#!/usr/bin/env python

import phylip
import sys

# Create an infile for fastDNAml

#Version  11/25/06
#Synopsis: fastDNAml.csh infile qadd global\
#                       jmble jseed bstrap tratio spout outgrp usertree ufn

#Convert arguments to variables
INFILE      = sys.argv[1]
QADD        = sys.argv[2]
GLOBAL      = sys.argv[3]
JMBLE       = sys.argv[4]
JSEED       = sys.argv[5]
BSTRAP      = sys.argv[6]
TRATIO      = sys.argv[7]
SPOUT       = sys.argv[8]
OUTGRP      = sys.argv[9]
USERTREE    = sys.argv[10]
UFN         = sys.argv[11]

# Bootstrapping will automatically jumble the sequence.
# If fastDNAml_boot finds a Jumble auxiliary line, it
# will generate an error message and quit.
if BSTRAP == "y":
    JMBLE = "N"

################################################
# Set up $INFILE for fastDNAml
################################################
#----------------- generate first line  -----------------

infile_h = open(INFILE, "r")
infile_lines = infile_h.readlines()
FIRSTLINE = infile_lines[0]
infile_h.close()
FIRSTLINE = FIRSTLINE + " Y F T"

if QADD == "Y":
    FIRSTLINE = FIRSTLINE + " Q"
if GLOBAL == "Y":
    FIRSTLINE = FIRSTLINE + " G"
if JMBLE == "Y":
    FIRSTLINE = FIRSTLINE + " J"
if SPOUT == "Y":
    FIRSTLINE = FIRSTLINE + " O"
if USERTREE == "Y":
    FIRSTLINE = FIRSTLINE + " U"

#---------------- Write first line and optional command lines------
print FIRSTLINE
print "T " + TRATIO

if JMBLE == "Y":
    print "J " + JSEED
if SPOUT == "Y":
    print "O " + OUTGRP

#--------------- Write sequence part of file ----------------------
#tail +2 $INFILE 
# We can no longer use tail +n because the syntax is no longer consistent
# between Unix and Linux
@ NUMLINES = (`wc -l $INFILE | sed -e "s/^[ ]*//" | cut -f1 -d" "`) - 1
tail -$NUMLINES $INFILE
for infile_lines[1:]
   
#--------------- Write user treefile, if supplied ----------------------
if USERTREE == "Y":
    phylip.ufn(UFN, "", False)