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
sat_subfam2fam_multi_support.py
#!/usr/bin/python
import sys
from subprocess import call
print "sat_subfam2fam.py AlignFile PatternFile"
try:
dat = sys.argv[1]
except:
dat = raw_input("Introduce align file: ")
try:
pat = sys.argv[2]
except:
pat = raw_input("Introduce pattern file: ")
pat = open(pat).readlines()
patterns = {}
for line in pat:
info = line.split()
patterns[info[0]] = info[1]
data = open(dat).readlines()
w = open(dat+".fam", "w")
for line in data:
for el in patterns:
line = line.replace(el,patterns[el])
w.write(line)
w.close()