pheval-exomiser 0.3.0__tar.gz → 0.3.2__tar.gz

{pheval_exomiser-0.3.0 → pheval_exomiser-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pheval_exomiser
-Version: 0.3.0
+Version: 0.3.2
 Summary: 
 Author: Yasemin Bridges
 Author-email: y.bridges@qmul.ac.uk
@@ -162,6 +162,9 @@ e.g.,
    └── vcf
 ```
 
+> [!IMPORTANT]  
+> If a `vcf` directory is not found in the testdata directory then the path to the VCF will be taken from the phenopacket if `variant_analysis` is set to True.
+
 ## Run command
 
 Once the testdata and input directories are correctly configured for the run, the `pheval run` command can be executed.

{pheval_exomiser-0.3.0 → pheval_exomiser-0.3.2}/README.md

@@ -139,6 +139,9 @@ e.g.,
    └── vcf
 ```
 
+> [!IMPORTANT]  
+> If a `vcf` directory is not found in the testdata directory then the path to the VCF will be taken from the phenopacket if `variant_analysis` is set to True.
+
 ## Run command
 
 Once the testdata and input directories are correctly configured for the run, the `pheval run` command can be executed.

{pheval_exomiser-0.3.0 → pheval_exomiser-0.3.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pheval_exomiser"
-version = "0.3.0"
+version = "0.3.2"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
     "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",

{pheval_exomiser-0.3.0 → pheval_exomiser-0.3.2}/src/pheval_exomiser/post_process/post_process_results_format.py

@@ -136,7 +136,7 @@ def create_standardised_results(
 ):
     sort_order = SortOrder.ASCENDING if sort_order.lower() == "ascending" else SortOrder.DESCENDING
     for exomiser_json_result_path in files_with_suffix(result_dir, ".json"):
-        exomiser_json_result = pl.read_json(exomiser_json_result_path)
+        exomiser_json_result = pl.read_json(exomiser_json_result_path, infer_schema_length=None)
         if gene_analysis:
             gene_results = extract_gene_results_from_json(exomiser_json_result, score_name)
             generate_gene_result(

{pheval_exomiser-0.3.0 → pheval_exomiser-0.3.2}/src/pheval_exomiser/prepare/create_batch_commands.py

@@ -100,8 +100,14 @@ class CommandCreator:
             )
 
     def add_variant_analysis_arguments(self, vcf_dir: Path) -> ExomiserCommandLineArguments:
-        vcf_file_data = PhenopacketUtil(self.phenopacket).vcf_file_data(
-            self.phenopacket_path, vcf_dir
+        vcf_file_data = (
+            PhenopacketUtil(self.phenopacket).vcf_file_data(self.phenopacket_path, vcf_dir)
+            if vcf_dir.exists()
+            else [
+                file
+                for file in self.phenopacket.files
+                if file.file_attributes["fileFormat"] == "vcf"
+            ][0]
         )
         output_options_file = self.assign_output_options_file()
         if self.environment == "local":