https://github.com/fjruizruano/ngs-protocols
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
get_var_library.py
#!/usr/bin/python
ra = open("ref_alt3.txt").readlines()
var = open("toico4.txt").readlines()
header = var[0]
samples = header.split()
n_samples = len(samples)
n_samples = (n_samples-2)/6
w = open("out.txt","w")
ra_list = []
for i in range(0,len(ra)):
ra_line = ra[i]
ra_info = ra_line.split()
r = int(ra_info[2])
a = int(ra_info[3])
var_line = var[i]
var_info = var_line.split()
res = []
for j in range(0,n_samples):
r_num = 2+(j*6)+r
a_num = 2+(j*6)+a
res.append(var_info[r_num])
res.append(var_info[a_num])
w.write("%s\t%s\n" % ("\t".join(ra_info[0:2]),"\t".join(res)))
w.close()