pgx-main from prod added

pgx-main/combine_outside_calls.py

@@ -0,0 +1,25 @@
+from argparse import ArgumentParser
+import pandas as pd
+import os
+
+
+def combine(sample):
+    files = os.listdir("data/")
+    dfs = []
+    for f in files:
+        f = "data/" + f
+        if f.startswith(sample + "_cyp") and f.endswith(".tsv"):
+            dfs.append(pd.read_csv(f, sep="\t", header=None))
+            os.unlink(f)
+    df = pd.concat(dfs, ignore_index=True).dropna()
+    df.to_csv(f"{sample}_outside_call.tsv", sep="\t", index=False, header=False)
+
+
+def main():
+    parser = ArgumentParser(description="Combine StellarPGx Output")
+    parser.add_argument('sample', type=str, help="StellarPGx allele file prefix")
+    args = parser.parse_args()
+    combine(args.sample.replace("_calls", ""))
+
+if __name__ == '__main__':
+    main()