install

#!/usr/bin/env python3
################################################################
#  This file part of GALA Gap-free Long-reads Assembler        #
#  Auther: Mohamed awad                                        #
#  Company: Xiangchao Gan lab (MPIPZ)                          #
#  Released under the (MIT) license (see LICENSE file)         #
################################################################
import os
import argparse
parser = argparse.ArgumentParser(prog="install",usage='%(prog)s -h  [options] description=Add Gala modules to path')
parser.add_argument("--prefix",nargs=1, type=str, default=['/usr/bin/'], metavar='The installation path\t [default /usr/bin/]',dest="path")
parser.add_argument("-y",nargs=1, type=str, default=['/usr/bin/env'], metavar='The path to Python\t [default /usr/bin/env]',dest="py")
parser.add_argument("-x",nargs=1, type=int, default=[3], metavar='Python Version\t [default 3]',dest="version")
args = parser.parse_args()
path=args.path[0]
py=args.py[0]
version=args.version[0]
a=['ccm','comp','mdm','newgenome','readsep','reformat','seprator','gala']
for i in a:
    b=path
    c=''.join(list(open(i)))
    c=c.replace('path=os.getcwd()','path="'+b)
    d=open(os.path.join(b,i),'w')
    if version==2: 
        d.writelines(c.replace('#!/usr/bin/env python3','!#'+py+' python2'))
        d.close()
    else:
        d.writelines(c.replace('#!/usr/bin/env','!#'+py))
        d.close()
    os.system('chmod +x '+os.path.join(b,i))
os.system('cp -RT src '+b)