phc-ingestion 0.8.24__tar.gz → 0.8.25__tar.gz

{phc-ingestion-0.8.24 → phc-ingestion-0.8.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.8.24
+Version: 0.8.25
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

{phc-ingestion-0.8.24 → phc-ingestion-0.8.25}/ingestion/nextgen/util/pre_filter_somatic_vcf.py

@@ -1,6 +1,7 @@
-import gzip
 from logging import Logger
 
+from ingestion.shared_util.open_maybe_gzipped import open_maybe_gzipped
+
 
 def build_variant_key_from_vcf_line(line: str) -> str:
     split_line = line.strip().split("\t")
@@ -22,12 +23,12 @@ def pre_filter_somatic_vcf(
     log.info("Pre-filtering somatic VCF file")
 
     valid_variant_keys = set()
-    with gzip.open(somatic_vcf_snv_file, "rt") as f:
+    with open_maybe_gzipped(somatic_vcf_snv_file, "rt") as f:
         for line in f:
             if line.startswith("#"):
                 continue
             valid_variant_keys.add(build_variant_key_from_vcf_line(line))
-    with gzip.open(somatic_vcf_indel_file, "rt") as f:
+    with open_maybe_gzipped(somatic_vcf_indel_file, "rt") as f:
         for line in f:
             if line.startswith("#"):
                 continue
@@ -36,7 +37,10 @@ def pre_filter_somatic_vcf(
     log.info(f"Found {len(valid_variant_keys)} valid variants")
 
     output_vcf_path = f"{working_dir}/filtered_somatic.vcf.gz"
-    with gzip.open(somatic_vcf_file, "rt") as f, gzip.open(output_vcf_path, "wt") as w:
+    with (
+        open_maybe_gzipped(somatic_vcf_file, "rt") as f,
+        open_maybe_gzipped(output_vcf_path, "wt") as w,
+    ):
         for line in f:
             if line.startswith("#"):
                 w.write(line)

phc-ingestion-0.8.25/ingestion/shared_util/open_maybe_gzipped.py

@@ -0,0 +1,8 @@
+import gzip
+from typing import cast, TextIO
+
+
+def open_maybe_gzipped(filename: str, mode: str = "rt") -> TextIO:
+    return cast(
+        TextIO, gzip.open(filename, mode) if filename.endswith(".gz") else open(filename, mode)
+    )

{phc-ingestion-0.8.24 → phc-ingestion-0.8.25}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.8.24"
+version = "0.8.25"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },

phc-ingestion-0.8.24/ingestion/shared_util/open_maybe_gzipped.py

@@ -1,5 +0,0 @@
-import gzip
-
-
-def open_maybe_gzipped(filename: str, mode: str = "rt"):
-    return gzip.open(filename, mode) if filename.endswith(".gz") else open(filename, mode)