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         self.assertEqual(fq.compression_extension, '')
  21
  22     def test_init_single_filename_gz(self):
  23         fq = FastqName(filename="12345_AABBCCDDXX_c100_l1.fastq.gz")
  24         self.assertEqual(fq.lib_id, "12345")
  25         self.assertEqual(fq['lib_id'], "12345")
  26         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  27         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  28         self.assertEqual(fq.cycle, "100")
  29         self.assertEqual(fq['cycle'], "100")
  30         self.assertEqual(fq.lane, "1")
  31         self.assertEqual(fq['lane'], "1")
  32         self.assertEqual(fq.is_paired, False)
  33         self.assertEqual(fq.compression_extension, '.gz')
  34
  35     def test_init_single_filename(self):
  36         fq = FastqName(filename="12345_AABBCCDDXX_c100_l1_r2.fastq")
  37         self.assertEqual(fq.lib_id, "12345")
  38         self.assertEqual(fq['lib_id'], "12345")
  39         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  40         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  41         self.assertEqual(fq.cycle, "100")
  42         self.assertEqual(fq['cycle'], "100")
  43         self.assertEqual(fq.lane, "1")
  44         self.assertEqual(fq['lane'], "1")
  45         self.assertEqual(fq.read, "2")
  46         self.assertEqual(fq['read'], "2")
  47         self.assertEqual(fq.is_paired, True)
  48         self.assertEqual(fq.compression_extension, None)
  49
  50     def test_init_bad_filename(self):
  51         attribs = {'filename': 'asdf.bam'}
  52         self.assertRaises(ValueError, FastqName, **attribs)
  53
  54     def test_init_single_attributes(self):
  55         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  56                        cycle = "100", lane="1")
  57         self.assertEqual(fq.is_valid, True)
  58         self.assertEqual(fq.lib_id, "12345")
  59         self.assertEqual(fq['lib_id'], "12345")
  60         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  61         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  62         self.assertEqual(fq.cycle, "100")
  63         self.assertEqual(fq['cycle'], "100")
  64         self.assertEqual(fq.lane, "1")
  65         self.assertEqual(fq['lane'], "1")
  66         self.assertEqual(fq.is_paired, False)
  67         self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1.fastq")
  68         self.assertEqual(fq.compression_extension, None)
  69
  70     def test_init_single_attributes_set_single(self):
  71         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  72                        cycle = "100", lane="1", is_paired=False)
  73         self.assertEqual(fq.is_valid, True)
  74         self.assertEqual(fq.is_paired, False)
  75
  76     def test_init_single_attributes_set_paired(self):
  77         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  78                        cycle = "100", lane="1", is_paired=True)
  79         self.assertEqual(fq.is_valid, False)
  80         self.assertEqual(fq.is_paired, True)
  81
  82     def test_init_single_attributes_set_paired_bzip2(self):
  83         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  84                        cycle = "100", lane="1", is_paired=True,
  85                        compression_extension='.bzip2')
  86         self.assertEqual(fq.is_valid, False)
  87         self.assertEqual(fq.is_paired, True)
  88         self.assertEqual(fq.compression_extension, '.bzip2')
  89
  90     def test_init_paired_attributes(self):
  91         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
  92                        cycle = "100", lane="1", read="2")
  93         self.assertEqual(fq.is_valid, True)
  94         self.assertEqual(fq.lib_id, "12345")
  95         self.assertEqual(fq['lib_id'], "12345")
  96         self.assertEqual(fq.flowcell, "AABBCCDDXX")
  97         self.assertEqual(fq['flowcell'], "AABBCCDDXX")
  98         self.assertEqual(fq.cycle, "100")
  99         self.assertEqual(fq['cycle'], "100")
 100         self.assertEqual(fq.lane, "1")
 101         self.assertEqual(fq['lane'], "1")
 102         self.assertEqual(fq.read, "2")
 103         self.assertEqual(fq['read'], "2")
 104         self.assertEqual(fq.is_paired, True)
 105         self.assertEqual(fq.filename, "12345_AABBCCDDXX_c100_l1_r2.fastq")
 106
 107     def test_init_paired_attributes_set_single(self):
 108         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
 109                        cycle = "100", lane="1", read="2", is_paired=False)
 110         self.assertEqual(fq.is_valid, True)
 111         self.assertEqual(fq.is_paired, False)
 112
 113     def test_init_paired_attributes_set_paired(self):
 114         fq = FastqName(lib_id="12345", flowcell="AABBCCDDXX",
 115                        cycle = "100", lane="1", read="2", is_paired=True)
 116         self.assertEqual(fq.is_valid, True)
 117         self.assertEqual(fq.is_paired, True)
 118
 119     def test_init_insufficient_attributes(self):
 120         attribs = dict(lib_id="12345", flowcell="AABBCCDDXX")
 121         fq = FastqName(**attribs)
 122         self.assertEqual(fq.is_valid, False)
 123
 124
 125 def suite():
 126     from unittest2 import TestSuite, defaultTestLoader
 127     suite = TestSuite()
 128     suite.addTests(defaultTestLoader.loadTestsFromTestCase(TestFastqName))
 129     return suite
 130
 131 if __name__ == "__main__":
 132     from unittest2 import main
 133     main(defaultTest='suite')