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)
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)
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)
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)
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)
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)
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)
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)
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)
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)