#!/usr/bin/env python

import os
import os.path
import phylip
import shutil
import subprocess
import sys
import time

#Version  Feb. 26, 2020
# Run proml as a command
#Synopsis: proml.py infile utree_ufn program pmodel speedy global method bseed\
#                  replicates blocksize percent jumble jseed numjum outgroup termout printdata\
#                  outfile treefile

#Convert arguments to variables
INFILE        = sys.argv[1]
#print 'INFILE: ' + INFILE
# bltree: If no file has been chosen for UFN, UFN will be blank.
# Simply substituting $UFN into the command for restml.csh would
# therefore result in a missing parameter. Here we concatenate
# UTREE and UFN in the form UTREE_UFN. restml.csh has been
# modified to read both parameters from the UTREE variable,
# and UFN is no longer passed as a separate variable.
UTREEPARAM = sys.argv[2]
UTREE = UTREEPARAM[0]
UFN           = UTREEPARAM[1:]
PROGRAM       = sys.argv[3]
PMODEL        = sys.argv[4]
SPEEDY        = sys.argv[5]
GLOBAL        = sys.argv[6]
METHOD        = sys.argv[7]
REPLICATES    = sys.argv[8]
BLOCKSIZE     = sys.argv[9]
PERCENT       = sys.argv[10]
JUMBLE        = sys.argv[11]
NUMJUM        = sys.argv[12]
OUTGROUP      = sys.argv[13]
TERMOUT       = sys.argv[14]
PRINTDATA     = sys.argv[15]
OUTFILE       = sys.argv[16]
TREEFILE      = sys.argv[17]


# Make a temporary directory in which to run the program
STARTDIR = os.getcwd()
TEMPDIR  = 'DNAML.' + str(os.getpid())
os.mkdir(TEMPDIR)
shutil.copyfile(INFILE, os.path.join(TEMPDIR, 'infile.temp'))

if UTREE == 'y':
    # Turn off bootstrapping when evaluating a user tree.
    # If bootstrapping is on, an empty file may be generated
    # which could cause drawtree or drawgram to loop infinitely
    METHOD = 'n'

    # Make sure that treefile begins with number of trees on first
    # line of file. If first line in file has parentheses, the
    # number must be added.
    phylip.ufn(UFN, TEMPDIR)

os.chdir(TEMPDIR)
# Debug statement.
#p_testinfile = subprocess.call(["nedit", "infile.temp"])
# Debug statement.
#p_testinfile = subprocess.call(["nedit", "intree"])

#----------------- generate keyboard input to send to program -----
msgfile_h = open("MSGFILE", "w")
# only two options, and the default is proml
if PROGRAM == "promlk":
    msgfile_h.write("--------  PROMLK - PROTEIN MAXIMUM LIKELIHOOD WITH EVOLUTIONARY CLOCK ---------\n")
else:
    msgfile_h.write("---------------------  PROML - PROTEIN MAXIMUM LIKELIHOOD ---------------------\n")
msgfile_h.write(" \n")

# Percent of characters to sample
if int(PERCENT) < 5 or int(PERCENT) > 100:
    PERCENT = 100


if METHOD == "n":
    msgfile_h.write(" \n")
    shutil.copyfile('infile.temp', 'infile')
if METHOD in ("b", "d"):
    phylip.stdresample(METHOD, PERCENT, REPLICATES, '1', msgfile_h, 's', 'i')
elif METHOD in ("ps", "po", "pw"):
    phylip.weightless_resample(METHOD, PERCENT, REPLICATES, '1',  msgfile_h, 's', 'i')
# Debug statement.
#p_testinfile = subprocess.call(["nedit", "infile"])

#-------- Run proml -----------
termout_h = open(TERMOUT, 'w')
RSEED = phylip.phylip_random()
msgfile_h.write(PROGRAM + ":  SEED= " + str(RSEED) + "\n")

# This statement reads from infile, so we have to run it before
# running TREEPROGRAM, which also reads infile.
NUMSEQ = phylip.get_numseq("infile")

comfile_h = open('PromlComfile', 'w')

if UTREE == 'y':
    comfile_h.write('u\n')

# Jumble - When multiple datasets are analyzed, some programs automatically
# jumbles, and prompts for a random number seed for jumbling. Othersise,
# jumbling must be explicitly set. From a scripting perspecitve, it is safest therefore
# to set jumbling first, so that we don't need to handle a bunch of special cases in
# which the program asks for jumbling at a later time.
if METHOD != "n":
    JUMBLE = "J"
if JUMBLE == "J":
    phylip.jumble(comfile_h, msgfile_h, NUMJUM)

# Unlike other programs, dnaml doesn't prompt for a random number
# seed if jumbling is set.y
if METHOD in ("b", "d"):
    comfile_h.write('m\n')
    comfile_h.write('w\n')
    comfile_h.write(REPLICATES + '\n')
#    comfile_h.write(str(RSEED) + '\n')
elif METHOD in ("ps", "po", "pw"):
    comfile_h.write('m\n')
    comfile_h.write('d\n')
    comfile_h.write(REPLICATES + '\n')
#    comfile_h.write(str(RSEED) + '\n')


# Speedier but rougher analysis
if SPEEDY == 'n':
    comfile_h.write('s\n')

# Global rearrangements
if GLOBAL == 'y':
    comfile_h.write( 'g\n')

# Outgroup
OUTGROUP = phylip.do_outgroup(OUTGROUP, NUMSEQ, comfile_h, msgfile_h)


# Genetic code
if PMODEL == "h":
    # echo 'Using Henikoff/Tiller PMG model' >> MSGFILE
    comfile_h.write('p\n')
elif PMODEL == "d":
    # echo 'Using Dayoff PAM model' >> MSGFILE
    comfile_h.write('p\n')
    comfile_h.write('p\n')


# Should sequence data be printed?
if PRINTDATA == 'y' and METHOD == 'n':
    comfile_h.write("1\n")

# When resampling or jumbling, turn off printing trees to outfile
if METHOD in ('b', 'd', 'ps', 'po', 'pw'):
    comfile_h.write("3\n")

#accept current settings and do the analysis
comfile_h.write("y\n")
comfile_h.close()

#-------- run proml -----------

os.nice(4)
start_time = time.time()
comfile_h = open('PromlComfile', 'r')
p_PROGRAM = subprocess.Popen([PROGRAM], stdin=comfile_h)
p_PROGRAM.wait()
comfile_h.close()
termout_h.close()
msgfile_h.close()
time_elapsed = time.time() - start_time
os.nice(0)

outfile_h = open('outfile', 'a')
outfile_h.write("Elapsed time on " + os.uname()[1] + ": " + str(time_elapsed) + " seconds")
outfile_h.close()


#----------- Return results to calling directory----------------
# When using resampling, filter the treefile through
# consense to generate an unrooted consensus tree.
if METHOD in ('b', 'd', 'ps', 'po', 'pw'):
    outfile_h = open('outfile', 'a')
    outfile_h.write(" \n")
    outfile_h.write('-------------------------------------------\n')
    outfile_h.close()

    subprocess.call(['consense.py', 'outtree', 'e', '1', str(OUTGROUP), 'n', 'outfile.consense', TREEFILE])
    shutil.move(TREEFILE, os.path.join(STARTDIR, TREEFILE))
    phylip.merge_msg(os.path.join(STARTDIR, OUTFILE))
else:
    shutil.move('outtree', os.path.join(STARTDIR, TREEFILE))
    phylip.merge_msg(os.path.join(STARTDIR, OUTFILE), False)

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

print("PROML completed.")