pg-main from prod server added

pgx-main/create_overview.py

@@ -0,0 +1,54 @@
+import pandas as pd
+import os
+import zipfile
+import functools as ft
+
+
+dir = "pgx_results"
+diplotypes = []
+
+for z in os.listdir(dir):
+    s = z[:-4]
+    z = f"{dir}/{z}"
+    d = z[:-4]
+    if not z.endswith('.zip'):
+        continue
+        
+    print("Working on sample ", z)
+    with zipfile.ZipFile(z, "r") as zip_ref:
+        zip_ref.extractall(d)
+    os.unlink(z)
+    df = pd.read_csv(f"{d}/diplotypes.tsv", sep="\t")
+    df = df.groupby("name").agg({"genotype": lambda x: ", ".join(list(set(x)))})
+    df.rename(columns={"genotype": s}, inplace=True)
+    diplotypes.append(df)
+
+df_final = ft.reduce(lambda left, right: left.join(right, how="outer"), diplotypes)
+dfx = df_final.transpose().sort_index()
+
+fulgent_ids = [f for f in pd.read_csv("pgx_fulgent_panel.tsv", sep="\t")["variants"].to_list() if f.startswith("rs")]
+
+a = []
+b = []
+c = []
+e = []
+for d in dfx.index:
+    filename = f"{dir}/{d}/pharmgkb_annotations.json"
+    x = pd.read_json(filename)
+    x = x[x["Variant"].apply(lambda t: t.startswith("rs"))]
+    #x = x[x["Level of Evidence"] < "3"]
+    y = x[x["Variant"].apply(lambda t: t.split()[0] in fulgent_ids)].copy()
+    b.append(", ".join(sorted(x.Variant.unique())))
+    e.append(", ".join(sorted(y.Variant.unique())))
+
+    x = x[x["Phenotype(s)"].isna()]
+    y = y[y["Phenotype(s)"].isna()]
+    a.append(", ".join(sorted(x.Variant.unique())))
+    c.append(", ".join(sorted(y.Variant.unique())))
+
+dfx["rsids (no phenotype)"] = a
+dfx["rsids (all)"] = b
+dfx["rsids (fulgent/no phenotype)"] = c
+dfx["rsids (fulgent/all)"] = e
+
+dfx.to_csv("pgx_diplotypes_rsids.tsv", sep="\t")