updated clustalw unittests for nopgap option

modules/bindings/tests/test_clustalw.py

@@ -13,6 +13,7 @@ class TestClustalWBindings(unittest.TestCase):
     self.templseq = io.LoadSequence("testfiles/similar.fasta")
     self.multseq = io.LoadSequenceList("testfiles/multiple.fasta")
     self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.fasta")
+    self.nopgap_pw_alignment = io.LoadAlignment("testfiles/nopgap_pairwise_aln.fasta")
     self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
     
   def testPairwiseClustalW(self):
@@ -20,6 +21,11 @@ class TestClustalWBindings(unittest.TestCase):
     assert self.pw_alignment.ToString(80) == aln.ToString(80), \
            "Pairwise alignment differs from precomputed one"
   
+  def testNoPGapPariwiseClustalW(self):
+    aln=clustalw.ClustalW(self.targetseq, self.templseq, nopgap=True)
+    assert self.nopgap_pw_alignment.ToString(80) == aln.ToString(80), \
+           "NoPGap pairwise alignment differs from precomputed one"
+
   def testAttachedViewClustalW(self):
     aln=clustalw.ClustalW(self.targetseq, self.templseq)
     assert aln.FindSequence("testseq").HasAttachedView(), \

modules/bindings/tests/testfiles/nopgap_pairwise_aln.fasta

+>testseq
+------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADIN---LEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATE----MTERLVADEEFTDWLCKR-----TPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL