예제 #1
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    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'
        }))
예제 #2
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 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)
예제 #3
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 def setUp(self):
     self.run = munge_path('/home/genetics/data/130321_HA00211_OncoPlex64')
     self.outdir = self.mkoutdir()
예제 #4
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 def setUp(self):
     self.run=munge_path('/home/genetics/data/2013-03-21_HiSeq_OncoPlex_Run14_v2')
     self.outdir = self.mkoutdir()