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)
