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corr. vcf_to_sfs

master
tforest 2022-02-14 10:32:11 +01:00
parent 257c713458
commit 017bf2c4ed
1 changed files with 8 additions and 11 deletions
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19
vcf_to_sfs.py
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@ -17,9 +17,7 @@ import sys
def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, verbose = False): def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, verbose = False):
""" """ Returns an SFS from a VCF file.
Multiplication de deux nombres entiers.
Cette fonction ne sert pas à grand chose.
Parameters Parameters
---------- ----------
@ -42,7 +40,8 @@ def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, ver
n *= 2 n *= 2
# initiate SFS_values with a zeros dict # initiate SFS_values with a zeros dict
SFS_values = dict.fromkeys(range(n),0) SFS_values = dict.fromkeys(range(n),0)
# store nb polyallellic sites
polyall = 0
with gzip.open(vcf_file, "rb") as inputgz: with gzip.open(vcf_file, "rb") as inputgz:
line = inputgz.readline() line = inputgz.readline()
genotypes = [] genotypes = []
@ -88,17 +87,13 @@ def sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False, ver
allele_counts[snp_genotypes.count(k)] = k allele_counts[snp_genotypes.count(k)] = k
allele_counts_list.append(snp_genotypes.count(k)) allele_counts_list.append(snp_genotypes.count(k))
if folded and len(ALT) >= 2: if folded and len(ALT) >= 2:
pass polyall += 1
# 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: else:
SFS_values[min(allele_counts_list)-1] += 1 SFS_values[min(allele_counts_list)-1] += 1
line = inputgz.readline() line = inputgz.readline()
if verbose: if verbose:
print(SFS_values) print(SFS_values)
return SFS_values return SFS_values, polyall
if __name__ == "__main__": if __name__ == "__main__":
@ -106,8 +101,10 @@ if __name__ == "__main__":
print("Need 2 args") print("Need 2 args")
exit(0) exit(0)
# PARAM : vcf_file
vcf_file = sys.argv[1]
# PARAM : Nb of indiv # PARAM : Nb of indiv
n = int(sys.argv[2]) n = int(sys.argv[2])
sfs = sfs_from_vcf(n, sys.argv[1], folded = True, diploid = True, phased = False) sfs, nb_polyall = sfs_from_vcf(n, vcf_file, folded = True, diploid = True, phased = False)
print(sfs) print(sfs)