phc-ingestion 0.10.17__tar.gz → 0.10.18__tar.gz

{phc-ingestion-0.10.17 → phc-ingestion-0.10.18}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.10.17
+Version: 0.10.18
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.10.17 → phc-ingestion-0.10.18}/ingestion/foundation/util/ga4gh.py

@@ -111,17 +111,23 @@ def get_hrd_status(genes) -> Optional[str]:
     hrd_dict = {
         "HRD Positive": "positive",
         "HRD Not Detected": "negative",
+        "HRDsig Positive": "positive",
+        "HRDsig Not Detected": "negative",
+        "HRDsig Negative": "negative",
     }
-    hrd_entry = [
-        entry
-        for entry in genes.get("Gene", {})
-        if entry.get("Name", "") == "Homologous Recombination status"
-    ]
-    if hrd_entry:
-        hrd_val = hrd_entry[0].get("Alterations", "").get("Alteration", "").get("Name", "")
-        return [value for (key, value) in hrd_dict.items() if key == hrd_val][0]
-    else:
+    hrd_entry = next(
+        (
+            entry
+            for entry in genes.get("Gene", {})
+            if entry.get("Name", "") == "Homologous Recombination status"
+            or entry.get("Name", "") == "HRD signature"
+        ),
+        None,
+    )
+    if not hrd_entry:
         return None
+    hrd_val = hrd_entry.get("Alterations", {}).get("Alteration", {}).get("Name", "")
+    return hrd_dict.get(hrd_val, None)
 
 
 def get_test_yml(
@@ -155,6 +161,14 @@ def get_test_yml(
         (prop for prop in properties if prop.get("@key") == "ComprehensiveTumorFractionScore"),
         {},
     ).get("value")
+    hrd_score = next(
+        (
+            prop
+            for prop in properties
+            if prop.get("@key") == "HomologousRecombinationDeficiencyScore"
+        ),
+        {},
+    ).get("value")
     plasma_tumor_fraction_score = None
     if plasma_tumor_fraction_score_value:
         plasma_tumor_fraction_score = get_plasma_tumor_fraction_score_from_value(
@@ -325,5 +339,7 @@ def get_test_yml(
     # add homologous recombination deficiency
     if hrd_status:
         yaml_file["hrdStatus"] = hrd_status
+    if hrd_score != None and is_number(hrd_score):
+        yaml_file["hrdScore"] = float(hrd_score)
 
     return yaml_file

{phc-ingestion-0.10.17 → phc-ingestion-0.10.18}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.10.17"
+version = "0.10.18"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },