pheval-exomiser 0.2.4__py3-none-any.whl → 0.2.6__py3-none-any.whl

pheval_exomiser/post_process/post_process_results_format.py

@@ -182,7 +182,12 @@ class PhEvalDiseaseResultFromExomiserJsonCreator:
                     )
             except KeyError:
                 pass
-        return simplified_exomiser_result
+        return list(
+            {
+                (result.disease_identifier, result.score): result
+                for result in simplified_exomiser_result
+            }.values()
+        )
 
 
 def create_standardised_results(

pheval_exomiser/prepare/tool_specific_configuration_options.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import List
+from typing import List, Optional
 
 from pydantic import BaseModel, Field
 
@@ -20,17 +20,17 @@ class ApplicationProperties(BaseModel):
         cache_caffeine_spec (int): Cache limit
     """
 
-    remm_version: str = Field(None)
-    cadd_version: str = Field(None)
-    hg19_data_version: str = Field(None)
-    hg19_local_frequency_path: Path = Field(None)
-    hg19_whitelist_path: Path = Field(None)
-    hg38_data_version: str = Field(None)
-    hg38_local_frequency_path: Path = Field(None)
-    hg38_whitelist_path: Path = Field(None)
-    phenotype_data_version: str = Field(None)
-    cache_type: str = Field(None)
-    cache_caffeine_spec: int = Field(None)
+    remm_version: Optional[str] = Field(None)
+    cadd_version: Optional[str] = Field(None)
+    hg19_data_version: Optional[str] = Field(None)
+    hg19_local_frequency_path: Optional[Path] = Field(None)
+    hg19_whitelist_path: Optional[Path] = Field(None)
+    hg38_data_version: Optional[str] = Field(None)
+    hg38_local_frequency_path: Optional[Path] = Field(None)
+    hg38_whitelist_path: Optional[Path] = Field(None)
+    phenotype_data_version: Optional[str] = Field(None)
+    cache_type: Optional[str] = Field(None)
+    cache_caffeine_spec: Optional[int] = Field(None)
 
 
 class PostProcessing(BaseModel):
@@ -64,5 +64,5 @@ class ExomiserConfigurations(BaseModel):
     analysis_configuration_file: Path = Field(...)
     max_jobs: int = Field(...)
     application_properties: ApplicationProperties = Field(...)
-    output_formats: List[str] = Field(None)
+    output_formats: Optional[List[str]] = Field(None)
     post_process: PostProcessing = Field(...)

{pheval_exomiser-0.2.4.dist-info → pheval_exomiser-0.2.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pheval_exomiser
-Version: 0.2.4
+Version: 0.2.6
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk
@@ -10,6 +10,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: click (>=8.1.3,<9.0.0)
 Requires-Dist: docker (>=6.0.1,<7.0.0)
 Requires-Dist: google (>=3.0.0,<4.0.0)

{pheval_exomiser-0.2.4.dist-info → pheval_exomiser-0.2.6.dist-info}/RECORD

@@ -3,16 +3,16 @@ pheval_exomiser/cli.py,sha256=0SR1-L2sREEkFRfUPwYwkbSaBsz_L_Sxq1S4c9LQLJg,350
 pheval_exomiser/constants.py,sha256=o_pLWF8kX74BqyTsAZa7twwSKzedLnpupCI90k_bMqY,517
 pheval_exomiser/post_process/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval_exomiser/post_process/post_process.py,sha256=ZLIGPeADGZn08jFc152QraiJnYSADlL35GOwxkCQDwA,901
-pheval_exomiser/post_process/post_process_results_format.py,sha256=WVtCQv5uiFk-6xL6zKsB0VWR2L52kCji_1fsXLitX3o,12112
+pheval_exomiser/post_process/post_process_results_format.py,sha256=F1TpgLgeoNFFZTk7XaXLptCLOr6G3tdZC2cltXFtHx8,12261
 pheval_exomiser/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval_exomiser/prepare/create_batch_commands.py,sha256=tDUBtpfSmNGqHte-vrGnusYZzM59pOX1IAumqRDlnBE,17205
-pheval_exomiser/prepare/tool_specific_configuration_options.py,sha256=Fd7Jfr6QwHhL1JK69D8FMwaAXe3cnG4IrBrB9JyEKlg,2792
+pheval_exomiser/prepare/tool_specific_configuration_options.py,sha256=4gedZ9iadRXK6tF9P-ju-dhj8-F2-fhrXVhfYIsAxFQ,2922
 pheval_exomiser/prepare/write_application_properties.py,sha256=KmG7GvkQo8AhnhRyqohTFvqjfhEhbcs78UYYoigxJ3w,8933
 pheval_exomiser/prepare/yaml_to_family_phenopacket.py,sha256=Hz77dHpVaRMV1fQWKmOCqCKJfmk_hdpZh_6o7hq9Sec,14452
 pheval_exomiser/run/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval_exomiser/run/run.py,sha256=bK_gL52zRl71Lxe-i-P6L4-dMstxFAG6SVNPO6G823o,7109
 pheval_exomiser/runner.py,sha256=LaWhC0F9LoPvP0Ie1sG2GkC8EG-tWjBBY_tFYmx6dxA,2548
-pheval_exomiser-0.2.4.dist-info/METADATA,sha256=BAfOlCbgucdlTto6PvpqYUZKqxb6alQfFKm0DxGEwUA,7475
-pheval_exomiser-0.2.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pheval_exomiser-0.2.4.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
-pheval_exomiser-0.2.4.dist-info/RECORD,,
+pheval_exomiser-0.2.6.dist-info/METADATA,sha256=sGthFcX63xsOR0YPiC-cWC4jowGaMm0pT81NHOCrpAo,7526
+pheval_exomiser-0.2.6.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+pheval_exomiser-0.2.6.dist-info/entry_points.txt,sha256=lbZMu-x7ns8UrFveWSqEQ1UB5l33TbRMomqBUyGYIwI,131
+pheval_exomiser-0.2.6.dist-info/RECORD,,

{pheval_exomiser-0.2.4.dist-info → pheval_exomiser-0.2.6.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.9.0
+Generator: poetry-core 1.9.1
 Root-Is-Purelib: true
 Tag: py3-none-any