htsworkflow/util/test/test_makebed.py

   1 import os
   2 from StringIO import StringIO
   3 import unittest
   4
   5 from htsworkflow.util import makebed
   6
   7 class testMakeBed(unittest.TestCase):
   8     def test_multi_1_0_0_limit_1(self):
   9       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:112:383    TCAAATCTTATGCTANGAATCNCAAATTTTCT 1:0:0   mm9_chr13_random.fa:1240R0')
  10       out = StringIO()
  11
  12       makebed.parse_multi_eland(instream, out, 'mm9_chr', 1)
  13       self.failUnlessEqual(out.getvalue(), 'mm9_chr13_random 1240 1272 read 0 - - - 255,255,0\n')
  14
  15     def test_multi_1_0_0_limit_255(self):
  16       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:112:383    TCAAATCTTATGCTANGAATCNCAAATTTTCT 1:0:0   mm9_chr13_random.fa:1240R0')
  17       out = StringIO()
  18
  19       makebed.parse_multi_eland(instream, out, 'mm9_chr', 255)
  20       self.failUnlessEqual(out.getvalue(), 'mm9_chr13_random 1240 1272 read 0 - - - 255,255,0\n')
  21
  22
  23     def test_multi_2_0_0_limit_1(self):
  24       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:104:586    GTTCTCGCATAAACTNACTCTNAATAGATTCA 2:0:0   mm9_chr4.fa:42995432F0,mm9_chrX.fa:101541458F0')
  25       out = StringIO()
  26
  27       makebed.parse_multi_eland(instream, out, 'mm9_chr', 1)
  28       self.failUnlessEqual(out.len, 0)
  29
  30     def test_multi_2_0_0_limit_255(self):
  31       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:104:586    GTTCTCGCATAAACTNACTCTNAATAGATTCA 2:0:0   mm9_chr4.fa:42995432F0,mm9_chrX.fa:101541458F0')
  32       out = StringIO()
  33
  34       makebed.parse_multi_eland(instream, out, 'mm9_chr', 255)
  35       self.failUnlessEqual(out.len, 98)
  36
  37     def test_multi_0_2_0_limit_1(self):
  38       instream = StringIO('>HWI-EAS229_26_209LVAAXX:7:3:115:495    TCTCCCTGAAAAATANAAGTGNTGTTGGTGAG        0:2:1   mm9_chr14.fa:104434729F2,mm9_chr16.fa:63263818R1,mm9_chr2.fa:52265438R1')
  39       out = StringIO()
  40
  41       makebed.parse_multi_eland(instream, out, 'mm9_chr', 1)
  42       print out.getvalue()
  43       self.failUnlessEqual(out.len, 0)
  44
  45 def suite():
  46     return unittest.makeSuite(testMakeBed, 'test')
  47
  48 if __name__ == "__main__":
  49     unittest.main(defaultTest='suite')
  50
  51