Change unittest2 back into unittest.

[htsworkflow.git] / test / test_srf2fastq.py

diff --git a/test/test_srf2fastq.py b/test/test_srf2fastq.py
index f29cc7048ce205fe52c5e841b8bf2d1dfd46bfc0..e06ec82ed31e197e464665d2a68e9c99bb53d3b5 100644 (file)
--- a/test/test_srf2fastq.py
+++ b/test/test_srf2fastq.py
@@ -1,14 +1,16 @@
 import os
 from StringIO import StringIO
 import sys
-import unittest
+from unittest import TestCase
 
 _module_path, _module_name = os.path.split(__file__)
 sys.path.append(os.path.join(_module_path, '..', 'scripts'))
 
-import srf2named_fastq
+from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
 
-class testSrf2Fastq(unittest.TestCase):
+from htsworkflow.pipelines import srf2fastq
+
+class testSrf2Fastq(TestCase):
     def test_split_good(self):
         source = StringIO("""@header
 AGCTTTTT
@@ -18,7 +20,7 @@ IIIIB+++
         target1 = StringIO()
         target2 = StringIO()
 
-        srf2named_fastq.convert_single_to_two_fastq(source, target1, target2)
+        srf2fastq.convert_single_to_two_fastq(source, target1, target2)
 
         target1.seek(0)
         lines1 = target1.readlines()
@@ -49,7 +51,7 @@ IIIIB+++
         target1 = StringIO()
         target2 = StringIO()
 
-        srf2named_fastq.convert_single_to_two_fastq(source, target1, target2, header="foo_")
+        srf2fastq.convert_single_to_two_fastq(source, target1, target2, header="foo_")
 
         target1.seek(0)
         lines1 = target1.readlines()
@@ -79,7 +81,7 @@ IIIIB+++
 """)
         target1 = StringIO()
 
-        srf2named_fastq.convert_single_to_fastq(source, target1)
+        srf2fastq.convert_single_to_fastq(source, target1)
 
         target1.seek(0)
         lines1 = target1.readlines()
@@ -101,7 +103,7 @@ IIIIB+++
 """)
         target1 = StringIO()
 
-        srf2named_fastq.convert_single_to_fastq(source, target1, header="foo_")
+        srf2fastq.convert_single_to_fastq(source, target1, header="foo_")
 
         target1.seek(0)
         lines1 = target1.readlines()
@@ -111,9 +113,36 @@ IIIIB+++
         self.failUnlessEqual(lines1[2].rstrip(), '+')
         self.failUnlessEqual(lines1[3].rstrip(), '@IIIB+++')
 
+    def test_is_srf(self):        
+        cnf4_srf = 'woldlab_070829_USI-EAS44_0017_FC11055_1.srf'
+        cnf4_path = os.path.join(TESTDATA_DIR, cnf4_srf)
+        cnf1_srf = 'woldlab_090512_HWI-EAS229_0114_428NNAAXX_5.srf'
+        cnf1_path = os.path.join(TESTDATA_DIR, cnf1_srf)
+        
+        is_srf = srf2fastq.is_srf
+        self.failUnlessEqual(is_srf(__file__), False)
+        self.failUnlessEqual(is_srf(cnf4_path), True)
+        self.failUnlessEqual(is_srf(cnf1_path), True)
+
+    def test_is_cnf1(self):        
+        cnf4_srf = 'woldlab_070829_USI-EAS44_0017_FC11055_1.srf'
+        cnf4_path = os.path.join(TESTDATA_DIR, cnf4_srf)
+        cnf1_srf = 'woldlab_090512_HWI-EAS229_0114_428NNAAXX_5.srf'
+        cnf1_path = os.path.join(TESTDATA_DIR, cnf1_srf)
+        
+        is_cnf1 = srf2fastq.is_cnf1
+        self.failUnlessRaises(ValueError, is_cnf1, __file__)
+        self.failUnlessEqual(is_cnf1(cnf4_path), False)
+        self.failUnlessEqual(is_cnf1(cnf1_path), True)
+
 
 def suite():
-    return unittest.makeSuite(testSrf2Fastq,'test')
+    from unittest import TestSuite, defaultTestLoader
+    suite = TestSuite()
+    suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq))
+    return suite
+
 
 if __name__ == "__main__":
-    unittest.main(defaultTest="suite")
+    from unittest import main
+    main(defaultTest="suite")