Python cHGVS Examples

Example #1

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 #2

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #3

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #4

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #5

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

 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)

Example #6

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

 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)

Example #7

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

 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)

Example #8

File: test_chgvs.py Project: personalis/hgvslib

	def test_c_del_dup_4(self):
		self.check = c.NO_MATCH
		self.query='c.919_922delins'
		self.ref='c.919_922delinsAG'

		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_del_dup(hgvs1, hgvs2 ), self.check)

Example #9

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #10

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #11

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #12

File: test_chgvs.py Project: personalis/hgvslib

	def test_check_c_del_dup_3(self):
		self.check = c.EQUIVALENT
		self.query='c.222_223dup'
		self.ref='c.222_223dupTT'

		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_del_dup(hgvs1, hgvs2 ), self.check)

Example #13

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #14

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #15

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #16

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #17

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #18

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

    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)

Example #19

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

    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)

Example #20

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

    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)

Example #21

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

 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)

Example #22

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

    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)

Example #23

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

    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)

Example #24

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

    def test_check_c_del_dup_3(self):
        self.check = c.EQUIVALENT
        self.query = 'c.222_223dup'
        self.ref = 'c.222_223dupTT'

        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_del_dup(hgvs1, hgvs2), self.check)

Example #25

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

    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)

Example #26

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

    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)

Example #27

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

    def test_c_del_dup_4(self):
        self.check = c.NO_MATCH
        self.query = 'c.919_922delins'
        self.ref = 'c.919_922delinsAG'

        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_del_dup(hgvs1, hgvs2), self.check)

Example #28

File: test_chgvs.py Project: personalis/hgvslib

	def test_class_instance_function(self):
		hgvs1=cHGVS(self.query)
		hgvs2=cHGVS(self.query)

		self.assertEqual(hgvs1.name, hgvs2.name)
		self.assertEqual(hgvs1.transcript, hgvs2.transcript)
		self.assertEqual(hgvs1.bases, hgvs2.bases)
		self.assertEqual(hgvs1.alias, hgvs2.alias)
		#self.assertEqual(hgvs1.intronic, hgvs2.intronic)

		self.assertEqual(hgvs1.intronic, hgvs2.intronic)

Example #29

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

    def test_class_instance_function_with_transcipt(self):
        query = 'NM(GENE):c.22delC'

        hgvs1 = cHGVS(query)
        hgvs2 = cHGVS(query)

        self.assertEqual(hgvs1.name, hgvs2.name)
        self.assertEqual(hgvs1.transcript, hgvs2.transcript)
        self.assertEqual(hgvs1.bases, hgvs2.bases)
        self.assertEqual(hgvs1.alias, hgvs2.alias)
        self.assertEqual(hgvs1.intronic, hgvs2.intronic)

Example #30

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

    def test_class_instance_function(self):
        hgvs1 = cHGVS(self.query)
        hgvs2 = cHGVS(self.query)

        self.assertEqual(hgvs1.name, hgvs2.name)
        self.assertEqual(hgvs1.transcript, hgvs2.transcript)
        self.assertEqual(hgvs1.bases, hgvs2.bases)
        self.assertEqual(hgvs1.alias, hgvs2.alias)
        #self.assertEqual(hgvs1.intronic, hgvs2.intronic)

        self.assertEqual(hgvs1.intronic, hgvs2.intronic)

Example #31

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #32

File: test_chgvs.py Project: personalis/hgvslib

	def test_class_instance_function_with_transcipt(self):
		query ='NM(GENE):c.22delC'

		hgvs1=cHGVS(query)
		hgvs2=cHGVS(query)

		self.assertEqual(hgvs1.name, hgvs2.name)
		self.assertEqual(hgvs1.transcript, hgvs2.transcript)
		self.assertEqual(hgvs1.bases, hgvs2.bases)
		self.assertEqual(hgvs1.alias, hgvs2.alias)
		self.assertEqual(hgvs1.intronic, hgvs2.intronic)

Example #33

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

    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)

Example #34

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #35

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #36

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #37

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

    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)

Example #38

File: test_chgvs.py Project: personalis/hgvslib

	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)

Example #39

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

    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)

Example #40

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

    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)

Example #41

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

    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)

Example #42

	def __init__(self, chgvs_str, phgvs_str, id, transcript='', effect='', ghgvs=''):

		# parse the chgvs string with the cHGVS object
		self.chgvs_obj  = cHGVS(chgvs_str)
		self.chgvs      = self.chgvs_obj.name
		self.type       = self.chgvs_obj.type

		self.phgvs_obj  = pHGVS(phgvs_str)
		self.phgvs      = self.phgvs_obj.name
		self.ghgvs      = ghgvs

		self.id         = id
		self.effect     = effect
		self.alt        = ''
		self.ref        = ''
		self.chr        = ''
		self.start      = ''
		self.stop       = ''
		self.location   = ''
		self.gen_alt    = ''

		self.gene       = ''

		self.transcript = transcript

		# get transcript from cHGVS object if the transcript field is null
		if not is_null(self.chgvs_obj.transcript) and is_null(transcript):
			self.transcript = self.chgvs_obj.transcript

		self.protein    = ''
		self.version    = Transcript(self.transcript).version

		self.check      = ''
		self.refalt     = ''

