htsworkflow/util/test/test_ucsc.py

   1 """Test wrappers around ucsc file formats
   2 """
   3 import os
   4 from unittest2 import TestCase
   5 from htsworkflow.util.test import TEST_DATA_DIR
   6 from htsworkflow.util.ucsc import bigWigInfo
   7
   8 from distutils.spawn import find_executable
   9
  10 class TestUCSC(TestCase):
  11     def test_bigwig_info(self):
  12         if not find_executable('bigWigInfo'):
  13             self.skipTest('Need bigWigInfo on path to test')
  14
  15         filename = os.path.join(TEST_DATA_DIR, 'foo.bigWig')
  16         info = bigWigInfo(filename)
  17         self.assertEqual(info.version, 4)
  18         self.assertEqual(info.isCompressed, True)
  19         # what should i do for byteswapped arch?
  20         self.assertEqual(info.isSwapped, False)
  21         self.assertEqual(info.primaryDataSize, 48)
  22         self.assertEqual(info.primaryIndexSize, 6204)
  23         self.assertEqual(info.zoomLevels, 2)
  24         self.assertEqual(info.basesCovered, 30)
  25         self.assertAlmostEqual(info.mean, 0.0)
  26         self.assertAlmostEqual(info.min, -5.5)
  27         self.assertAlmostEqual(info.max, 5.5)
  28         self.assertAlmostEqual(info.std, 4.567501)
  29