def test_compare_function_on_frameshift_3(self): self.query = 'p.Gln188fs' self.ref = 'p.Gln188Glufs' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_hgvs_1(self): self.hgvs1 = 'c.652delG' self.hgvs2 = 'c.652del' self.check = c.EQUIVALENT check = compare_hgvs(self.hgvs1, self.hgvs2) print 'Check %s..' % (self._testMethodName) self.assertEqual(self.check, check)
def test_compare_function_on_mnv(self): self.query = 'p.Phe334_Val335delinsLeuMet' self.ref = 'p.PheVal334LeuMet' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_synonymous_2(self): self.query = 'p.Pro401Pro=' self.ref = 'p.Pro401Pro' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_ext_3(self): self.query = 'p.Ter330TrpextTer19' self.ref = 'p.Ter330Trp' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_nonsense_7(self): self.query = 'p.Arg168Ter' self.ref = 'p.Arg168*' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_frameshift_9(self): self.query = 'p.Gln64fs*>182' self.ref = 'p.Gln64LysfsTer218' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_frameshift_7(self): self.query = 'p.Arg1921Metfs*' self.ref = 'p.Arg1921MetfsTer9' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_frameshift_4(self): self.query = 'p.Arg1921fs' self.ref = '-' self.check = 'no' message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_function_on_frameshift_2(self): self.query = 'p.Glu78Gly' self.ref = 'p.Glu78Glyfs*7' self.check = 'no' message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.query, self.ref), self.check)
def test_compare_hgvs_8(self): self.hgvs1 = 'p.Ter257Ter' self.hgvs2 = 'p.*257*' self.check = c.EQUIVALENT check = compare_hgvs(self.hgvs1, self.hgvs2) print 'Check %s..' % (self._testMethodName) self.assertEqual(self.check, check)
def test_compare_function_on_ins_7(self): self.query = 'NM_033632.3:c.45_46insCCT' self.ref = 'c.45_46insCCT' self.check = c.EXACT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.ref, self.query), self.check)
def test_compare_hgvs_5(self): self.hgvs1 = 'p.Ala859Ala' self.hgvs2 = 'p.(=)' self.check = c.EQUIVALENT check = compare_hgvs(self.hgvs1, self.hgvs2) print 'Check %s..' % (self._testMethodName) self.assertEqual(self.check, check)
def test_compare_function_on_del_5(self): self.query = 'c.209delCinsCA' self.ref = 'c.210delA' self.check = 'no' message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.ref, self.query), self.check)
def test_compare_function_on_del_6(self): self.query = 'c.3324_3347delTGCAGCTGCAGCTGCAGCCGCAGCTGC' self.ref = 'c.3324_3347delAGCTGCTGCAGCTGCAGCTGCAGC' self.check = 'no' message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.ref, self.query), self.check)
def test_compare_function_on_del_4(self): self.query = 'c.843_846+4delCGAGGTGA' self.ref = 'c.843_846+4del8' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.ref, self.query), self.check)
def test_compare_function_on_del_2(self): self.query = 'c.302+1_302+4delGTGA' self.ref = 'c.302+1_302+4del' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.ref, self.query), self.check)
def test_compare_function_on_del_1(self): self.query = 'c.919_922del' self.ref = 'c.919_922delAG' self.check = c.EQUIVALENT message = '%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(compare_hgvs(self.ref, self.query), self.check)
def check_ref_list(ref_str, hgvs_list): ''' Compares hgvs given a reference hgvs, and list of hgvs string and corresponding transcripts. :param ref_str: reference hgvs string :param hgvs_list: list of hgvs strings e.g. [c.4324A>T, c.4324A>T, c.4324A>T] :return: list of comparison results in order e.g. [yes, yes, yes] ''' r = [] for num in range(0,len(hgvs_list)): query_str = hgvs_list[num] result = compare_hgvs(ref_str, query_str) r.append(result) return '\t'.join(r)
def check_ref_list(ref_str, hgvs_list, transcripts): ''' Compares hgvs given a reference hgvs, and list of hgvs string and corresponding transcripts. :param ref_str: reference hgvs string :param hgvs_list: list of hgvs strings e.g. [c.4324A>T, c.4324A>T, c.4324A>T] :param transcripts: list of transcripts e.g [NM_0000342.1, NM_0000342.1, NM_0000342.1] *order must correspond with the hgvs strings* :return: list of comparison results in order e.g. [yes, yes, yes] ''' r = [] for num in [0, 1, 2]: query_str = hgvs_list[num] transcript = transcripts[num] if transcript == NO_MATCH: # only compare transcripts with exact match result = NO_MATCH else: result = compare_hgvs(ref_str, query_str) r.append(result) return '\t'.join(r)
def check_ref_list(ref_str, hgvs_list, transcripts): ''' Compares hgvs given a reference hgvs, and list of hgvs string and corresponding transcripts. :param ref_str: reference hgvs string :param hgvs_list: list of hgvs strings e.g. [c.4324A>T, c.4324A>T, c.4324A>T] :param transcripts: list of transcripts e.g [NM_0000342.1, NM_0000342.1, NM_0000342.1] *order must correspond with the hgvs strings* :return: list of comparison results in order e.g. [yes, yes, yes] ''' r = [] for num in [0,1,2]: query_str = hgvs_list[num] transcript = transcripts[num] if transcript == NO_MATCH: # only compare transcripts with exact match result = NO_MATCH else: result = compare_hgvs(ref_str, query_str) r.append(result) return '\t'.join(r)