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Commit e67796eb authored by Tobias Schmidt's avatar Tobias Schmidt Committed by Marco Biasini
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updated clustalw unittests for nopgap option

parent 6424dafe
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...@@ -13,6 +13,7 @@ class TestClustalWBindings(unittest.TestCase): ...@@ -13,6 +13,7 @@ class TestClustalWBindings(unittest.TestCase):
self.templseq = io.LoadSequence("testfiles/similar.fasta") self.templseq = io.LoadSequence("testfiles/similar.fasta")
self.multseq = io.LoadSequenceList("testfiles/multiple.fasta") self.multseq = io.LoadSequenceList("testfiles/multiple.fasta")
self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.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") self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
def testPairwiseClustalW(self): def testPairwiseClustalW(self):
...@@ -20,6 +21,11 @@ class TestClustalWBindings(unittest.TestCase): ...@@ -20,6 +21,11 @@ class TestClustalWBindings(unittest.TestCase):
assert self.pw_alignment.ToString(80) == aln.ToString(80), \ assert self.pw_alignment.ToString(80) == aln.ToString(80), \
"Pairwise alignment differs from precomputed one" "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): def testAttachedViewClustalW(self):
aln=clustalw.ClustalW(self.targetseq, self.templseq) aln=clustalw.ClustalW(self.targetseq, self.templseq)
assert aln.FindSequence("testseq").HasAttachedView(), \ assert aln.FindSequence("testseq").HasAttachedView(), \
......
>testseq
------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADIN---LEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-
>P50199.1
MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATE----MTERLVADEEFTDWLCKR-----TPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL
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