Python AlasccaClassRule Examples

Example #1

File: test_rules.py Project: ClinSeq/reportgen

 def test_apply_pik3ca_class_a_test2(self):
     input_symbol2gene = {"PIK3CA": self._pik3ca_gene_missense_a_and_b}
     rule = AlasccaClassRule("reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx", input_symbol2gene)
     test_report = rule.apply()
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME: AlasccaClassReport.MUTN_CLASS_A}
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #2

File: test_rules.py Project: ClinSeq/reportgen

 def test_apply_single_pik3r1_missense(self):
     input_symbol2gene = {"PIK3R1": self._pik3r1_gene_missense}
     rule = AlasccaClassRule("reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx", input_symbol2gene)
     test_report = rule.apply()
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME: AlasccaClassReport.MUTN_CLASS_B}
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #3

File: test_rules.py Project: ClinSeq/reportgen

 def test_apply_double_pten(self):
     input_symbol2gene = {"PTEN": self._pten_gene_double_mutation}
     rule = AlasccaClassRule("reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx", input_symbol2gene)
     test_report = rule.apply()
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME: AlasccaClassReport.MUTN_CLASS_B}
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #4

File: test_rules.py Project: ClinSeq/reportgen

 def test_apply_single_pik3r1_frameshift_off(self):
     input_symbol2gene = {"PIK3R1": self._pik3r1_gene_frameshift_off}
     rule = AlasccaClassRule("reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx", input_symbol2gene)
     test_report = rule.apply()
     # ALASCCA class definitions changed => This is now Class B.
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME: AlasccaClassReport.MUTN_CLASS_B}
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #5

File: test_rules.py Project: ClinSeq/reportgen

 def test_apply_single_pten_not_enough(self):
     input_symbol2gene = {"PTEN": self._pten_gene_single_mutation_not_enough}
     rule = AlasccaClassRule("reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx", input_symbol2gene)
     test_report = rule.apply()
     # ALASCCA class definitions changed => This is now Class B.
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME: AlasccaClassReport.MUTN_CLASS_B}
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #6

 def test_apply_pik3ca_class_a_test2(self):
     input_symbol2gene = {"PIK3CA": self._pik3ca_gene_missense_a_and_b}
     rule = AlasccaClassRule(
         "reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx",
         input_symbol2gene)
     test_report = rule.apply()
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME:
         AlasccaClassReport.MUTN_CLASS_A
     }
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #7

 def test_apply_single_pik3r1_missense(self):
     input_symbol2gene = {"PIK3R1": self._pik3r1_gene_missense}
     rule = AlasccaClassRule(
         "reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx",
         input_symbol2gene)
     test_report = rule.apply()
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME:
         AlasccaClassReport.MUTN_CLASS_B
     }
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #8

 def test_apply_double_pten(self):
     input_symbol2gene = {"PTEN": self._pten_gene_double_mutation}
     rule = AlasccaClassRule(
         "reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx",
         input_symbol2gene)
     test_report = rule.apply()
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME:
         AlasccaClassReport.MUTN_CLASS_B
     }
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #9

 def test_apply_single_pik3r1_frameshift_off(self):
     input_symbol2gene = {"PIK3R1": self._pik3r1_gene_frameshift_off}
     rule = AlasccaClassRule(
         "reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx",
         input_symbol2gene)
     test_report = rule.apply()
     # ALASCCA class definitions changed => This is now Class B.
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME:
         AlasccaClassReport.MUTN_CLASS_B
     }
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)

Example #10

 def test_apply_single_pten_not_enough(self):
     input_symbol2gene = {
         "PTEN": self._pten_gene_single_mutation_not_enough
     }
     rule = AlasccaClassRule(
         "reportgen/assets/ALASCCA_MUTATION_TABLE_SPECIFIC.xlsx",
         input_symbol2gene)
     test_report = rule.apply()
     # ALASCCA class definitions changed => This is now Class B.
     expected_output_dict = {
         AlasccaClassReport.ALASCCA_CLASS_FEATURENAME:
         AlasccaClassReport.MUTN_CLASS_B
     }
     self.assertDictEqual(test_report.to_dict(), expected_output_dict)