From ad1f0029097e0b88a46221d717f066b3dda09a80 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 16 Jan 2019 15:41:20 +0100
Subject: [PATCH] make testBlastExec unit test less stringent
Depending on the used BLAST version, there might be one low quality hit more
or less. The unit test is now less stringent in a sense that we check whether
the perfect hits are found.
---
modules/bindings/tests/test_blast.py | 29 +++++++++++++++-------------
1 file changed, 16 insertions(+), 13 deletions(-)
diff --git a/modules/bindings/tests/test_blast.py b/modules/bindings/tests/test_blast.py
index 48cb56068..18311abd9 100644
--- a/modules/bindings/tests/test_blast.py
+++ b/modules/bindings/tests/test_blast.py
@@ -32,21 +32,23 @@ class TestBlastBindings(unittest.TestCase):
def testBlastExec(self):
- hits=blast.Blast(self.query, 'testfiles/seqdb')
-
- expected_hits=['1griA','1fhsA','3n84E','1mw9X']
- self.assertEqual(len(hits), 4)
-
- found=0
- hit_ids=[]
+ hits = blast.Blast(self.query, 'testfiles/seqdb')
+ expected_perfect_hit_ids = ["1fhsA", "3n84E", "1griA"]
+ perfect_hit_ids = []
+
for h in hits:
- hit_ids.append(h.identifier)
-
- for identifier in expected_hits:
- if identifier in hit_ids:
- found+=1
- self.assertEqual(found, 4)
+ perfect_match = False
+ for aln_patch in h.aligned_patches:
+ if aln_patch.seqid == 1.0:
+ perfect_match = True
+ if perfect_match:
+ perfect_hit_ids.append(h.identifier)
+
+ expected_perfect_hit_ids.sort()
+ perfect_hit_ids.sort()
+
+ self.assertEqual(perfect_hit_ids, expected_perfect_hit_ids)
def testBlastParseOutput(self):
@@ -54,6 +56,7 @@ class TestBlastBindings(unittest.TestCase):
parsed_out=blast.ParseBlastOutput(raw_out)
+ # numbers and ids can be specific to a certain blast version
expected_ids=['1griA','1fhsA','3n84E','1mw9X']
expected_evalues=[4.80893e-59,4.80893e-59,9.06925e-58,2.96523]
expected_scores=[534,534,523,27]
--
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