def test_delins_6(self): self.query ='c.711_729delTGAGAGCCGGCTGGCGGATinsCCC' self.ref='c.711_729delinsCC' self.check = c.NO_MATCH message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(cHGVS.check_c_hgvs(self.query, self.ref ), self.check)
def compare_hgvs(str1, str2):
'''
Checks whether is coding or protein hgvs from string, calls check_p_hgvs or check_c_hgvs functions
:param str1: hgvs string
:param str2: hgvs string
:return: exact (yes), yes modified or equivalent (yes_m), no match (no)
'''
if is_null(str1) and is_null(str2):
return c.EXACT
if pHGVS.is_protein(str1) or pHGVS.is_protein(str2):
hgvs1 = pHGVS(str1)
hgvs2 = pHGVS(str2)
return pHGVS.check_p_hgvs(hgvs1, hgvs2)
elif cHGVS.is_coding(str1) or cHGVS.is_coding(str2):
hgvs1 = cHGVS(str1)
hgvs2 = cHGVS(str2)
return cHGVS.check_c_hgvs(hgvs1, hgvs2)
elif str1.startswith('g.') and str2.startswith('g.'):
logging.error('Cannot compare g. hgvs %s, %s' % (str1, str2))
else:
logging.error('Unknown input reference:%s,%s' % (str1, str2) )
return c.UNKNOWN
def test_sub_3(self): self.check = c.NO_MATCH self.query='c.222T>C' self.ref='c.222T=' hgvs1=cHGVS(self.query) hgvs2=cHGVS(self.ref) message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(cHGVS.check_c_hgvs(hgvs1, hgvs2 ), self.check)
def test_delins_9(self): ref='c.1077_1090>GCTTTGA' query='c.1077_1093delinsGCTTTGA' check='no' message='%s, %s, %s, %s.' % (self._testMethodName, ref, query, check) var1=cHGVS(query) var2=cHGVS(ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), check)
def test_delins_9(self):
ref = 'c.1077_1090>GCTTTGA'
query = 'c.1077_1093delinsGCTTTGA'
check = 'no'
message = '%s, %s, %s, %s.' % (self._testMethodName, ref, query, check)
var1 = cHGVS(query)
var2 = cHGVS(ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), check)
def test_delins_1(self): self.check = c.EQUIVALENT self.query='c.222_223delTTinsGA' self.ref='c.222_223delinsGA' hgvs1=cHGVS(self.query) hgvs2=cHGVS(self.ref) message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(cHGVS.check_c_hgvs(hgvs1, hgvs2 ), self.check)
def test_delins_6(self):
self.query = 'c.711_729delTGAGAGCCGGCTGGCGGATinsCCC'
self.ref = 'c.711_729delinsCC'
self.check = c.NO_MATCH
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(cHGVS.check_c_hgvs(self.query, self.ref), self.check)
def test_check_delins_3(self): self.query='c.919_922delins' self.ref ='c.919_922delinsAG' self.check = c.NO_MATCH message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_sub_3(self):
self.check = c.NO_MATCH
self.query = 'c.222T>C'
self.ref = 'c.222T='
hgvs1 = cHGVS(self.query)
hgvs2 = cHGVS(self.ref)
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(cHGVS.check_c_hgvs(hgvs1, hgvs2), self.check)
def test_del_6(self): self.query='c.209_210delCA' self.ref ='c.209_210delCG' self.check = c.NO_MATCH message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) var1=cHGVS(self.query) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_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) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_dup_4(self): self.query='c.30_38dup' self.ref='c.30_38dupGCTGCTGCT' self.check = c.EQUIVALENT message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_dup_1(self): self.query='c.424-16_424-14dupTTC' self.ref='c.424-19_424-14dupTTCTTC' self.check = c.NO_MATCH message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_ins_2(self): self.query='c.764_765insAACCTGACAGTTGCAGTTTTCACCCATGGAAAGT' self.ref='c.764_765insAACCTGACAGTTGCAGTTTTCACCCATGGAAAGT' self.check = c.EXACT message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_delins_1(self):
self.check = c.EQUIVALENT
self.query = 'c.222_223delTTinsGA'
self.ref = 'c.222_223delinsGA'
hgvs1 = cHGVS(self.query)
hgvs2 = cHGVS(self.ref)
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(cHGVS.check_c_hgvs(hgvs1, hgvs2), self.check)
