From e67796eb7e021d2767eba88c47fe1117d087d47b Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 22 Oct 2010 17:30:34 +0200
Subject: [PATCH] updated clustalw unittests for nopgap option
---
modules/bindings/tests/test_clustalw.py | 6 ++++++
modules/bindings/tests/testfiles/nopgap_pairwise_aln.fasta | 4 ++++
2 files changed, 10 insertions(+)
create mode 100644 modules/bindings/tests/testfiles/nopgap_pairwise_aln.fasta
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
index fc93a19b6..cf8b2753e 100644
--- a/modules/bindings/tests/test_clustalw.py
+++ b/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(), \
diff --git a/modules/bindings/tests/testfiles/nopgap_pairwise_aln.fasta b/modules/bindings/tests/testfiles/nopgap_pairwise_aln.fasta
new file mode 100644
index 000000000..4ec347261
--- /dev/null
+++ b/modules/bindings/tests/testfiles/nopgap_pairwise_aln.fasta
@@ -0,0 +1,4 @@
+>testseq
+------MRLDGKTALITGSARGIGRAFAEAYVREGARVAIADIN---LEAARATAAEIGPAACAIALDVTDQASIDRCVAELLDRWGSIDILVNNAALFDLAPIVEITRESYDRLFAINVSGTLFMMQAVARAMIAGGRGGKIINMASQAGRRGEALVGVYCATKAAVISLTQSAGLNLIRHGINVNAIAPGVVDGEHWDGVDAKFADYENLPRGEKKRQVGAAVPFGRMGRAEDLTGMAIFLATPEADYIVAQTYNVDGGNWMS-
+>P50199.1
+MSHPDLFSLSGARALVTGASRGIGLTLAKGLARYGAEVVLNGRNAESLDSAQSGFEAEGLKASTAVFDVTDQDAVIDGVAAIERDMGPIDILINNAGIQRRAPLEEFSRKDWDDLMSTNVNAVFFVGQAVARHMIPRGRG-KIVNICSVQSELARPGIAPYTATKGAVKNLTKGMATDWGRHGLQINGLAPGYFATE----MTERLVADEEFTDWLCKR-----TPAGRWGQVEELVGAAVFLSSRASSFVNGQVLMVDGGITVSL
--
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