replace TSV with CSV for variant outputs

ffpe_damage_v2.py

@@ -33,7 +33,8 @@ Outputs (in --outdir):
   strand_damage_profile_3prime.csv                (3' profile)
   end_enrichment.csv
   candidate_CtoT.bed / candidate_GtoA.bed         (IGV tracks)
-  candidate_variants.tsv                          (per-position context)
+  candidate_variants.csv                          (per-position context)
+  clean_variants.csv / ffpe_suspect_variants.csv
   CtoT_R1.png CtoT_R2.png GtoA_R1.png GtoA_R2.png (5' plots)
   CtoT_R1_3prime.png ... GtoA_R2_3prime.png       (3' plots)
 """
@@ -616,15 +617,15 @@ def write_beds_and_variants(d, args):
         df["is_ffpe_suspect"] = [x[0] for x in flags]
         df["ffpe_reason"] = [x[1] for x in flags]
 
-        df.to_csv(os.path.join(args.outdir, "candidate_variants.tsv"),
-                  index=False, sep="\t")
+        df.to_csv(os.path.join(args.outdir, "candidate_variants.csv"),
+                  index=False)
 
         clean = df[~df["is_ffpe_suspect"]]
         damaged = df[df["is_ffpe_suspect"]]
-        clean.to_csv(os.path.join(args.outdir, "clean_variants.tsv"),
-                     index=False, sep="\t")
-        damaged.to_csv(os.path.join(args.outdir, "ffpe_suspect_variants.tsv"),
-                       index=False, sep="\t")
+        clean.to_csv(os.path.join(args.outdir, "clean_variants.csv"),
+                     index=False)
+        damaged.to_csv(os.path.join(args.outdir, "ffpe_suspect_variants.csv"),
+                       index=False)
 
         for name, subset, fname in [
             ("clean", clean, "candidate_CtoT_clean.bed"),
@@ -647,8 +648,8 @@ def write_beds_and_variants(d, args):
             f.writelines(clean_ga)
         return df
     else:
-        open(os.path.join(args.outdir, "clean_variants.tsv"), "w").close()
-        open(os.path.join(args.outdir, "ffpe_suspect_variants.tsv"), "w").close()
+        open(os.path.join(args.outdir, "clean_variants.csv"), "w").close()
+        open(os.path.join(args.outdir, "ffpe_suspect_variants.csv"), "w").close()
         return pd.DataFrame()
 
 
@@ -886,7 +887,7 @@ def main():
         n_flag = int(flagged_df["is_ffpe_suspect"].sum())
         n_clean = len(flagged_df) - n_flag
         print(f"variants flagged FFPE : {n_flag} / {len(flagged_df)} "
-              f"-> ffpe_suspect_variants.tsv / clean_variants.tsv")
+              f"-> ffpe_suspect_variants.csv / clean_variants.csv")
 
 
 if __name__ == "__main__":