Python check_p_hgvs Examples

Example #1

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #2

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #3

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #4

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #5

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #6

File: test_phgvs.py Project: slu-gh/hgvslib

 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)

Example #7

File: test_phgvs.py Project: slu-gh/hgvslib

 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)

Example #8

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #9

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

Example #10

File: test_phgvs.py Project: slu-gh/hgvslib

 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)

Example #11

File: test_phgvs.py Project: slu-gh/hgvslib

 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)

Example #12

File: test_phgvs.py Project: slu-gh/hgvslib

 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)

Example #13

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #14

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #15

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #16

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #17

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #18

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #19

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #20

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #21

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #22

File: test_phgvs.py Project: personalis/hgvslib

	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')

Example #23

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #24

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #25

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #26

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #27

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #28

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #29

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #30

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #31

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #32

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #33

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #34

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #35

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #36

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #37

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #38

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #39

File: test_phgvs.py Project: slu-gh/hgvslib

    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')

Example #40

File: test_phgvs.py Project: slu-gh/hgvslib

    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)

Example #41

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #42

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #43

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #44

File: test_phgvs.py Project: personalis/hgvslib

	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)

Example #45

File: test_phgvs.py Project: personalis/hgvslib

	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)