creates dummy ped file

src/create_dummy_ped.py

+"""
+Create dummy ped file by project
+"""
+
+from pathlib import Path
+
+
+def main(project_name, outpath):
+
+    project_path = Path("/data/project/worthey_lab/projects") / project_name / "analysis"
+
+    samples = (
+        f.name for f in project_path.iterdir() if f.is_dir() and f.name.startswith(("LW", "UDN"))
+    )
+
+    header = ["#family_id", "sample_id", "paternal_id", "maternal_id", "sex", "phenotype"]
+    with open(Path(outpath) / f"{project_name}.ped", "w") as out_handle:
+        out_handle.write("\t".join(header) + "\n")
+
+        for sample in samples:
+            data = ["unknown", sample, "-9", "-9", "-9", "-9"]
+            out_handle.write("\t".join(data) + "\n")
+
+    return None
+
+
+if __name__ == "__main__":
+    OUT_PATH = "data/raw/ped"  # not so raw, is it?
+    # PROJECT_NAME = "MuscDyst_SU_MAlexander"
+    for PROJECT_NAME in [
+        "CF_TLOAF_PFarrell",
+        "CF_CFF_PFarrell",
+        "EDS3_unkn_DGreenspan",
+        "MuscDyst_SU_MAlexander",
+        "UDN_Phase1_EAWorthey",
+    ]:
+        main(PROJECT_NAME, OUT_PATH)