#45 write cooocurring_mutations.csv in the beginning of main

viloca/shorah_snv.py

@@ -546,7 +546,7 @@ def main(args):
 
     logging.info(str(inspect.getfullargspec(main)))
 
-    # write: "cooccurring_mutations.csv"
+    # start write: "cooccurring_mutations.csv"
     tmp_df =[]
     # iterate over haplotype files
     with open("coverage.txt") as cov_file:
@@ -557,8 +557,9 @@ def main(args):
             file_stem = "w-%s-%s-%s" % (chrom, beg, end)
             haplo_filename = os.path.join(working_dir, "haplotypes", file_stem + ".reads-support.fas")
             ref_name = os.path.join(working_dir, "haplotypes", file_stem + ".ref.fas")
-            tmp_df.append(get_cooccuring_muts_df(fname_haplo, fname_ref, beg,end,chrom))
+            tmp_df.append(get_cooccuring_muts_haplo_df(fname_haplo, fname_ref, beg,end,chrom))
     pd.concat(tmp_df).to_csv("cooccurring_mutations.csv")
+    # finish  write: "cooccurring_mutations.csv"
 
     # snpD_m is the file with the 'consensus' SNVs (from different windows)
     logging.debug("now parsing SNVs")