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vcf_to_sfs.py

 """
 Caution : At the moment for gzipped files only.
 
+ARGS
+--------
+
+usage : vcf_to_sfs.py VCF.gz nb_indiv
 
 """
 
 # default folded SFS
 folded = True
 diploid = True
+phased = False
 
 # PARAM : Nb of indiv
 n = int(sys.argv[2])
 
 if diploid and not folded:
     n *= 2
-
+# initiate SFS_values with a zeros dict
 SFS_values = dict.fromkeys(range(n),0)
 
-
 with gzip.open(sys.argv[1], "rb") as inputgz:
     line = inputgz.readline()
     genotypes = []
-    #SFS_values = {}
     while line:
+        # decode gzipped binary lines
         line = line.decode('utf-8').strip()
+        # every snp line, not comment or header
         if not line.startswith("##") and not line.startswith("#"):
             FORMAT = line.split("\t")[8:9]
             SAMPLES = line.split("\t")[9:]
             allele_counts = {}
             for sample in SAMPLES:
                 # for UNPHASED data
-                smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']                    
+                smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']
+                
                 nb_alleles = set(smpl_genotype)
                 snp_genotypes += smpl_genotype
+            # skip if all individuals have the same genotype
             if len(set(snp_genotypes)) == 1:
                 line = inputgz.readline()
                 continue
-            #print(snp_genotypes)
             for k in set(snp_genotypes):
                 allele_counts[snp_genotypes.count(k)] = k
-            if 7 in allele_counts.keys():
-                print(allele_counts)
-                #print(allele_counts)
             if folded :
-                #for count in allele_counts.keys():
-                # for count in allele_counts.keys():
-                #     if count <= len(snp_genotypes)/2 :
-                #         SFS_values[count-1] += 1
-                #     else:
-                #         SFS_values[len(snp_genotypes)-count-1] += 1
                 SFS_values[min(allele_counts.keys())-1] += 1
         line = inputgz.readline()
-        #print(SFS_values)
-
-
-# Note : tout est doublé là
+        print(SFS_values)