transposonPSI

#!/usr/bin/env python

from shutil import copyfile, rmtree
from os import path
import os.path
import sys

# Methods
def getArgument(args, title):
    for i in range(0, len(args)):
        if(args[i].startswith("-"+title)):
            if(i<len(args)-1):
                return args[i+1]
            else:
                return ""
    return ""

args = sys.argv

# Parameters
tempFolder   = getArgument(args, "tempFolder")
resultFolder = getArgument(args, "resultFolder")
fastaFile    = getArgument(args, "fastaFile")
mode         = getArgument(args, "mode")

# Localize share folder
script_dir = os.path.dirname(__file__)
parent_dir = os.path.abspath(os.path.join(script_dir, os.pardir))
share_dir  = os.path.join(parent_dir, "share", "transposonPSIcli")
print(script_dir)
print(parent_dir)
print(share_dir)

# Create temp folder
if(path.isdir(tempFolder)):
    rmtree(tempFolder)
os.mkdir(tempFolder)

# Copy code into temp folder
os.system("cp -r "+share_dir+" "+tempFolder)

# Copy fasta to temp folder
os.system("cp "+fastaFile+" "+os.path.join(tempFolder,"transposonPSIcli"))

# Go to folder and run transposonPSI
fastaFileName = os.path.basename(fastaFile)
os.system("cd "+os.path.join(tempFolder,"transposonPSIcli")+" && ./transposonPSI.pl "+fastaFileName+" "+mode)

# Copy results back
if(not path.isdir(resultFolder)):
    os.mkdir(resultFolder)
os.system("cp "+os.path.join(tempFolder,"transposonPSIcli","*.TPSI.allHits*")+" "+resultFolder)

# Delete temp folder
rmtree(tempFolder)
    
print("finished completely...")