pheval 0.4.0__py3-none-any.whl → 0.4.2__py3-none-any.whl

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/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/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.

{pheval-0.4.0.dist-info → pheval-0.4.2.dist-info}/METADATA

@@ -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.dist-info → pheval-0.4.2.dist-info}/RECORD

@@ -9,7 +9,7 @@ pheval/analyse/binary_classification_stats.py,sha256=E35YjvGM-zFnuEt8M3pgN03vBab
 pheval/analyse/disease_prioritisation_analysis.py,sha256=1Ut4u6p9mDGbGBoXrVxTuUgv_nrqxzBhq5N9jbGWRWs,5725
 pheval/analyse/gene_prioritisation_analysis.py,sha256=_7r16BC0S2H9rOY016mLLUg6PcxaCQOh5FQcNKFTy-4,5582
 pheval/analyse/generate_plots.py,sha256=rMSdgawGYYc7BAAolqz73TAnanKtrxCC48bI6WQq6xc,21455
-pheval/analyse/generate_summary_outputs.py,sha256=9v9w7le_wLxyjgUgxl6f0RXb2Qt-B3XrKdlmfT6DSjo,4160
+pheval/analyse/generate_summary_outputs.py,sha256=nKqwbpA-9bbL5mCySiuyV_AUDIokmCg3vD8_JAsg1ls,4157
 pheval/analyse/parse_benchmark_summary.py,sha256=vyAOIdIWF4rZjGTPFE69ajhEC9AkkN3QBVqSe_uYZsg,2946
 pheval/analyse/parse_corpus.py,sha256=N88enptR4qG6cmqXU_TKg8DMmCeFog37eeK5nFEMQOQ,8678
 pheval/analyse/prioritisation_result_types.py,sha256=qJoB6O-lFYmzAMcTQeDJZQNLJ6hleoKDYATTkhvFF98,1228
@@ -29,7 +29,7 @@ pheval/prepare/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pheval/prepare/create_noisy_phenopackets.py,sha256=ydhA4mpqKTDc4hBu8YfvNW2nMubHK3dbO-cv0lA4JFQ,11504
 pheval/prepare/create_spiked_vcf.py,sha256=90A-Mi8QKhvN036vtFEVWAHgzHO37itiLYrqYlG4LiA,23953
 pheval/prepare/custom_exceptions.py,sha256=_G3_95dPtHIs1SviYBV1j7cYc-hxlhuw8hhnYdzByYY,1719
-pheval/prepare/prepare_corpus.py,sha256=eRvozzezIgAqHAumtqul0WfXfBO1iOBaSlN8fPSn0Nw,4223
+pheval/prepare/prepare_corpus.py,sha256=mwI3FJJ6GGSbmbvz4enrVP86MBoHSssMIRebkapmu5Y,4484
 pheval/prepare/update_phenopacket.py,sha256=21fzUPbwKN6Ey5TSh9PFzjT2x86U19RAE6WmkjG8u28,4770
 pheval/resources/alternate_ouputs/CADA_results.txt,sha256=Rinn2TtfwFNsx0aEWegKJOkjKnBm-Mf54gdaT3bWP0k,547
 pheval/resources/alternate_ouputs/DeepPVP_results.txt,sha256=MF9MZJYa4r4PEvFzALpi-lNGLxjENOnq_YgrgFMn-oQ,1508
@@ -47,11 +47,11 @@ pheval/utils/docs_gen.py,sha256=6FGtHicBC0rZKi0tdL3Epsg8d4osE44I9f1Ga0j4JLA,3193
 pheval/utils/docs_gen.sh,sha256=LyKLKjaZuf4UJ962CWfM-XqkxtvM8O2N9wHZS5mcb9A,477
 pheval/utils/exomiser.py,sha256=m2u0PH2z9lFPaB3LVkZCmPmH5e55q1NoTzNl46zRRP8,683
 pheval/utils/file_utils.py,sha256=m21cz-qjDYqnI8ClUv3J9fKizex98a-9bSEerQ75i_c,3576
-pheval/utils/phenopacket_utils.py,sha256=W9T_X48EJ-xn5GghzbZlt-lI-DxWoSm7_SHr8DCJg2Q,26856
+pheval/utils/phenopacket_utils.py,sha256=6xQ8WCLdR1VhiU3nCDzaqEVKjGvDWrzvPA50_6ZAHXM,27310
 pheval/utils/semsim_utils.py,sha256=s7ZCR2VfPYnOh7ApX6rv66eGoVSm9QJaVYOWBEhlXpo,6151
 pheval/utils/utils.py,sha256=9V6vCT8l1g4O2-ZATYqsVyd7AYZdWGd-Ksy7_oIC3eE,2343
-pheval-0.4.0.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-pheval-0.4.0.dist-info/METADATA,sha256=JXpNQPIx-5qBaP3ZDR96_hiasIdBHhaESiHUOJvT1s0,6418
-pheval-0.4.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pheval-0.4.0.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
-pheval-0.4.0.dist-info/RECORD,,
+pheval-0.4.2.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+pheval-0.4.2.dist-info/METADATA,sha256=thGGkAFHrqcTeinQ4gSBiPg-RihcKED9fFUK0_Rph4g,6469
+pheval-0.4.2.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+pheval-0.4.2.dist-info/entry_points.txt,sha256=o9gSwDkvT4-lqKy4mlsftd1nzP9WUOXQCfnbqycURd0,81
+pheval-0.4.2.dist-info/RECORD,,

{pheval-0.4.0.dist-info → pheval-0.4.2.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