phc-ingestion 0.8.24__tar.gz → 0.8.26__tar.gz

{phc-ingestion-0.8.24 → phc-ingestion-0.8.26}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phc-ingestion
-Version: 0.8.24
+Version: 0.8.26
 Summary: Functions for LifeOmic PHC genomic ingestions
 License: MIT
 Author-email: LifeOmic Development <development@lifeomic.com>

phc-ingestion-0.8.26/ingestion/nextgen/util/pre_filter_somatic_vcf.py

@@ -0,0 +1,67 @@
+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")
+    chrom, pos, ref, alt = split_line[0], split_line[1], split_line[3], split_line[4]
+    return f"{chrom}:{pos}:{ref}:{alt}"
+
+
+def extract_filter_from_vcf_line(line: str) -> str:
+    split_line = line.strip().split("\t")
+    return split_line[6]
+
+
+def replace_filter_in_vcf_line(line: str, new_filter: str) -> str:
+    split_line = line.strip().split("\t")
+    split_line[6] = new_filter
+    return "\t".join(split_line) + "\n"
+
+
+def pre_filter_somatic_vcf(
+    somatic_vcf_file: str,
+    somatic_vcf_snv_file: str,
+    somatic_vcf_indel_file: str,
+    working_dir: str,
+    log: Logger,
+) -> str:
+    """
+    Removes all variants from the `somatic_vcf_file` that are not
+    also in the `somatic_vcf_snv_file` or `somatic_vcf_indel_file`.
+
+    Also updates the FILTER field in the `somatic_vcf_file` to match
+    the FILTER field of the corresponding variant in the
+    `somatic_vcf_snv_file` or `somatic_vcf_indel_file`.
+    """
+    log.info("Pre-filtering somatic VCF file")
+
+    valid_variants_with_filters: dict[str, str] = {}
+
+    for file in [somatic_vcf_snv_file, somatic_vcf_indel_file]:
+        with open_maybe_gzipped(file, "rt") as f:
+            for line in f:
+                if line.startswith("#"):
+                    continue
+                valid_variants_with_filters[build_variant_key_from_vcf_line(line)] = (
+                    extract_filter_from_vcf_line(line)
+                )
+
+    log.info(f"Found {len(valid_variants_with_filters)} valid variants")
+
+    output_vcf_path = f"{working_dir}/filtered_somatic.vcf.gz"
+    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)
+            else:
+                key = build_variant_key_from_vcf_line(line)
+                if key in valid_variants_with_filters:
+                    w.write(replace_filter_in_vcf_line(line, valid_variants_with_filters[key]))
+
+    log.info(f"Successfully pre-filtered somatic VCF file to {output_vcf_path}")
+    return output_vcf_path

phc-ingestion-0.8.26/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-0.8.26}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "phc-ingestion"
-version = "0.8.24"
+version = "0.8.26"
 description = "Functions for LifeOmic PHC genomic ingestions"
 authors = [
     { name = "LifeOmic Development", email = "development@lifeomic.com" },

phc-ingestion-0.8.24/ingestion/nextgen/util/pre_filter_somatic_vcf.py

@@ -1,48 +0,0 @@
-import gzip
-from logging import Logger
-
-
-def build_variant_key_from_vcf_line(line: str) -> str:
-    split_line = line.strip().split("\t")
-    chrom, pos, ref, alt = split_line[0], split_line[1], split_line[3], split_line[4]
-    return f"{chrom}:{pos}:{ref}:{alt}"
-
-
-def pre_filter_somatic_vcf(
-    somatic_vcf_file: str,
-    somatic_vcf_snv_file: str,
-    somatic_vcf_indel_file: str,
-    working_dir: str,
-    log: Logger,
-) -> str:
-    """
-    Removes all variants from the `somatic_vcf_file` that are not
-    also in the `somatic_vcf_snv_file` or `somatic_vcf_indel_file`.
-    """
-    log.info("Pre-filtering somatic VCF file")
-
-    valid_variant_keys = set()
-    with gzip.open(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:
-        for line in f:
-            if line.startswith("#"):
-                continue
-            valid_variant_keys.add(build_variant_key_from_vcf_line(line))
-
-    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:
-        for line in f:
-            if line.startswith("#"):
-                w.write(line)
-            else:
-                if build_variant_key_from_vcf_line(line) in valid_variant_keys:
-                    w.write(line)
-
-    log.info(f"Successfully pre-filtered somatic VCF file to {output_vcf_path}")
-    return output_vcf_path

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)