#!/usr/bin/env python

import birchenv
import birchscript
import os
import os.path
import shutil
import subprocess
import sys

# For each name in INFILE, call a SeqHound method, and return
# the result (a list). Results for each name are converted into
# a GDE flat file. Flat files are concatenated into a single
# flatfile to be read back into GDE.

# Make sure that the user has a $HOME/.shoundremrc file
if not os.path.exists(os.path.join(birchenv.HOME, ".shoundremrc")):
    shutil.copyfile(os.path.join(birchenv.BIRCH, "java", "Leash", "shoundremrc"), os.path.join(os.getcwd(), os.path.join(birchenv.HOME, ".shoundremrc")))
   
h_INFILE  = open(sys.argv[1], "r")
OUTFILE  = sys.argv[2]
TYPE     = sys.argv[3]
TEMPFILE = "leash." + os.getpid()

for name in h_INFILE:
    namefile = name + "." + TYPE
    command = ["java", "-jar", os.path.join(birchenv.BIRCH, "java", "Leash", "Leash.jar"), "-mpi", name]
    command[5:] = sys.argv[3:]
    command[-1:] = [command[-1][0], "-of", namefile]
    subprocess.call(command)
    subprocess.call([os.path.join(birchenv.BIRCH, "script", "list2flat.py"), namefile, TEMPFILE])
    birchscript.cat_to(TEMPFILE, h_OUTFILE)
    os.remove(namefile)
    os.remove(TEMPFILE)