extra/ucsc_encode_submission/test_ucsc_gather.py

   1 import unittest
   2
   3 import ucsc_gather
   4
   5 class testUCSCGather(unittest.TestCase):
   6     def test_view_attribute_map(self):
   7         view_map = ucsc_gather.NameToViewMap()
   8         view_map.lib_cache["0"] = {
   9             "cell_line": "NLHF",
  10             "replicate": "1",
  11             "lane_set": {},
  12             }
  13
  14         a = view_map.find_attributes("foo.ini", "0")
  15         self.failUnless(a["view"] is None)
  16
  17         a = view_map.find_attributes("asdf.fdsa", "0")
  18         self.failUnless(a is None)
  19
  20         a = view_map.find_attributes("foo.fastq", "0")
  21         self.failUnlessEqual(a["view"], "Fastq", "0")
  22
  23         a = view_map.find_attributes("foo_r1.fastq", "0")
  24         self.failUnlessEqual(a["view"], "FastqRd1", "0")
  25
  26     def test_get_library_info_paired(self):
  27         view_map = ucsc_gather.NameToViewMap()
  28         view_map.lib_cache["11588"] = {
  29             u'antibody_id': None,
  30             u'cell_line': u'NHLF',
  31             u'cell_line_id': 13,
  32             u'experiment_type': u'RNA-seq',
  33             u'experiment_type_id': 4,
  34             u'gel_cut_size': 300,
  35             u'hidden': False,
  36             u'id': u'11588',
  37             u'insert_size': 200,
  38             u'lane_set': [{u'flowcell': u'61PKCAAXX',
  39                            u'lane_number': 8,
  40                            u'paired_end': True,
  41                            u'read_length': 76,
  42                            u'status': u'Unknown',
  43                            u'status_code': None},
  44                           {u'flowcell': u'61PKLAAXX',
  45                            u'lane_number': 8,
  46                            u'paired_end': True,
  47                            u'read_length': 76,
  48                            u'status': u'Unknown',
  49                            u'status_code': None}],
  50             u'library_id': u'11588',
  51             u'library_name': u'Paired ends 254 NHLF 31',
  52             u'library_species': u'Homo sapiens',
  53             u'library_species_id': 8,
  54             u'library_type': u'Paired End',
  55             u'library_type_id': 2,
  56             u'made_by': u'Brian',
  57             u'made_for': u'Brian',
  58             u'notes': u'300 bp gel fragment, SPRI beads cleanup',
  59             u'replicate': 2,
  60             u'stopping_point': u'1Aa',
  61             u'successful_pM': None,
  62             u'undiluted_concentration': u'26.2'}
  63
  64         a = view_map.find_attributes("foo.bam", "11588")
  65         self.failUnlessEqual(a["view"], "Paired")
  66         self.failUnlessEqual(a["insertLength"], 200)
  67
  68
  69 def suite():
  70     return unittest.makeSuite(testUCSCGather,"test")
  71
  72 if __name__ == "__main__":
  73     unittest.main(defaultTest="suite")
  74