htsworkflow/pipelines/test/test_sequences.py

   1 #!/usr/bin/env python
   2 import os
   3 import unittest
   4
   5 from htsworkflow.pipelines import sequences
   6
   7 class SequenceFileTests(unittest.TestCase):
   8     """
   9     Make sure the sequence archive class works
  10     """
  11     def test_srf(self):
  12         path = '/root/42BW9AAXX/C1-38'
  13         name = 'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_4.srf'
  14         pathname = os.path.join(path,name)
  15         f = sequences.parse_srf(path, name)
  16
  17         self.failUnlessEqual(f.filetype, 'srf')
  18         self.failUnlessEqual(f.path, pathname)
  19         self.failUnlessEqual(f.flowcell, '42BW9AAXX')
  20         self.failUnlessEqual(f.lane, 4)
  21         self.failUnlessEqual(f.read, None)
  22         self.failUnlessEqual(f.pf, None)
  23         self.failUnlessEqual(f.cycle, None)
  24
  25     def test_qseq(self):
  26         path = '/root/42BW9AAXX/C1-36'
  27         name = 'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l4_r1.tar.bz2'
  28         pathname = os.path.join(path,name)
  29         f = sequences.parse_qseq(path, name)
  30
  31         self.failUnlessEqual(f.filetype, 'qseq')
  32         self.failUnlessEqual(f.path, pathname)
  33         self.failUnlessEqual(f.flowcell, '42BW9AAXX')
  34         self.failUnlessEqual(f.lane, 4)
  35         self.failUnlessEqual(f.read, 1)
  36         self.failUnlessEqual(f.pf, None)
  37         self.failUnlessEqual(f.cycle, None)
  38
  39     def test_fastq(self):
  40         path = '/root/42BW9AAXX/C1-38'
  41         name = 'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l4_r1_pass.fastq.bz2'
  42         pathname = os.path.join(path,name)
  43         f = sequences.parse_fastq(path, name)
  44
  45         self.failUnlessEqual(f.filetype, 'fastq')
  46         self.failUnlessEqual(f.path, pathname)
  47         self.failUnlessEqual(f.flowcell, '42BW9AAXX')
  48         self.failUnlessEqual(f.lane, 4)
  49         self.failUnlessEqual(f.read, 1)
  50         self.failUnlessEqual(f.pf, True)
  51         self.failUnlessEqual(f.cycle, None)
  52
  53         name = 'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l4_r2_nopass.fastq.bz2'
  54         pathname = os.path.join(path,name)
  55         f = sequences.parse_fastq(path, name)
  56
  57         self.failUnlessEqual(f.filetype, 'fastq')
  58         self.failUnlessEqual(f.path, pathname)
  59         self.failUnlessEqual(f.flowcell, '42BW9AAXX')
  60         self.failUnlessEqual(f.lane, 4)
  61         self.failUnlessEqual(f.read, 2)
  62         self.failUnlessEqual(f.pf, False)
  63         self.failUnlessEqual(f.cycle, None)
  64
  65     def test_eland(self):
  66         path = '/root/42BW9AAXX/C1-38'
  67         name = 's_4_eland_extended.txt.bz2'
  68         pathname = os.path.join(path,name)
  69         f = sequences.parse_eland(path, name)
  70
  71         self.failUnlessEqual(f.filetype, 'eland')
  72         self.failUnlessEqual(f.path, pathname)
  73         self.failUnlessEqual(f.flowcell, '42BW9AAXX')
  74         self.failUnlessEqual(f.lane, 4)
  75         self.failUnlessEqual(f.read, None)
  76         self.failUnlessEqual(f.pf, None)
  77         self.failUnlessEqual(f.cycle, 'C1-38')
  78
  79         path = '/root/42BW9AAXX/C1-152'
  80         name = 's_4_1_eland_extended.txt.bz2'
  81         pathname = os.path.join(path,name)
  82         f = sequences.parse_eland(path, name)
  83
  84         self.failUnlessEqual(f.filetype, 'eland')
  85         self.failUnlessEqual(f.path, pathname)
  86         self.failUnlessEqual(f.flowcell, '42BW9AAXX')
  87         self.failUnlessEqual(f.lane, 4)
  88         self.failUnlessEqual(f.read, 1)
  89         self.failUnlessEqual(f.pf, None)
  90         self.failUnlessEqual(f.cycle, 'C1-152')
  91
  92     def test_sequence_file_equality(self):
  93         path = '/root/42BW9AAXX/C1-38'
  94         name = 'woldlab_090622_HWI-EAS229_0120_42BW9AAXX_l4_r1.tar.bz2'
  95
  96         f1_qseq = sequences.parse_qseq(path, name)
  97         f2_qseq = sequences.parse_qseq(path, name)
  98
  99         self.failUnlessEqual(f1_qseq, f2_qseq)
 100
 101 def suite():
 102     return unittest.makeSuite(SequenceFileTests,'test')
 103
 104 if __name__ == "__main__":
 105     unittest.main(defaultTest="suite")