"""More direct synthetic test cases for the eland output file processing
"""
from StringIO import StringIO
-import unittest
+from unittest import TestCase
-from htsworkflow.pipelines.eland import ElandLane, MatchCodes, MappedReads
+from htsworkflow.pipelines.eland import ELAND, ElandLane, ElandMatches, \
+ SampleKey, MatchCodes, MappedReads
-class MatchCodeTests(unittest.TestCase):
+class MatchCodeTests(TestCase):
def test_initializer(self):
self.assertRaises(ValueError, MatchCodes, {'foo':'bar'})
self.assertRaises(ValueError, MatchCodes, 3)
self.assertEqual(mc1['U0'], 100)
-class TestMappedReads(unittest.TestCase):
+class TestMappedReads(TestCase):
def test_initializer(self):
mr1 = MappedReads()
self.assertEqual(len(mr1), 0)
mr3['Lambda3'] = 2
self.assertEqual(mr3['Lambda3'], 2)
-class ElandTests(unittest.TestCase):
+class ElandTests(TestCase):
"""Test specific Eland modules
"""
def compare_match_array(self, current, expected):
self.assertEqual(len(match_reads), 0)
self.assertEqual(reads, 1)
+ def test_ordering(self):
+ e = ELAND()
+ sl3 = SampleKey(lane=3, read=1, sample='33333')
+ sl1 = SampleKey(lane=1, read=1, sample='11111')
+ sl5 = SampleKey(lane=5, read=1, sample='55555')
+ e.results[sl5] = 'Lane5'
+ e.results[sl3] = 'Lane3'
+ e.results[sl1] = 'Lane1'
+
+ e_list = e.values()
+ self.assertEqual(e_list[0], 'Lane1')
+ self.assertEqual(e_list[1], 'Lane3')
+ self.assertEqual(e_list[2], 'Lane5')
+
+class TestElandMatches(TestCase):
+ def test_eland_replacing(self):
+ key = SampleKey(1, 1, 's')
+ e = ELAND()
+ em = ElandMatches(e)
+ em.add('s_1_sequence.txt')
+ self.assertEqual(len(em), 1)
+ self.assertEqual(len(em[key]), 1)
+ filename = iter(em[key]).next().filename
+ self.assertEqual(filename, 's_1_sequence.txt')
+ self.assertEqual(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])
+
+ def test_parts(self):
+ key11111 = SampleKey(1, 1, '11111')
+ key11112 = SampleKey(1, 1, '11112')
+ e = ELAND()
+ em = ElandMatches(e)
+ em.add('11111_CCAATT_L001_R1_001_export.txt.gz')
+ em.add('11111_CCAATT_L001_R1_002_export.txt.gz')
+ em.add('11111_CCAATT_L001_R1_003_export.txt.gz')
+ em.add('11112_AAGGTT_L001_R1_001_export.txt.gz')
+ em.add('11112_AAGGTT_L001_R1_002_export.txt.gz')
+ self.assertEqual(len(em), 2)
+ self.assertEqual(len(em[key11111]), 3)
+ self.assertEqual(len(em[key11112]), 2)
+
+def suite():
+ from unittest import TestSuite, defaultTestLoader
+ suite = TestSuite()
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(MatchCodeTests))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestMappedReads))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(ElandTests))
+ suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestElandMatches))
+ return suite
+
if __name__ == "__main__":
- unittest.main()
+ from unittest import main
+ main(defaultTest="suite")