Python MutationInfo.fuzzy_hgvs_corrector示例

示例#1

文件： test.py 项目： zzygyx9119/MutationInfo

    def test_FYZZY_HGVS_CORRECTOR(self):
        print '------FUZZY HGVS CORRECTOR---------'
        ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C')
        print ret
        self.assertEqual(ret, None)

        ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1')
        print ret
        self.assertEqual(ret, None)

        try: 
            MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1', ref_type='p')
        except Exception as e:
            self.assertEqual(str(e), 'Available values for ref_type: None, "c" and "g" . Found: p')

        ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1', ref_type='c')
        print ret
        self.assertEqual(ret, 'NM_001042351.1:c.1048G>C')

        ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A', transcript='NM_001042351.1', ref_type='c')
        print ret
        self.assertEqual(ret, ['NM_001042351.1:c.1387C>T', 'NM_001042351.1:c.1387C>A'])

        ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A')
        print ret
        self.assertEqual(ret, None)

        ret = MutationInfo.fuzzy_hgvs_corrector('-1923(A>C)', transcript='NT_005120.15', ref_type='g')
        print ret
        self.assertEqual(ret, 'NT_005120.15:g.-1923A>C')

        ret = MutationInfo.fuzzy_hgvs_corrector('NT_005120.15:c.1160(CC>GT)')
        print ret
        self.assertEqual(ret, 'NT_005120.15:c.1160_1161delinsGT')

示例#2

文件： test.py 项目： kantale/MutationInfo

    def test_FYZZY_HGVS_CORRECTOR(self):
        print '------FUZZY HGVS CORRECTOR---------'
        ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C')
        print ret
        self.assertEqual(ret, None)

        ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1')
        print ret
        self.assertEqual(ret, None)

        try: 
            MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1', ref_type='p')
        except Exception as e:
            self.assertEqual(str(e), 'Available values for ref_type: None, "c" and "g" . Found: p')

        ret = MutationInfo.fuzzy_hgvs_corrector('1048G->C', transcript='NM_001042351.1', ref_type='c')
        print ret
        self.assertEqual(ret, 'NM_001042351.1:c.1048G>C')

        ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A', transcript='NM_001042351.1', ref_type='c')
        print ret
        self.assertEqual(ret, ['NM_001042351.1:c.1387C>T', 'NM_001042351.1:c.1387C>A'])

        ret = MutationInfo.fuzzy_hgvs_corrector('1387C->T/A')
        print ret
        self.assertEqual(ret, None)

        ret = MutationInfo.fuzzy_hgvs_corrector('-1923(A>C)', transcript='NT_005120.15', ref_type='g')
        print ret
        self.assertEqual(ret, 'NT_005120.15:g.-1923A>C')

        ret = MutationInfo.fuzzy_hgvs_corrector('NT_005120.15:c.1160(CC>GT)')
        print ret
        self.assertEqual(ret, 'NT_005120.15:c.1160_1161delinsGT')