richard
/
geinf
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Before clean comments

master
tforest 2021-10-25 11:23:08 +02:00
parent c1e2cc9192
commit 77991f07ad
1 changed files with 10 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
vcf_to_sfs.py
View File

@ -82,16 +82,16 @@ with gzip.open(sys.argv[1], "rb") as inputgz:
if folded : if folded :
#allele_counts_list = list(allele_counts.keys()) #allele_counts_list = list(allele_counts.keys())
##print("ALC", allele_counts_list, "POLY", polyallelic, ALT) ##print("ALC", allele_counts_list, "POLY", polyallelic, ALT)
# for al in range(polyallelic-1): for al in range(polyallelic-1):
# SFS_values[min(allele_counts_list)-1] += 1/len(ALT) SFS_values[min(allele_counts_list)-1] += 1/len(ALT)
# allele_counts_list.remove(min(allele_counts_list)) allele_counts_list.remove(min(allele_counts_list))
if len(ALT) == 1: # if len(ALT) == 1:
SFS_values[min(allele_counts_list)-1] += 1 # SFS_values[min(allele_counts_list)-1] += 1
else: # else:
for al in range(polyallelic-1): # for al in range(polyallelic-1):
SFS_values[min(allele_counts_list)-1] += 1/len(ALT) # SFS_values[min(allele_counts_list)-1] += 1/len(ALT)
allele_counts_list.remove(min(allele_counts_list)) # allele_counts_list.remove(min(allele_counts_list))
polycount += 1 # polycount += 1
line = inputgz.readline() line = inputgz.readline()
print(SFS_values) print(SFS_values)
print(polycount) print(polycount)