def test_check_ext_1(self): self.query = 'p.*463Arg' self.ref="p.Ter463Argext*?" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_check_ext_2(self): self.query = 'p.Ter1313Tyr' self.ref="p.Ter1313TyrextTer66" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_check_null_1(self): self.query = None self.ref="p.?" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_check_null_2(self): self.query ="-" self.ref="" self.check="yes" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_missense_p2(self): self.query ="p.Pro559Ser" self.ref="p.Pro559Ser" self.check="yes" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_protein_delins_1(self):
self.query = "p.Glu22_Val23delinsLys"
self.ref = "p.Glu22_Val23delGluValinsLys"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_check_null_3(self):
self.query = ""
self.ref = "p.Gly23Gly"
self.check = "no"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_del_3(self): self.query ="p.Cys28_Met30delArgLys" self.ref="p.Cys28_Met30del" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_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_protein_delins_1(self):
self.query = "p.Gln256>ArgGlu"
self.ref = "p.Gln256delinsArgGlu"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_start_lost(self):
self.query = 'p.Met1?'
self.ref = "p.Met1Ile"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_protein_delins_1(self):
self.query = "p.GluValThrTrp33359ValLysGluLys"
self.ref = "p.Glu33359_Trp33362delinsValLysGluLys"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_check_null_2(self):
self.query = "-"
self.ref = ""
self.check = "yes"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_check_null_1(self):
self.query = None
self.ref = "p.?"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_check_ext_2(self):
self.query = 'p.Ter1313Tyr'
self.ref = "p.Ter1313TyrextTer66"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_check_ext_1(self):
self.query = 'p.*463Arg'
self.ref = "p.Ter463Argext*?"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_missense_p2(self):
self.query = "p.Pro559Ser"
self.ref = "p.Pro559Ser"
self.check = "yes"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_del_3(self):
self.query = "p.Cys28_Met30delArgLys"
self.ref = "p.Cys28_Met30del"
self.check = "yes_m"
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_nonsense_1(self): self.query ="p.Tyr567Ter" self.ref="p.Tyr567*" self.check="yes_m" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2 ), self.check)
def test_frameshift_4(self): self.query ="p.Arg1921fs" self.ref="-" self.check="no" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_frameshift_2(self): self.query ="p.Glu78Gly" self.ref="p.Glu78Glyfs*7" self.check="no" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_dup_p2(self): self.query ="p.Gly54_Arg55dupArgArg" self.ref="p.Gly54_Arg55dup" self.check="p.Gly54_Arg55dup" self.hgvs = pHGVS(self.query) self.ref = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.ref, self.hgvs.alias), 'yes_m')
def test_frameshift_5(self): self.query ="p.Thr655Asnfs" self.ref="p.Thr655Asnfs*49" self.check="yes_m" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_dup_1(self): self.query ="p.Pro559dup" self.ref="p.Pro559dup" self.check="yes" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2 ), self.check)
def test_nonsense_2(self): self.query ="p.Gln136Profs*13" self.ref="p.Gln136Ter13" self.check="no" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_synonymous_9(self): self.query ="p.Ter257=" self.ref="p.(=)" self.check="yes_m" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2 ), self.check)
def test_ins_2(self): self.query ="p.Lys2_Met3insGlnSerLysArg" self.ref="p.Lys2_Met3ins4" self.check="yes_m" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) #self.assertEqual(pHGVS.check_insertion(hgvs1, hgvs2 ), self.check) self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2 ), self.check)
def test_synonymous_8(self): self.query ="p.Pro559Glu" self.ref="p.(=)" self.check="no" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2 ), self.check)
def test_nonsense_2(self):
self.query = "p.Gln136Profs*13"
self.ref = "p.Gln136Ter13"
self.check = "no"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_frameshift_5(self):
self.query = "p.Thr655Asnfs"
self.ref = "p.Thr655Asnfs*49"
self.check = "yes_m"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_frameshift_4(self):
self.query = "p.Arg1921fs"
self.ref = "-"
self.check = "no"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_nonsense_1(self):
self.query = "p.Tyr567Ter"
self.ref = "p.Tyr567*"
self.check = "yes_m"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_frameshift_2(self):
self.query = "p.Glu78Gly"
self.ref = "p.Glu78Glyfs*7"
self.check = "no"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref), self.check)
def test_synonymous_8(self):
self.query = "p.Pro559Glu"
self.ref = "p.(=)"
self.check = "no"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_synonymous_9(self):
self.query = "p.Ter257="
self.ref = "p.(=)"
self.check = "yes_m"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_dup_1(self):
self.query = "p.Pro559dup"
self.ref = "p.Pro559dup"
self.check = "yes"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_frameshift_1(self): self.query = "p.Glu78fs" self.ref= "p.Glu78Glyfs*7" self.refcheck = "p.Glu78fs*" self.new_ref = "p.Glu78Glyfs" self.check="yes_m" hgvs1 = pHGVS(self.query) hgvs2 = pHGVS(self.ref) message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_ins_2(self):
self.query = "p.Lys2_Met3insGlnSerLysArg"
self.ref = "p.Lys2_Met3ins4"
self.check = "yes_m"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
#self.assertEqual(pHGVS.check_insertion(hgvs1, hgvs2 ), self.check)
self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_dup_p2(self):
self.query = "p.Gly54_Arg55dupArgArg"
self.ref = "p.Gly54_Arg55dup"
self.check = "p.Gly54_Arg55dup"
self.hgvs = pHGVS(self.query)
self.ref = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(self.ref, self.hgvs.alias),
'yes_m')
def test_frameshift_1(self):
self.query = "p.Glu78fs"
self.ref = "p.Glu78Glyfs*7"
self.refcheck = "p.Glu78fs*"
self.new_ref = "p.Glu78Glyfs"
self.check = "yes_m"
hgvs1 = pHGVS(self.query)
hgvs2 = pHGVS(self.ref)
message = "%s, %s, %s, %s." % (self._testMethodName, self.query,
self.ref, self.check)
self.assertEqual(pHGVS.check_p_hgvs(hgvs1, hgvs2), self.check)
def test_protein_delins_1(self): self.query ="p.Gln256>ArgGlu" self.ref="p.Gln256delinsArgGlu" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_protein_delins_1(self): self.query ="p.GluValThrTrp33359ValLysGluLys" self.ref="p.Glu33359_Trp33362delinsValLysGluLys" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_protein_delins_1(self): self.query ="p.Glu22_Val23delinsLys" self.ref="p.Glu22_Val23delGluValinsLys" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_start_lost(self): self.query = 'p.Met1?' self.ref="p.Met1Ile" self.check="yes_m" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
def test_check_null_3(self): self.query ="" self.ref="p.Gly23Gly" self.check="no" message = "%s, %s, %s, %s." % (self._testMethodName, self.query, self.ref, self.check) self.assertEqual(pHGVS.check_p_hgvs(self.query, self.ref ), self.check)
