pheval 0.4.0__tar.gz → 0.4.2__tar.gz

{pheval-0.4.0 → pheval-0.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pheval
-Version: 0.4.0
+Version: 0.4.2
 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: class-resolver (>=0.4.2)
 Requires-Dist: click (>=8.1.3)
 Requires-Dist: deprecation (>=2.1.0)

{pheval-0.4.0 → pheval-0.4.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pheval"
-version = "0.4.0"
+version = "0.4.2"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>",
   "Julius Jacobsen <j.jacobsen@qmul.ac.uk>",

{pheval-0.4.0 → pheval-0.4.2}/src/pheval/analyse/generate_summary_outputs.py

@@ -39,7 +39,7 @@ def create_comparison_table(
         table_name (str): Name of the table to extract ranks from
     """
     connector.drop_table(comparison_table_name)
-    excluded_columns = (", ".join(drop_columns), "identifier") if drop_columns else ("identifier",)
+    excluded_columns = tuple(drop_columns + ["identifier"]) if drop_columns else ("identifier",)
     connector.conn.execute(
         f'CREATE TABLE "{comparison_table_name}" AS SELECT * '
         f"EXCLUDE {excluded_columns} FROM {table_name}"

{pheval-0.4.0 → pheval-0.4.2}/src/pheval/prepare/prepare_corpus.py

@@ -57,6 +57,11 @@ def prepare_corpus(
                     f"Removed {phenopacket_path.name} from the corpus due to missing variant fields."
                 )
                 continue
+            elif phenopacket_util.check_variant_alleles():
+                info_log.warning(
+                    f"Removed {phenopacket_path.name} from the corpus due to identical "
+                    "reference and alternate allele fields."
+                )
         if gene_analysis:
             if phenopacket_util.check_incomplete_gene_record():
                 info_log.warning(

{pheval-0.4.0 → pheval-0.4.2}/src/pheval/utils/phenopacket_utils.py

@@ -503,6 +503,19 @@ class PhenopacketUtil:
                 return True
         return False
 
+    def check_variant_alleles(self) -> bool:
+        """
+        Check if any variant record in the phenopacket has identical reference and alternate alleles.
+
+        Returns:
+            bool: True if the reference and alternate alleles are identical, False otherwise.
+        """
+        variants = self.diagnosed_variants()
+        for variant in variants:
+            if variant.ref == variant.alt:
+                return True
+        return False
+
     def check_incomplete_gene_record(self) -> bool:
         """
         Check if any gene record in the phenopacket has incomplete information.