Example #43

File: test_chgvs.py Project: personalis/hgvslib

	def test_cHGVS_parse_hgvs_string(self):
		hgvs_str='NM_017547.3(FOXRED1):c.694C>T'
		var=cHGVS(hgvs_str)
		transcript='NM_017547.3'
		chgvs='c.694C>T'
		print 'Check %s..' % (self._testMethodName)
		self.assertEqual((chgvs, transcript), (var.name, var.transcript))

Example #44

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

 def test_cHGVS_parse_hgvs_string(self):
     hgvs_str = 'NM_017547.3(FOXRED1):c.694C>T'
     var = cHGVS(hgvs_str)
     transcript = 'NM_017547.3'
     chgvs = 'c.694C>T'
     print 'Check %s..' % (self._testMethodName)
     self.assertEqual((chgvs, transcript), (var.name, var.transcript))

Example #45

File: test_chgvs.py Project: personalis/hgvslib

	def test_get_cHGVS_type_6(self):
		self.query='NM_000240.3:c.-1241_-1212ACCGGCACCGGCACCAGTACCCGCACCAGT(3_5)'
		self.check='del'
		hgvs=cHGVS(self.query)
		message='%s, %s, %s' % (self._testMethodName, self.query, self.check)
		self.assertEqual(hgvs.type, (self.check), msg=message)

Example #46

File: test_chgvs.py Project: personalis/hgvslib

	def test_get_cHGVS_type_5(self):
		self.query='NM_000602.4:c.-820_-817G(4_5)'
		self.check='del'
		hgvs=cHGVS(self.query)
		message='%s, %s, %s' % (self._testMethodName, self.query, self.check)
		self.assertEqual(hgvs.type, (self.check), msg=message)

Example #47

File: test_chgvs.py Project: personalis/hgvslib

	def test_get_cHGVS_type_4(self):
		self.query='c.23insCC'
		self.check='ins'
		hgvs=cHGVS(self.query)
		message='%s, %s, %s' % (self._testMethodName, self.query, self.check)
		self.assertEqual(hgvs.type, (self.check), msg=message)

Example #48

File: test_chgvs.py Project: personalis/hgvslib

	def test_get_cHGVS_type_2(self):
		self.check='delins' #### self.check='delins'
		self.query='c.22_23delTTinsCC'
		hgvs=cHGVS(self.query)
		message='%s, %s, %s' % (self._testMethodName, self.query, self.check)
		self.assertEqual(hgvs.type, (self.check), msg=message)

Example #49

File: test_chgvs.py Project: personalis/hgvslib

	def test_get_cHGVS_type_1(self):
		hgvs=cHGVS(self.query)
		message='%s, %s, %s' % (self._testMethodName, self.query, self.check)
		self.assertEqual(hgvs.type, (self.check), msg=message)

Example #50

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

 def test_get_cHGVS_type_1(self):
     hgvs = cHGVS(self.query)
     message = '%s, %s, %s' % (self._testMethodName, self.query, self.check)
     self.assertEqual(hgvs.type, (self.check), msg=message)

Example #51

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

 def test_get_cHGVS_type_6(self):
     self.query = 'NM_000240.3:c.-1241_-1212ACCGGCACCGGCACCAGTACCCGCACCAGT(3_5)'
     self.check = 'del'
     hgvs = cHGVS(self.query)
     message = '%s, %s, %s' % (self._testMethodName, self.query, self.check)
     self.assertEqual(hgvs.type, (self.check), msg=message)

Example #52

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

 def test_get_cHGVS_type_2(self):
     self.check = 'delins'  #### self.check='delins'
     self.query = 'c.22_23delTTinsCC'
     hgvs = cHGVS(self.query)
     message = '%s, %s, %s' % (self._testMethodName, self.query, self.check)
     self.assertEqual(hgvs.type, (self.check), msg=message)

Example #53

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

 def test_get_cHGVS_type_4(self):
     self.query = 'c.23insCC'
     self.check = 'ins'
     hgvs = cHGVS(self.query)
     message = '%s, %s, %s' % (self._testMethodName, self.query, self.check)
     self.assertEqual(hgvs.type, (self.check), msg=message)

Example #54

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

 def test_get_cHGVS_type_5(self):
     self.query = 'NM_000602.4:c.-820_-817G(4_5)'
     self.check = 'del'
     hgvs = cHGVS(self.query)
     message = '%s, %s, %s' % (self._testMethodName, self.query, self.check)
     self.assertEqual(hgvs.type, (self.check), msg=message)