htsworkflow/util/test/test_validate.py

   1 import os
   2 from StringIO import StringIO
   3 from unittest import TestCase
   4
   5 from htsworkflow.util import validate
   6
   7 class TestValidate(TestCase):
   8     def test_phred33_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_phred64_works(self):
  14         q = StringIO(u"@ abc\nAGCT\n+\nfgh]\n")
  15         errors = validate.validate_fastq(q, 'phred64')
  16         self.failUnlessEqual(0, errors)
  17
  18     def test_fasta_fails(self):
  19         q = StringIO(u">abc\nAGCT\n>foo\nCGAT\n")
  20         errors = validate.validate_fastq(q)
  21         self.failUnlessEqual(3, errors)
  22
  23     def test_fastq_diff_length_uniform(self):
  24         q = StringIO(u"@ abc\nAGCT\n+\nBBBB\n@ abcd\nAGCTT\n+\nJJJJJ\n")
  25         errors = validate.validate_fastq(q, 'phred33', True)
  26         self.failUnlessEqual(2, errors)
  27
  28     def test_fastq_diff_length_variable(self):
  29         q = StringIO(u"@ abc\nAGCT\n+\n@@@@\n@ abcd\nAGCTT\n+\nJJJJJ\n")
  30         errors = validate.validate_fastq(q, 'phred33', False)
  31         self.failUnlessEqual(0, errors)
  32
  33     def test_fastq_qual_short(self):
  34         q = StringIO(u"@ abc\nAGCT\n+\nJJ\n")
  35         errors = validate.validate_fastq(q)
  36         self.failUnlessEqual(1, errors)
  37
  38     def test_fastq_seq_invalid_char(self):
  39         q = StringIO(u"@ abc\nAGC\u1310\n+\nEFGH\n")
  40         errors = validate.validate_fastq(q)
  41         self.failUnlessEqual(1, errors)
  42
  43     def test_fastq_qual_invalid_char(self):
  44         q = StringIO(u"+ abc\nAGC.\n+\n!@#J\n")
  45         errors = validate.validate_fastq(q)
  46         self.failUnlessEqual(1, errors)
  47
  48
  49 def suite():
  50     from unittest import TestSuite, defaultTestLoader
  51     suite = TestSuite()
  52     suite.addTests(defaultTestLoader.loadTestsFromTestCase(testValidate))
  53     return suite
  54
  55
  56 if __name__ == "__main__":
  57     from unittest import main
  58     main(defaultTest="suite")