refactors ped creator to include sex

src/create_dummy_ped.py

 """
 Create dummy ped file by project
+
+Usage:
+ml reset
+ml Anaconda3
+conda activate quac_common
+python src/create_dummy_ped.py
 """
 
 from pathlib import Path
+import pandas as pd
 
 
-def main(project_name, outpath):
+def read_project_tracker(project_tracker_f):
 
-    project_path = Path("/data/project/worthey_lab/projects") / project_name / "analysis"
+    df = pd.read_excel(project_tracker_f, usecols=["CGDS ID", "Sex"])
+
+    df["sex_ped"] = df["Sex"].str.lower().map({"m": "1", "f": "2"})
+    df["sex_ped"] = df["sex_ped"].fillna("-9")  # unknown sex
+
+    sample_sex_dict = df.set_index("CGDS ID")["sex_ped"].to_dict()
+
+    return sample_sex_dict
 
+
+def nbbbb():
+
+    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"))
     )
@@ -24,14 +42,49 @@ def main(project_name, outpath):
     return None
 
 
+def main(outpath):
+
+    project_dict = {
+        "CF_CFF_PFarrell": {
+            "tracking_sheet": "data/external/project_tracker/PROJECT TRACKING -CF.xlsx",
+            "affected": "all",
+        },
+        # "CF_TLOAF_PFarrell",
+        # "EDS3_unkn_DGreenspan",
+        # "MuscDyst_SU_MAlexander",
+        # "UDN_Phase1_EAWorthey",
+    }
+
+    for project_name in project_dict:
+        # get sample's sex info from project tracking sheet
+        sample_sex_dict = read_project_tracker(project_dict[project_name]["tracking_sheet"])
+
+        # get samples from cheaha for the project
+        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 sorted(samples):
+                data = [
+                    "unknown",
+                    sample,
+                    "-9",  # father
+                    "-9",  # mother
+                    sample_sex_dict[sample],  # sample sex
+                    "1" if project_dict[project_name]["affected"] == "all" else "-9",  # affected
+                ]
+                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)
+    main(OUT_PATH)