114 lines
3.6 KiB
Python
Executable File
114 lines
3.6 KiB
Python
Executable File
#!/usr/bin/env python3
|
|
|
|
"""
|
|
FOREST Thomas (thomas.forest@college-de-france.fr)
|
|
|
|
Caution : At the moment for gzipped files only.
|
|
|
|
ARGS
|
|
--------
|
|
|
|
standalone usage : vcf_to_sfs.py VCF.gz nb_indiv
|
|
|
|
"""
|
|
|
|
import gzip
|
|
import sys
|
|
|
|
def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, verbose = False):
|
|
|
|
"""
|
|
Multiplication de deux nombres entiers.
|
|
Cette fonction ne sert pas à grand chose.
|
|
|
|
Parameters
|
|
----------
|
|
n : int
|
|
Nb of individuals in sample.
|
|
vcf_file : str
|
|
SNPs in VCF file format.
|
|
|
|
Used to generate a Site Frequency Spectrum (SFS) from a VCF.
|
|
|
|
Returns
|
|
-------
|
|
dict
|
|
Site Frequency Spectrum (SFS)
|
|
|
|
|
|
"""
|
|
|
|
if diploid and not folded:
|
|
n *= 2
|
|
# initiate SFS_values with a zeros dict
|
|
SFS_values = dict.fromkeys(range(n),0)
|
|
|
|
with gzip.open(vcf_file, "rb") as inputgz:
|
|
line = inputgz.readline()
|
|
genotypes = []
|
|
print("Parsing VCF", vcf_file, "... Please wait...")
|
|
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("#"):
|
|
FIELDS = line.split("\t")
|
|
# REF is col 4 of VCF
|
|
REF = FIELDS[3].split(",")
|
|
# ALT is col 5 of VCF
|
|
ALT = FIELDS[4].split(",")
|
|
FORMAT = line.split("\t")[8:9]
|
|
SAMPLES = line.split("\t")[9:]
|
|
snp_genotypes = []
|
|
allele_counts = {}
|
|
allele_counts_list = []
|
|
# SKIP the SNP if :
|
|
# 1 : missing
|
|
# 2 : deletion among REF
|
|
# 3 : deletion among ALT
|
|
if "./.:." in line \
|
|
or len(ALT[0]) > 1 \
|
|
or len(REF[0]) > 1:
|
|
line = inputgz.readline()
|
|
continue
|
|
for sample in SAMPLES:
|
|
if not phased:
|
|
# for UNPHASED data
|
|
smpl_genotype = [int(a) for a in sample.split(':')[0].split('/') if a != '.']
|
|
else:
|
|
# for PHASED
|
|
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
|
|
for k in set(snp_genotypes):
|
|
allele_counts[snp_genotypes.count(k)] = k
|
|
allele_counts_list.append(snp_genotypes.count(k))
|
|
if folded and len(ALT) >= 2:
|
|
pass
|
|
# TODO - work in progress
|
|
# for al in range(len(ALT)-1):
|
|
# SFS_values[min(allele_counts_list)-1] += 1/len(ALT)
|
|
# allele_counts_list.remove(min(allele_counts_list))
|
|
else:
|
|
SFS_values[min(allele_counts_list)-1] += 1
|
|
line = inputgz.readline()
|
|
if verbose:
|
|
print(SFS_values)
|
|
return SFS_values
|
|
|
|
if __name__ == "__main__":
|
|
|
|
if len(sys.argv) != 3:
|
|
print("Need 2 args")
|
|
exit(0)
|
|
|
|
# PARAM : Nb of indiv
|
|
n = int(sys.argv[2])
|
|
|
|
sfs = sfs_from_vcf(n, sys.argv[1], folded = True, diploid = True, phased = False)
|
|
print(sfs)
|