--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/micropita_prepare.py	Tue May 13 21:58:57 2014 -0400
@@ -0,0 +1,202 @@
+#!/usr/bin/env python
+
+"""
+Author: George Weingart
+Description: Prepare parameters to call micropita
+"""
+
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#####################################################################################
+
+__author__ = "George Weingart"
+__copyright__ = "Copyright 2012"
+__credits__ = ["George Weingart"]
+__license__ = "MIT"
+__maintainer__ = "George Weingart"
+__email__ = "george.weingart@gmail.com"
+__status__ = "Development"
+
+import argparse
+from cStringIO import StringIO
+import sys,string,time
+import os
+from time import gmtime, strftime
+from pprint import pprint
+import subprocess  
+import blist
+import shlex
+import tempfile
+
+##################################################################################
+#   Modification by George Weingart    5/6/2014                                  #
+#   Using subprocess to invoke the calls to Micropita                            #
+#   and allocating the temporary file using trmpfile                             #
+##################################################################################
+
+
+
+
+##################################################################################
+#  Decode Parms                                                                  #
+##################################################################################
+def read_params(x):
+	parser = argparse.ArgumentParser(description='Micropita Annotate Argparser')
+	parser.add_argument('--input', action="store",dest='inputname')
+	parser.add_argument('--output', action="store",dest='outputname')
+	parser.add_argument('-m', action="store",dest='MParameter')
+	parser.add_argument('-n', action="store",dest='NSamples')
+	parser.add_argument('--lastmeta', action="store",dest='lastmeta')
+	parser.add_argument('--stratify_value', action="store",dest='stratify_value')
+
+
+	try:
+		parser.add_argument('--feature_method', action="store",dest='feature_method')
+	except:
+		pass
+	try:
+		parser.add_argument('--targets', action="store",dest='targets')
+	except:
+		pass
+	try:
+		parser.add_argument('--label_value', action="store",dest='label_value')
+	except:
+		pass
+	return  parser
+	
+
+##################################################################################
+#  Main Program                                                                  #
+##################################################################################
+parser = read_params( sys.argv )
+results = parser.parse_args()
+root_dir = os.environ.get('micropita_SCRIPT_PATH')
+
+
+fname =  results.inputname
+input_file = open(fname,'rU')
+input_lines = input_file.readlines()
+input_file.close()
+table_lines = []
+for x in input_lines:
+	first_column = x.split('\t')[0]
+	table_lines.append(first_column)
+
+
+
+FileTimeStamp =  strftime("%Y%m%d%H%M%S", gmtime())
+LastMetaInt = 0
+if results.lastmeta and not results.lastmeta == "None":
+	LastMetaInt = int(results.lastmeta) - 1
+
+StratifyValueInt = 0
+if  results.stratify_value and not   results.stratify_value == "None":
+	StratifyValueInt = int(results.stratify_value) - 2 
+
+LabelValueInt = 0
+if results.label_value and not results.label_value == "None":
+	LabelValueInt = int(results.label_value) - 1
+
+stratify_string = ""
+q = '"'
+if  not results.stratify_value == '1':
+	stratify_string = " --stratify " + q + table_lines[StratifyValueInt] + q + " "
+
+if results.MParameter == "features":
+	TBTargets = list()
+	TableTargets = results.targets.split(',')
+	for t in TableTargets:
+		tb_entry = int(t) + LastMetaInt 
+		TBTargets.append(int(tb_entry))
+
+
+	OutTargetsFile  = tempfile.NamedTemporaryFile('w', delete=False )   
+	TempTargetsFileName = OutTargetsFile.name 
+	indx = -1
+	for  c in table_lines:
+		indx+=1
+		if  indx in TBTargets:
+			OutputString = table_lines[indx] + "\n"
+			OutTargetsFile.write(OutputString)
+	OutTargetsFile.close()
+	os_command = "python " + \
+		root_dir + \
+		"/MicroPITA.py "+\
+		"--lastmeta " + table_lines[LastMetaInt]+ " " +\
+		"--feature_method " + results.feature_method + " " + \
+		"--target " + TempTargetsFileName + " " +\
+		"-m " + results.MParameter + " " + \
+		"-n " + results.NSamples + " " +\
+	stratify_string + " " +\
+	results.inputname + " " +\
+	results.outputname
+	#print os_command
+	os.system(os_command)
+	argsx = shlex.split(os_command)					#Split the command
+	try:
+			subprocess.check_call(argsx , shell=False)
+	except:
+			print "The call to micropita failed============="
+	sys.exit(0)
+
+
+
+if results.MParameter == "representative"\
+or results.MParameter == "diverse"\
+or results.MParameter == "extreme": 
+		os_command = "python " + \
+		root_dir +  \
+		"/MicroPITA.py "+\
+		"--lastmeta " + table_lines[LastMetaInt]+ " " +\
+		"-m " + results.MParameter + " " + \
+		"-n " + results.NSamples + " " +\
+		stratify_string + " " + \
+		results.inputname + " " +\
+		results.outputname
+		argsx = shlex.split(os_command)					#Split the command
+		try:
+				###os.system(os_command)
+				subprocess.check_call(argsx , shell=False)
+		except:
+				print "The call to micropita failed============="
+		sys.exit(0)
+ 
+	
+	
+	
+if results.MParameter == "distinct"\
+or results.MParameter == "discriminant": 
+	os_command = "python " + \
+		root_dir + \
+		"/MicroPITA.py "+\
+		"--lastmeta " + table_lines[LastMetaInt]+ " " +\
+		"--label " + table_lines[LastMetaInt]+ " " +\
+		"-m " + results.MParameter + " " + \
+		"-n " + results.NSamples + " " +\
+		stratify_string + " " + \
+	results.inputname + " " +\
+	results.outputname
+	#print os_command
+	argsx = shlex.split(os_command)					#Split the command
+	try:
+			subprocess.check_call(argsx , shell=False)
+	except:
+			print "The call to micropita failed============="
+	sys.exit(0)