -y) if x in breaks else (-2000 -y)#Very expensive to open a gap in seq2 unless it is in one of the allowed positions
+        nogaps = lambda x, y: -2000 - y
-        alignments = pairwise2.align.globalmc(seq1,seq2,1,-1,nogaps,specificgaps)
+        #Very expensive to open a gap in seq2 unless it is in one of the allowed positions:
-        self.assertEqual(len(alignments),1)
+        specificgaps = lambda x, y: (-2 - y) if x in breaks else (-2000 - y)
+        alignments = pairwise2.align.globalmc(seq1, seq2, 1, -1, nogaps, specificgaps)
+        self.assertEqual(len(alignments), 1)
         formatted = pairwise2.format_alignment(*alignments[0])
-        self.assertEqual(formatted,"""\
+        self.assertEqual(formatted, """\
 AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA
 ||||||||||||||||||||||||||||||||||||
 --AAB----------BBAAAACCCCAAAABBBAA--