def testMungePath(self):
test_id1 = munge_path('140915_HA000_ColoTestFiles')
test_id2 = munge_path('testfiles/140915_MA0001_OncoPlexKapa')
test_id3 = munge_path('testfiles/160727_MB0745_GEN005-GLTv1')
test_id4 = munge_path('testfiles/160820_MD0020_HP66-HHv1')
test_id5 = munge_path('testfiles/160209_MA0829_GEN06-STHv1')
self.assertEqual(test_id1, ({
'date': '2014-09-15',
'run': 'HA000',
'machine': 'hiseq',
'assay': 'coloseq',
'project': 'colotestfiles',
'prep_type': 'sure_select'
}))
self.assertEqual(test_id2, ({
'date': '2014-09-15',
'run': 'MA0001',
'machine': 'miseq',
'assay': 'oncoplex',
'prep_type': 'kapa',
'project': 'oncoplexkapa'
}))
self.assertEqual(test_id3, ({
'date': '2016-07-27',
'run': 'MB0745',
'machine': 'miseq',
'assay': 'hotspot-hereditary',
'prep_type': 'truseq',
'project': 'gen005-gltv1'
}))
self.assertEqual(test_id4, ({
'date': '2016-08-20',
'run': 'MD0020',
'machine': 'miseq',
'assay': 'hotspot-heme',
'prep_type': 'truseq',
'project': 'hp66-hhv1'
}))
self.assertEqual(test_id5, ({
'date': '2016-02-09',
'run': 'MA0829',
'machine': 'miseq',
'assay': 'hotspot-heme',
'prep_type': 'truseq',
'project': 'gen06-sthv1'
}))
def testMungeWrongPath(self):
"""
Test that a ValueError is raised if wrong path is given
"""
run=munge_path('/home/genetics/data/Broca_v6')
self.assertRaises(ValueError)
def setUp(self):
self.run = munge_path('/home/genetics/data/130321_HA00211_OncoPlex64')
self.outdir = self.mkoutdir()
def setUp(self):
self.run=munge_path('/home/genetics/data/2013-03-21_HiSeq_OncoPlex_Run14_v2')
self.outdir = self.mkoutdir()