#!/usr/bin/env python

import os
import os.path
import shutil
import subprocess
import sys

#Version  6/23/98
# Run reticulate as a command
#Synopsis: reticulate.csh infile title method outputtype fontsize outfile 

""" ensure that there are enough command line arguments to parse """
if len(sys.argv) < 7:
    print("Usage: reticulate.py  INFILE  TFILE  METHOD  OUTPUTTYPE  FONTSIZE  OUTFILE")
    exit();

#Convert arguments to variables
INFILE        = sys.argv[1]
TFILE         = sys.argv[2]
METHOD        = sys.argv[3]
OUTPUTTYPE    = sys.argv[4]
FONTSIZE      = sys.argv[5]
OUTFILE       = sys.argv[6]

# Remember where we started
STARTDIR = os.getcwd()

IFN = os.path.splitext(str(INFILE))[0]

# Make a temporary directory to run the program in 
TEMPDIR = 'reticulate.' + os.getpid()
os.mkdir(TEMPDIR)
shutil.copyfile(INFILE, os.path.join(TEMPDIR, 'infile.temp'))
shutil.copyfile(TFILE, os.path.join(TEMPDIR, os.path.basename(TFILE)))
os.chdir(TEMPDIR)

# Determine whether sequence is protein or DNA
# Only check for amino acid characters that are not also
# used as DNA ambiguity codes.
temphandle = open (INFILE, 'r')
for line in temphandle:
    if not line.startswith('>'):
        string = line.upper()
        for char in string:
            if char == 'X':
                CONTAINSX = true
            elif char == 'N':
                CONTAINSN = true
temphandle.close()

#------ reticulate -----------------------
os.nice(10)
p = subprocess.Popen(['reticulate'], stdin=subprocess.PIPE)
os.nice(0)

#----------------- generate keyboard input to send to program -----
p.stdin.write('infile.temp\n') # name of sequence file
p.stdin.write('n\n')  # init. gaps not marked in brackets

if CONTAINSX:
    p.stdin.write('n\n')  # X's are not unknowns
if CONTAINSN:
    p.stdin.write('n\n')  # N's are not unknowns

temphandle = open (TFILE, 'r')
p.stdin.write(temphandle.readline())  # title line
temphandle.close()


# Choose site polymorphism method
if METHOD == 2:
    p.stdin.write('2\n') # As transversion sites (DNA/RNA only)
elif METHOD == 3:
    p.stdin.write('3\n') # As sites with more than two characters
else:
    # call this whether or not METHOD = 1
    p.stdin.write('1\n') # Ignore these sites, use binary sites only

p.stdin.write('y\n')      # save informative sites to a file
p.stdin.write(IFN + '\n')
p.stdin.write('p\n')      # print the output


if OUTPUTTYPE == "eps": # Encapsulated Postscript
    OFN = IFN + '.eps'
    p.stdin.write('e\n')
else:                   # Postscript
    OFN = IFN + '.ps'
    p.stdin.write('p\n')

#echo IFN >> inputfile # name for window

p.stdin.write(FONTSIZE + '\n')
p.stdin.write(IFN + '\n')       # base name for file
p.stdin.write(" \n")            # name for printout (blank)
p.stdin.write('q\n')            # quit
p.stdin.close()
p.wait()

#----------- Return results to calling directory----------------
shutil.copyfile(OFN, os.path.join(STARTDIR, OUTFILE))
shutil.copyfile(IFN + '.sit', os.path.join(IFN + '.sit'))

os.chdir(STARTDIR)
shutil.rmtree(TEMPDIR)