phc-ingestion 0.9.2__tar.gz → 0.9.3__tar.gz

{phc-ingestion-0.9.2 → phc-ingestion-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.9.2
+Version: 0.9.3
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

phc-ingestion-0.9.3/ingestion/nebula/__init__.py

@@ -0,0 +1 @@
+from ingestion.nebula.process import process

phc-ingestion-0.9.3/ingestion/nebula/process.py

@@ -0,0 +1,46 @@
+import os
+from pathlib import Path
+from ingestion.vcf_standardization.standardize import standardize_vcf
+from lifeomic_logging import scoped_logger
+
+
+def process(vcf_file: str, source_file_id: str, out_path: str, case_id: str) -> dict:
+    with scoped_logger(__name__) as log:
+        # TODO: do we need to take in + process the manifest file here?
+
+        # Process VCF
+        base_vcf_file = os.path.basename(vcf_file)
+        vcf_out = base_vcf_file.replace(".vcf", ".modified.vcf")
+        vcf_final = base_vcf_file.replace(".vcf", ".modified.nrm.filtered.vcf")
+        if not vcf_final.endswith(".gz"):
+            vcf_final = vcf_final + ".gz"
+
+        # Assuming Nebula VCFs are germline
+        sample_name = f"germline_{case_id}"
+        vcf_line_count = standardize_vcf(
+            vcf_file, vcf_out, out_path, sample_name, log, compression=True
+        )
+
+        # Create a basic manifest for the Nebula VCF
+        manifest = {
+            "testType": "Nebula",
+            "sourceFileId": source_file_id,
+            "reference": "GRCh38",  # Assuming GRCh38, adjust as needed
+            "resources": [{"fileName": f".lifeomic/nebula/{case_id}/{base_vcf_file}"}],
+            "files": [
+                {
+                    "fileName": f".lifeomic/nebula/{case_id}/{vcf_final}",
+                    "sequenceType": "germline",
+                    "type": "shortVariant",
+                }
+            ],
+        }
+
+        case_metadata = {
+            "test_type": "Nebula",
+            "vcf_line_count": vcf_line_count,
+            "case_id": case_id,
+            "germline_genome_reference": manifest["reference"],
+        }
+
+        return case_metadata, manifest

{phc-ingestion-0.9.2 → phc-ingestion-0.9.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.9.2"
+version = "0.9.3"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },