Merge branch '262-is-rna-available' into 'develop'

Resolve "`is_rna_available` is set to False if it is not provided in the patient-data"

See merge request tron/addannot!229

.gitlab-ci.yml

@@ -67,4 +67,5 @@ publish_package:
     - python3 setup.py sdist bdist_wheel
     - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python -m twine upload --repository-url https://gitlab.rlp.net/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/*
   only:
+    # deploys in private gitlab package repository only the develop branch, the master branch is published in PyPI
     - develop

docs/source/03_03_usage.md

@@ -15,7 +15,7 @@ neofox --input-file neoantigens_candidates.tsv \
     [--output-prefix out_prefix]  \
     [--organism human|mouse]  \
     [--rank-mhci-threshold 2.0] \
-    [--rank-mhcii-threshold 4.0] \
+    [--rank-mhcii-threshold 5.0] \
     [--num-cpus] \
     [--config] \
     [--patient-id] \

docs/source/05_models.md

@@ -195,7 +195,6 @@ The metadata required for analysis for a given patient + its patient identifier
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
 | identifier | [string](#string) |  | Patient identifier |
-| isRnaAvailable | [bool](#bool) |  | Is RNA expression available? |
 | tumorType | [string](#string) |  | Tumor entity in TCGA study abbrevation style as described here: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations |
 | mhc1 | [Mhc1](#neoantigen.Mhc1) | repeated | MHC I classic molecules |
 | mhc2 | [Mhc2](#neoantigen.Mhc2) | repeated | MHC II classic molecules |

neofox/__init__.py

@@ -18,8 +18,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.#
 
 
-VERSION = "1.0.6"
-
+VERSION = "1.1.0b1"
 
 REFERENCE_FOLDER_ENV = "NEOFOX_REFERENCE_FOLDER"
 NEOFOX_BLASTP_ENV = "NEOFOX_BLASTP"

neofox/command_line.py

@@ -213,16 +213,6 @@ def _read_data(input_file, patients_data, mhc_database: MhcDatabase) -> Tuple[Li
     else:
         raise ValueError('Not supported input file extension: {}'.format(input_file))
 
-    patients_dict : Dict[str, Patient]
-    patients_dict = {p.identifier: p for p in patients}
-
-    for n in neoantigens:
-        patient = patients_dict.get(n.patient_identifier)
-        if not patient.is_rna_available:
-            # removes RNA vaf if indicated in patient that this information is no good
-            # iCam legacy
-            n.rna_variant_allele_frequency = None
-
     return neoantigens, patients
 
 
@@ -386,16 +376,6 @@ def _read_data_epitopes(
     else:
         raise ValueError('Not supported input file extension: {}'.format(input_file))
 
-    patients_dict : Dict[str, Patient]
-    patients_dict = {p.identifier: p for p in patients}
-
-    for n in neoepitopes:
-        patient = patients_dict.get(n.patient_identifier)
-        if patient is not None and not patient.is_rna_available:
-            # removes RNA vaf if indicated in patient that this information is no good
-            # iCam legacy
-            n.rna_variant_allele_frequency = None
-
     return neoepitopes, patients
 
 

neofox/model/conversion.py

@@ -111,7 +111,6 @@ def parse_patients_file(patients_file: str, mhc_database: MhcDatabase) -> List[P
             patient_dict = row.to_dict()
             patient = PatientFactory.build_patient(
                 identifier=patient_dict.get("identifier"),
-                is_rna_available=patient_dict.get("isRnaAvailable", False),
                 tumor_type=patient_dict.get("tumorType"),
                 mhc_alleles=patient_dict.get("mhcIAlleles", []),
                 mhc2_alleles=patient_dict.get("mhcIIAlleles", []),

neofox/model/factories.py

@@ -173,11 +173,10 @@ def build_neoepitope(mutated_peptide=None, wild_type_peptide=None, patient_ident
 
 class PatientFactory(object):
     @staticmethod
-    def build_patient(identifier, is_rna_available=False, tumor_type=None, mhc_alleles: List[str] = [],
+    def build_patient(identifier, tumor_type=None, mhc_alleles: List[str] = [],
                       mhc2_alleles: List[str] = [], mhc_database: MhcDatabase =None):
         patient = Patient(
             identifier=identifier,
-            is_rna_available=is_rna_available,
             tumor_type=tumor_type,
             mhc1=MhcFactory.build_mhc1_alleles(mhc_alleles, mhc_database),
             mhc2=MhcFactory.build_mhc2_alleles(mhc2_alleles, mhc_database)

neofox/model/models.md

@@ -195,7 +195,6 @@ The metadata required for analysis for a given patient + its patient identifier
 | Field | Type | Label | Description |
 | ----- | ---- | ----- | ----------- |
 | identifier | [string](#string) |  | Patient identifier |
-| isRnaAvailable | [bool](#bool) |  | Is RNA expression available? |
 | tumorType | [string](#string) |  | Tumor entity in TCGA study abbrevation style as described here: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations |
 | mhc1 | [Mhc1](#neoantigen.Mhc1) | repeated | MHC I classic molecules |
 | mhc2 | [Mhc2](#neoantigen.Mhc2) | repeated | MHC II classic molecules |

neofox/model/neoantigen.proto

@@ -78,21 +78,17 @@ message Patient {
 	*/
 	string identifier = 1;
 	/**
-	Is RNA expression available?
-	*/
-	bool isRnaAvailable = 2;
-	/**
 	Tumor entity in TCGA study abbrevation style as described here: https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations
 	*/
-	string tumorType = 3;
+	string tumorType = 2;
 	/**
 	MHC I classic molecules
 	*/
-	repeated Mhc1 mhc1 = 4;
+	repeated Mhc1 mhc1 = 3;
 	/**
 	MHC II classic molecules
 	*/
-	repeated Mhc2 mhc2 = 5;
+	repeated Mhc2 mhc2 = 4;
 }
 
 /**

neofox/neofox.py

@@ -110,10 +110,6 @@ def __init__(
         for neoantigen in self.neoantigens:
             expression_per_patient[neoantigen.patient_identifier].append(neoantigen.rna_expression)
 
-        for patient in self.patients:
-            self.patients[patient].is_rna_available = all(e is not None for e in
-                                                          expression_per_patient[self.patients[patient].identifier])
-
         # only performs the expression imputation for humans
         if self.reference_folder.organism == ORGANISM_HOMO_SAPIENS:
             # impute expresssion from TCGA, ONLY if isRNAavailable = False for given patient,
@@ -137,7 +133,7 @@ def _conditional_expression_imputation(self) -> List[Neoantigen]:
             gene_expression = expression_annotator.get_gene_expression_annotation(
                 gene_name=neoantigen.gene, tcga_cohort=patient.tumor_type
             )
-            if not patient.is_rna_available and patient.tumor_type is not None and patient.tumor_type != "":
+            if expression_value is None and patient.tumor_type is not None and patient.tumor_type != "":
                 expression_value = gene_expression
             neoantigen_transformed.rna_expression = expression_value
             neoantigen.imputed_gene_expression = gene_expression

neofox/neofox_epitope.py

@@ -211,8 +211,6 @@ def _conditional_expression_imputation(self) -> List[PredictedEpitope]:
                 neoepitope_transformed = neoepitope
                 gene_expression = expression_annotator.get_gene_expression_annotation(
                     gene_name=neoepitope.gene, tcga_cohort=patient.tumor_type)
-                if not patient.is_rna_available and patient.tumor_type is not None and patient.tumor_type != "":
-                    neoepitope_transformed.rna_expression = gene_expression
                 neoepitope.imputed_gene_expression = gene_expression
                 neoepitopes_transformed.append(neoepitope_transformed)
             else:

neofox/tests/integration_tests/test_neofox.py

@@ -345,8 +345,6 @@ def test_neofox_without_mhc1(self):
 
     def test_gene_expression_imputation(self):
         neoantigens, patients = self._get_test_data()
-        for p in patients:
-            p.is_rna_available = False
         neofox = NeoFox(
             neoantigens=neoantigens,
             patients=patients,

neofox/tests/synthetic_data/factories.py

@@ -78,7 +78,6 @@ def patient(self) -> Patient:
             try:
                 patient = Patient(
                     identifier=self.generator.unique.uuid4(),
-                    is_rna_available=True,
                     tumor_type=self.random_elements(self.available_tumor_types, length=1)[0],
                     # by setting unique=True we enforce that all patients are heterozygous
                     mhc1=MhcFactory.build_mhc1_alleles(

neofox/tests/unit_tests/test_model_converter.py

@@ -193,7 +193,6 @@ def test_patients_csv_file2model(self):
         self.assertEqual(
             9, len([a for m in patients[0].mhc2 for g in m.genes for a in g.alleles])
         )
-        self.assertEqual(patients[0].is_rna_available, False)
 
     def test_patients_without_mhc2(self):
         patients_file = pkg_resources.resource_filename(
@@ -208,7 +207,6 @@ def test_patients_without_mhc2(self):
         self.assertEqual(3, len(patients[0].mhc1))
         self.assertEqual(6, len([a for m in patients[0].mhc1 for a in m.alleles]))
         self.assertEqual(0, len(patients[0].mhc2))
-        self.assertEqual(patients[0].is_rna_available, False)
 
     def test_patients_csv_file2model_mouse(self):
         patients_file = pkg_resources.resource_filename(
@@ -226,7 +224,6 @@ def test_patients_csv_file2model_mouse(self):
         self.assertEqual(
             3, len([a for m in patients[0].mhc2 for g in m.genes for a in g.alleles])
         )
-        self.assertEqual(patients[0].is_rna_available, False)
 
     def test_patients_csv_file2model2(self):
         patients_file = pkg_resources.resource_filename(
@@ -244,7 +241,6 @@ def test_patients_csv_file2model2(self):
         self.assertEqual(
             9, len([a for m in patients[0].mhc2 for g in m.genes for a in g.alleles])
         )
-        self.assertEqual(patients[0].is_rna_available, True)
 
     def test_patients_csv_file2model3(self):
         patients_file = pkg_resources.resource_filename(
@@ -269,7 +265,6 @@ def test_patients_csv_file2model3(self):
             "HLA-DQA1*04:01"
             in [a.name for m in patients[0].mhc2 for g in m.genes for a in g.alleles]
         )
-        self.assertTrue(patients[0].is_rna_available)
 
     def test_patients_csv_file2model_without_mhc1(self):
         patients_file = pkg_resources.resource_filename(
@@ -287,7 +282,6 @@ def test_patients_csv_file2model_without_mhc1(self):
         self.assertEqual(
             9, len([a for m in patients[0].mhc2 for g in m.genes for a in g.alleles])
         )
-        self.assertEqual(patients[0].is_rna_available, True)
 
     def test_patients_csv_file2model_without_mhc2(self):
         patients_file = pkg_resources.resource_filename(

neofox/tests/unit_tests/test_neofox.py

@@ -191,11 +191,12 @@ def test_with_expression_imputation(self):
             reference_folder=FakeReferenceFolder(),
             configuration=FakeDependenciesConfiguration(),
         )
-        for neoantigen in original_neoantigens:
-            for neoantigen_imputed in neofox_runner.neoantigens:
-                self.assertFalse(
-                    neoantigen.rna_expression == neoantigen_imputed.rna_expression
-                )
+        for neoantigen, neoantigen_imputed in zip(original_neoantigens, neofox_runner.neoantigens):
+            self.assertIsNotNone(neoantigen_imputed.imputed_gene_expression)
+            if neoantigen.rna_expression is None:
+                self.assertNotEqual(neoantigen.rna_expression, neoantigen_imputed.rna_expression)
+            else:
+                self.assertEqual(neoantigen.rna_expression, neoantigen_imputed.rna_expression)
 
     def _get_test_neoantigen(self):
         return Neoantigen(
@@ -207,7 +208,7 @@ def _get_test_neoantigen(self):
         )
 
     def _get_test_patient(self):
-        return Patient(identifier="12345", is_rna_available=True)
+        return Patient(identifier="12345")
 
 
 if __name__ == "__main__":

neofox/tests/unit_tests/test_validation.py

@@ -42,12 +42,6 @@ def test_bad_type_raises_exception(self):
             Neoantigen(patient_identifier="1234", rna_expression="0.45"),
         )  # this should be a float)
 
-        self.assertRaises(
-            NeofoxDataValidationException,
-            ModelValidator.validate,
-            Patient(identifier="1234", is_rna_available="Richtig"),
-        )  # this should be a boolean)
-
         # TODO: make validation capture this data types errors!
         ModelValidator.validate(
             Neoantigen(
@@ -63,7 +57,7 @@ def test_good_data_does_not_raise_exceptions(self):
         neoantigen = Neoantigen(patient_identifier="1234", rna_expression=0.45)
         ModelValidator.validate(neoantigen)
 
-        patient = Patient(identifier="1234", is_rna_available=True)
+        patient = Patient(identifier="1234")
         ModelValidator.validate(patient)
 
     def test_enum_with_wrong_value(self):
@@ -695,20 +689,6 @@ def test_empty_patient_identifier(self):
             NeofoxDataValidationException, ModelValidator.validate_patient, patient, ORGANISM_HOMO_SAPIENS
         )
 
-    def test_bad_is_rna_available(self):
-        ModelValidator.validate_patient(
-            Patient(identifier="123", is_rna_available=True), ORGANISM_HOMO_SAPIENS
-        )
-        ModelValidator.validate_patient(
-            Patient(identifier="123", is_rna_available=False), ORGANISM_HOMO_SAPIENS
-        )
-        self.assertRaises(
-            NeofoxDataValidationException,
-            ModelValidator.validate_patient,
-            Patient(identifier="123", is_rna_available="False"),
-            ORGANISM_HOMO_SAPIENS
-        )
-
     def test_validate_neoepitope_mhci(self):
         neoepitope = PredictedEpitope(
             mutated_peptide="DILVTDQTR",