htsworkflow/submission/test/test_fastqname.py

   1 from unittest2 import TestCase
   2 from htsworkflow.submission.fastqname import FastqName
   3
   4 class TestFastqName(TestCase):
   5     def test_init_empty(self):
   6         fq = FastqName()
   7         self.assertEqual(fq.is_valid, False)
   8
   9     def test_init_single_filename(self):
  10         fq = FastqName(filename="12345_AABBCCDDXX_c100_l1.fastq")
  11         self.assertEqual(fq.lib_id, "12345")
  12         self.assertEqual(fq['lib_id'], "12345")
  13         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  14         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  15         self.assertEqual(fq.cycle, "100")
  16         self.assertEqual(fq['cycle'], "100")
  17         self.assertEqual(fq.lane, "1")
  18         self.assertEqual(fq['lane'], "1")
  19         self.assertEqual(fq.is_paired, False)
  20
  21     def test_init_single_filename(self):
  22         fq = FastqName(filename="12345_AABBCCDDXX_c100_l1_r2.fastq")
  23         self.assertEqual(fq.lib_id, "12345")
  24         self.assertEqual(fq['lib_id'], "12345")
  25         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  26         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  27         self.assertEqual(fq.cycle, "100")
  28         self.assertEqual(fq['cycle'], "100")
  29         self.assertEqual(fq.lane, "1")
  30         self.assertEqual(fq['lane'], "1")
  31         self.assertEqual(fq.read, "2")
  32         self.assertEqual(fq['read'], "2")
  33         self.assertEqual(fq.is_paired, True)
  34
  35     def test_init_bad_filename(self):
  36         attribs = {'filename': 'asdf.bam'}
  37         self.assertRaises(ValueError, FastqName, **attribs)
  38
  39     def test_init_single_attributes(self):
  40         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  41                        cycle = "100", lane="1")
  42         self.assertEqual(fq.is_valid, True)
  43         self.assertEqual(fq.lib_id, "12345")
  44         self.assertEqual(fq['lib_id'], "12345")
  45         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  46         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  47         self.assertEqual(fq.cycle, "100")
  48         self.assertEqual(fq['cycle'], "100")
  49         self.assertEqual(fq.lane, "1")
  50         self.assertEqual(fq['lane'], "1")
  51         self.assertEqual(fq.is_paired, False)
  52         self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1.fastq")
  53
  54     def test_init_single_attributes_set_single(self):
  55         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  56                        cycle = "100", lane="1", is_paired=False)
  57         self.assertEqual(fq.is_valid, True)
  58         self.assertEqual(fq.is_paired, False)
  59
  60     def test_init_single_attributes_set_paired(self):
  61         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  62                        cycle = "100", lane="1", is_paired=True)
  63         self.assertEqual(fq.is_valid, False)
  64         self.assertEqual(fq.is_paired, True)
  65
  66     def test_init_paired_attributes(self):
  67         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  68                        cycle = "100", lane="1", read="2")
  69         self.assertEqual(fq.is_valid, True)
  70         self.assertEqual(fq.lib_id, "12345")
  71         self.assertEqual(fq['lib_id'], "12345")
  72         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  73         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  74         self.assertEqual(fq.cycle, "100")
  75         self.assertEqual(fq['cycle'], "100")
  76         self.assertEqual(fq.lane, "1")
  77         self.assertEqual(fq['lane'], "1")
  78         self.assertEqual(fq.read, "2")
  79         self.assertEqual(fq['read'], "2")
  80         self.assertEqual(fq.is_paired, True)
  81         self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1_r2.fastq")
  82
  83     def test_init_paired_attributes_set_single(self):
  84         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  85                        cycle = "100", lane="1", read="2", is_paired=False)
  86         self.assertEqual(fq.is_valid, True)
  87         self.assertEqual(fq.is_paired, False)
  88
  89     def test_init_paired_attributes_set_paired(self):
  90         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  91                        cycle = "100", lane="1", read="2", is_paired=True)
  92         self.assertEqual(fq.is_valid, True)
  93         self.assertEqual(fq.is_paired, True)
  94
  95     def test_init_insufficient_attributes(self):
  96         attribs = dict(lib_id="12345", flowcell="AABBCCDDXX")
  97         fq = FastqName(**attribs)
  98         self.assertEqual(fq.is_valid, False)
  99
 100
 101 def suite():
 102     from unittest2 import TestSuite, defaultTestLoader
 103     suite = TestSuite()
 104     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
 105     return suite
 106
 107 if __name__ == "__main__":
 108     from unittest2 import main
 109     main(defaultTest='suite')