#!/usr/bin/env python
"""More direct synthetic test cases for the eland output file processing
"""
-from StringIO import StringIO
-from unittest2 import TestCase
+from io import StringIO
+from unittest import TestCase
from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
SampleKey, MatchCodes, MappedReads
'U0':0, 'U1':0, 'U2':0,
'R0':0, 'R1':0, 'R2':0,
}
- self.assertEqual(mc.keys(), match_codes.keys())
- self.assertEqual(mc.items(), match_codes.items())
- self.assertEqual(mc.values(), match_codes.values())
+ self.assertEqual(list(mc.keys()), list(match_codes.keys()))
+ self.assertEqual(list(mc.items()), list(match_codes.items()))
+ self.assertEqual(list(mc.values()), list(match_codes.values()))
self.assertRaises(KeyError, mc.__getitem__, 'foo')
def test_addition(self):
mr1['chr9'] = 7
self.assertEqual(list(mr1.keys()), ['chr9'])
self.assertEqual(mr1['chr9'], 7)
- self.assertEqual(mr1.items(), [('chr9', 7)])
+ self.assertEqual(list(mr1.items()), [('chr9', 7)])
del mr1['chr9']
self.assertEqual(len(mr1), 0)
"""Test specific Eland modules
"""
def compare_match_array(self, current, expected):
- for key in expected.keys():
+ for key in list(expected.keys()):
self.assertEqual(current[key], expected[key],
"Key %s: %s != %s" % (key,current[key],expected[key]))
e.results[sl3] = 'Lane3'
e.results[sl1] = 'Lane1'
- e_list = e.values()
+ e_list = list(e.values())
self.assertEqual(e_list[0], 'Lane1')
self.assertEqual(e_list[1], 'Lane3')
self.assertEqual(e_list[2], 'Lane5')
self.assertEqual(len(em[key]), 1)
filename = iter(em[key]).next().filename
self.assertEqual(filename, 's_1_sequence.txt')
- self.assertEqual(em.keys(), [key])
+ self.assertEqual(list(em.keys()), [key])
em.add('s_1_eland_result.txt')
self.assertEqual(len(em), 1)
self.assertEqual(len(em[key]), 1)
filename = iter(em[key]).next().filename
self.assertEqual(filename, 's_1_eland_result.txt')
- self.assertEqual(em.keys(), [key])
+ self.assertEqual(list(em.keys()), [key])
def test_parts(self):
key11111 = SampleKey(1, 1, '11111')
self.assertEqual(len(em[key11112]), 2)
def suite():
- from unittest2 import TestSuite, defaultTestLoader
+ from unittest import TestSuite, defaultTestLoader
suite = TestSuite()
suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests))
suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads))
if __name__ == "__main__":
- from unittest2 import main
+ from unittest import main
main(defaultTest="suite")