geinf/vcf_to_sfs.py

#!/usr/bin/env python3

"""
Caution : At the moment for gzipped files only.


"""

import gzip
import sys

# default folded SFS
folded = True
diploid = True

# PARAM : Nb of indiv
n = int(sys.argv[2])

if diploid and not folded:
    n *= 2

SFS_values = dict.fromkeys(range(n),0)


with gzip.open(sys.argv[1], "rb") as inputgz:
    line = inputgz.readline()
    genotypes = []
    #SFS_values = {}
    while line:
        line = line.decode('utf-8').strip()
        if not line.startswith("##") and not line.startswith("#"):
            FORMAT = line.split("\t")[8:9]
            SAMPLES = line.split("\t")[9:]
            snp_genotypes = []
            allele_counts = {}
            for sample in SAMPLES:
                # for UNPHASED data
                smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']                    
                nb_alleles = set(smpl_genotype)
                snp_genotypes += smpl_genotype
            for k in set(snp_genotypes):
                allele_counts[snp_genotypes.count(k)] = k
            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
        line = inputgz.readline()
        print(SFS_values)