import os
from StringIO import StringIO
import sys
-import unittest
+from unittest2 import TestCase
_module_path, _module_name = os.path.split(__file__)
sys.path.append(os.path.join(_module_path, '..', 'scripts'))
+from htsworkflow.pipelines.test.simulate_runfolder import TESTDATA_DIR
+
from htsworkflow.pipelines import srf2fastq
-class testSrf2Fastq(unittest.TestCase):
+class testSrf2Fastq(TestCase):
def test_split_good(self):
source = StringIO("""@header
AGCTTTTT
def test_is_srf(self):
cnf4_srf = 'woldlab_070829_USI-EAS44_0017_FC11055_1.srf'
- cnf4_path = os.path.join(_module_path, cnf4_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(_module_path, cnf1_srf)
+ cnf1_path = os.path.join(TESTDATA_DIR, cnf1_srf)
is_srf = srf2fastq.is_srf
self.failUnlessEqual(is_srf(__file__), False)
def test_is_cnf1(self):
cnf4_srf = 'woldlab_070829_USI-EAS44_0017_FC11055_1.srf'
- cnf4_path = os.path.join(_module_path, cnf4_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(_module_path, cnf1_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 unittest2 import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(testSrf2Fastq))
+ return suite
+
if __name__ == "__main__":
- unittest.main(defaultTest="suite")
+ from unittest2 import main
+ main(defaultTest="suite")