Merge pull request #46 from monarch-initiative/45-convert-expects-a-l…

…ist-of-omim-ids 45 convert expects a list of omim ids
monarch-initiative · Dec 12, 2024 · 273db47 · 273db47
2 parents ba3be0a + 7a4f457
commit 273db47
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phenotype2phenopacket"
-version = "0.6.6"
+version = "0.6.7"
 description = ""
 authors = ["Yasemin Bridges <y.bridges@qmul.ac.uk>"]
 readme = "README.md"

diff --git a/src/phenotype2phenopacket/convert/convert.py b/src/phenotype2phenopacket/convert/convert.py
@@ -37,9 +37,13 @@ def convert_to_phenopackets(
     grouped_omim_diseases = filter_diseases(
         num_disease, omim_id, omim_id_list, phenotype_annotation_data
     )
-    for omim_id, omim_disease in zip(read_omim_id_list(omim_id_list), grouped_omim_diseases):
+    omim_ids = (
+        read_omim_id_list(omim_id_list) if omim_id_list else [None] * len(grouped_omim_diseases)
+    )
+    for omim_id, omim_disease in zip(omim_ids, grouped_omim_diseases):
         if len(omim_disease) == 0:
-            print(f"Skipping... Could not find any phenotype entries for {omim_id}!")
+            id_message = f" for {omim_id}!" if omim_id else "!"
+            print(f"Skipping... Could not find any phenotype entries{id_message}")
             continue
         phenopacket_file = PhenotypeAnnotationToPhenopacketConverter(
             human_phenotype_ontology