diff --git a/vcf_to_sfs.py b/vcf_to_sfs.py index 5f27794..b48856c 100755 --- a/vcf_to_sfs.py +++ b/vcf_to_sfs.py @@ -38,13 +38,25 @@ 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 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(): - if count <= len(snp_genotypes)/2 : - SFS_values[count-1] += 1 - else: - SFS_values[len(snp_genotypes)-count] += 1 + #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) + #print(SFS_values) + + +# Note : tout est doublé là