def test_ins_3(self): self.query='c.764_765ins33' self.ref='c.764_765ins33' self.check = c.EXACT message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_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) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_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)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_del_6(self):
self.query = 'c.209_210delCA'
self.ref = 'c.209_210delCG'
self.check = c.NO_MATCH
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
var1 = cHGVS(self.query)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_ins_3(self):
self.query = 'c.764_765ins33'
self.ref = 'c.764_765ins33'
self.check = c.EXACT
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_ins_2(self):
self.query = 'c.764_765insAACCTGACAGTTGCAGTTTTCACCCATGGAAAGT'
self.ref = 'c.764_765insAACCTGACAGTTGCAGTTTTCACCCATGGAAAGT'
self.check = c.EXACT
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_dup_4(self):
self.query = 'c.30_38dup'
self.ref = 'c.30_38dupGCTGCTGCT'
self.check = c.EQUIVALENT
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_dup_1(self):
self.query = 'c.424-16_424-14dupTTC'
self.ref = 'c.424-19_424-14dupTTCTTC'
self.check = c.NO_MATCH
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_check_delins_3(self):
self.query = 'c.919_922delins'
self.ref = 'c.919_922delinsAG'
self.check = c.NO_MATCH
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_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)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_check_dup_2(self): """ For when the hgvs positions are not even close """ self.query='c.424-14_424-13insTTC' self.ref ='c.424-16_424-14dupTTC' self.check = c.NO_MATCH message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_check_dup_2(self):
"""
For when the hgvs positions are not even close
"""
self.query = 'c.424-14_424-13insTTC'
self.ref = 'c.424-16_424-14dupTTC'
self.check = c.NO_MATCH
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_dup_3(self): """ check dup equivalencies """ self.query='c.1011dup' self.ref='c.1011dupA' self.check = c.EQUIVALENT message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_check_delins_4(self): """ Test position of coding hgvs when the actual sequence output does not match. """ self.query ='c.919_922delinsAC' self.ref='c.919_922delinsAG' self.check = c.NO_MATCH message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_del_3(self): """ For preferred and non preferred deletion hgvs equivalencies """ 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) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_check_delins_4(self):
"""
Test position of coding hgvs when the actual sequence output does not match.
"""
self.query = 'c.919_922delinsAC'
self.ref = 'c.919_922delinsAG'
self.check = c.NO_MATCH
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_dup_3(self):
"""
check dup equivalencies
"""
self.query = 'c.1011dup'
self.ref = 'c.1011dupA'
self.check = c.EQUIVALENT
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_del_3(self):
"""
For preferred and non preferred deletion hgvs equivalencies
"""
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)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_delins_5(self): """ Test equivalency of separated del and ins syntax vs delins syntax. Preferred hgvs here is describing ins bases only. """ self.query ='c.711_729delTGAGAGCCGGCTGGCGGATinsCC' self.ref='c.711_729delinsCC' self.check = c.EQUIVALENT message='%s, %s, %s, %s.' % (self._testMethodName, self.query, self.ref, self.check) var1=cHGVS(self.query) var2=cHGVS(self.ref) self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
def test_delins_5(self):
"""
Test equivalency of separated del and ins syntax vs delins syntax.
Preferred hgvs here is describing ins bases only.
"""
self.query = 'c.711_729delTGAGAGCCGGCTGGCGGATinsCC'
self.ref = 'c.711_729delinsCC'
self.check = c.EQUIVALENT
message = '%s, %s, %s, %s.' % (self._testMethodName, self.query,
self.ref, self.check)
var1 = cHGVS(self.query)
var2 = cHGVS(self.ref)
self.assertEqual(cHGVS.check_c_hgvs(var1, var2), self.check)
