htsworkflow/util/test/test_validate.py

   1 import os
   2 from StringIO import StringIO
   3 import unittest
   4
   5 from htsworkflow.util import validate
   6
   7 class TestValidate(unittest.TestCase):
   8     def test_fastq_works(self):
   9         q = StringIO(u"> abc\nAGCT\n@\nBBBB\n")
  10         errors = validate.validate_fastq(q)
  11         self.failUnlessEqual(0, errors)
  12
  13     def test_fastq_diff_length_uniform(self):
  14         q = StringIO(u"> abc\nAGCT\n@\nBBBB\n> abcd\nAGCTT\n@\nJJJJJ\n")
  15         errors = validate.validate_fastq(q, True)
  16         self.failUnlessEqual(2, errors)
  17
  18     def test_fastq_diff_length_variable(self):
  19         q = StringIO(u"> abc\nAGCT\n@\n@@@@\n> abcd\nAGCTT\n@\nJJJJJ\n")
  20         errors = validate.validate_fastq(q, False)
  21         self.failUnlessEqual(0, errors)
  22
  23     def test_fastq_qual_short(self):
  24         q = StringIO(u"> abc\nAGCT\n@\nSS\n")
  25         errors = validate.validate_fastq(q)
  26         self.failUnlessEqual(1, errors)
  27
  28     def test_fastq_seq_invalid_char(self):
  29         q = StringIO(u"> abc\nAGC\u1310\n@\nPQRS\n")
  30         errors = validate.validate_fastq(q)
  31         self.failUnlessEqual(1, errors)
  32
  33     def test_fastq_qual_invalid_char(self):
  34         q = StringIO(u"> abc\nAGC.\n@\n!@#J\n")
  35         errors = validate.validate_fastq(q)
  36         self.failUnlessEqual(1, errors)
  37
  38 def suite():
  39     return unittest.makeSuite(testValidate, 'test')
  40
  41 if __name__ == "__main__":
  42     unittest.main(defaultTest='suite')
  43
  44