Cleaned

vcf_to_sfs.py

@@ -28,8 +28,6 @@ if diploid and not folded:
 # initiate SFS_values with a zeros dict
 SFS_values = dict.fromkeys(range(n),0)
 
-polycount = 0
-
 with gzip.open(sys.argv[1], "rb") as inputgz:
     line = inputgz.readline()
     genotypes = []
@@ -66,12 +64,6 @@ with gzip.open(sys.argv[1], "rb") as inputgz:
                     smpl_genotype = [int(a) for a in sample.split(':')[0].split('|') if a != '.']
                 nb_alleles = set(smpl_genotype)
                 snp_genotypes += smpl_genotype
-            # if set(snp_genotypes) > 2:
-            #     polyallelic = set(snp_genotypes)
-            # else:
-            #     polyallelic = False
-            polyallelic = len(ALT)
-            ##print(REF, ALT, snp_genotypes)
             # skip if all individuals have the same genotype
             if len(set(snp_genotypes)) == 1:
                 line = inputgz.readline()
@@ -80,18 +72,9 @@ with gzip.open(sys.argv[1], "rb") as inputgz:
                 allele_counts[snp_genotypes.count(k)] = k
                 allele_counts_list.append(snp_genotypes.count(k))
             if folded :
-                #allele_counts_list = list(allele_counts.keys())
-                ##print("ALC", allele_counts_list, "POLY", polyallelic, ALT)
                 for al in range(polyallelic-1):
                     SFS_values[min(allele_counts_list)-1] += 1/len(ALT)
                     allele_counts_list.remove(min(allele_counts_list))
-                # if len(ALT) == 1:
-                #     SFS_values[min(allele_counts_list)-1] += 1
-                # else:
-                #     for al in range(polyallelic-1):
-                #         SFS_values[min(allele_counts_list)-1] += 1/len(ALT)
-                #         allele_counts_list.remove(min(allele_counts_list))
-                #         polycount += 1
         line = inputgz.readline()
         print(SFS_values)
 print(polycount)