5 class testUCSCGather(unittest.TestCase):
6 def test_view_attribute_map(self):
7 view_map = ucsc_gather.NameToViewMap()
8 view_map.lib_cache["0"] = {
14 a = view_map.find_attributes("foo.ini", "0")
15 self.failUnless(a["view"] is None)
17 a = view_map.find_attributes("asdf.fdsa", "0")
18 self.failUnless(a is None)
20 a = view_map.find_attributes("foo.fastq", "0")
21 self.failUnlessEqual(a["view"], "Fastq", "0")
23 a = view_map.find_attributes("foo_r1.fastq", "0")
24 self.failUnlessEqual(a["view"], "FastqRd1", "0")
26 def test_get_library_info_paired(self):
27 view_map = ucsc_gather.NameToViewMap()
28 view_map.lib_cache["11588"] = {
30 u'cell_line': u'NHLF',
32 u'experiment_type': u'RNA-seq',
33 u'experiment_type_id': 4,
38 u'lane_set': [{u'flowcell': u'61PKCAAXX',
42 u'status': u'Unknown',
43 u'status_code': None},
44 {u'flowcell': u'61PKLAAXX',
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,
57 u'made_for': u'Brian',
58 u'notes': u'300 bp gel fragment, SPRI beads cleanup',
60 u'stopping_point': u'1Aa',
61 u'successful_pM': None,
62 u'undiluted_concentration': u'26.2'}
64 a = view_map.find_attributes("foo.bam", "11588")
65 self.failUnlessEqual(a["view"], "Paired")
66 self.failUnlessEqual(a["insertLength"], 200)
70 return unittest.makeSuite(testUCSCGather,"test")
72 if __name__ == "__main__":
73 unittest.main(defaultTest="suite")