Merge pull request #284 from NCI-CGR/213-create-header-only-files-for…

…-sample_levelconcordancegraftsv-sample_levelconcordancekingkin0-when-no-relatives

fix empty relatedness files

src/cgr_gwas_qc/workflow/scripts/sample_concordance.py

@@ -34,6 +34,7 @@
     - :mod:`cgr_gwas_qc.parsers.king`
     - :mod:`cgr_gwas_qc.parsers.graf`
 """
+import os
 from itertools import combinations
 from pathlib import Path
 from typing import List, Tuple
@@ -102,9 +103,18 @@ def read(filename: PathLike):
 
 @app.command()
 def main(
-    sample_sheet_csv: Path, plink_file: Path, graf_file: Path, king_file: Path, outfile: Path,
+    sample_sheet_csv: Path,
+    plink_file: Path,
+    graf_file: Path,
+    king_file: Path,
+    outfile: Path,
 ):
     ss = sample_sheet.read(sample_sheet_csv)
+
+    # Check if graf or king are empty (no related). If so add expected final headers to file
+    check_empty_add_headers(graf_file, ["GRAF_HGMR", "GRAF_AGMR", "GRAF_relationship"])
+    check_empty_add_headers(king_file, ["KING_Kinship", "KING_relationship"])
+
     concordance = (
         build(plink_file, graf_file, king_file)
         .pipe(_add_expected_replicates, ss)
@@ -119,6 +129,13 @@ def main(
     )
 
 
+def check_empty_add_headers(file_path: Path, headers: list):
+    """Check if the file is empty"""
+    if os.path.getsize(file_path) == 0:
+        with open(file_path, "w") as f:
+            f.write("\t".join(headers) + "\n")
+
+
 def build(plink_file: PathLike, graf_file: PathLike, king_file: PathLike):
     """Build the main concordance table."""
     return (
@@ -246,7 +263,8 @@ def _graf(filename: PathLike):
         .set_index(["ID1", "ID2"])
         .reindex(["HGMR", "AGMR", "relationship"], axis=1)
         .rename(
-            {"HGMR": "GRAF_HGMR", "AGMR": "GRAF_AGMR", "relationship": "GRAF_relationship"}, axis=1,
+            {"HGMR": "GRAF_HGMR", "AGMR": "GRAF_AGMR", "relationship": "GRAF_relationship"},
+            axis=1,
         )
     )