Mercurial > repos > george-weingart > micropita
annotate micropita_prepare.py @ 15:61e311c4d2d0
Updated test-data
| author | george-weingart |
|---|---|
| date | Mon, 19 May 2014 02:28:59 -0400 |
| parents | a206555874ee |
| children | a40a7a8c28d2 |
| rev | line source |
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| 0 | 1 #!/usr/bin/env python |
| 2 | |
| 3 """ | |
| 4 Author: George Weingart | |
| 5 Description: Prepare parameters to call micropita | |
| 6 """ | |
| 7 | |
| 8 ##################################################################################### | |
| 9 #Copyright (C) <2012> | |
| 10 # | |
| 11 #Permission is hereby granted, free of charge, to any person obtaining a copy of | |
| 12 #this software and associated documentation files (the "Software"), to deal in the | |
| 13 #Software without restriction, including without limitation the rights to use, copy, | |
| 14 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, | |
| 15 #and to permit persons to whom the Software is furnished to do so, subject to | |
| 16 #the following conditions: | |
| 17 # | |
| 18 #The above copyright notice and this permission notice shall be included in all copies | |
| 19 #or substantial portions of the Software. | |
| 20 # | |
| 21 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, | |
| 22 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A | |
| 23 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT | |
| 24 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION | |
| 25 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE | |
| 26 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. | |
| 27 ##################################################################################### | |
| 28 | |
| 29 __author__ = "George Weingart" | |
| 30 __copyright__ = "Copyright 2012" | |
| 31 __credits__ = ["George Weingart"] | |
| 32 __license__ = "MIT" | |
| 33 __maintainer__ = "George Weingart" | |
| 34 __email__ = "george.weingart@gmail.com" | |
| 35 __status__ = "Development" | |
| 36 | |
| 37 import argparse | |
| 38 from cStringIO import StringIO | |
| 39 import sys,string,time | |
| 40 import os | |
| 41 from time import gmtime, strftime | |
| 42 from pprint import pprint | |
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43 import subprocess |
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44 import blist |
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45 import shlex |
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46 import tempfile |
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47 |
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48 ################################################################################## |
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49 # Modification by George Weingart 5/6/2014 # |
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50 # Using subprocess to invoke the calls to Micropita # |
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51 # and allocating the temporary file using trmpfile # |
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52 ################################################################################## |
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53 |
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54 |
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55 |
| 0 | 56 |
| 57 ################################################################################## | |
| 58 # Decode Parms # | |
| 59 ################################################################################## | |
| 60 def read_params(x): | |
| 61 parser = argparse.ArgumentParser(description='Micropita Annotate Argparser') | |
| 62 parser.add_argument('--input', action="store",dest='inputname') | |
| 63 parser.add_argument('--output', action="store",dest='outputname') | |
| 64 parser.add_argument('-m', action="store",dest='MParameter') | |
| 65 parser.add_argument('-n', action="store",dest='NSamples') | |
| 66 parser.add_argument('--lastmeta', action="store",dest='lastmeta') | |
| 67 parser.add_argument('--stratify_value', action="store",dest='stratify_value') | |
| 68 | |
| 69 | |
| 70 try: | |
| 71 parser.add_argument('--feature_method', action="store",dest='feature_method') | |
| 72 except: | |
| 73 pass | |
| 74 try: | |
| 75 parser.add_argument('--targets', action="store",dest='targets') | |
| 76 except: | |
| 77 pass | |
| 78 try: | |
| 79 parser.add_argument('--label_value', action="store",dest='label_value') | |
| 80 except: | |
| 81 pass | |
| 82 return parser | |
| 83 | |
| 84 | |
| 85 ################################################################################## | |
| 86 # Main Program # | |
| 87 ################################################################################## | |
| 88 parser = read_params( sys.argv ) | |
| 89 results = parser.parse_args() | |
| 3 | 90 root_dir = os.environ.get('micropita_SCRIPT_PATH') |
| 91 | |
| 0 | 92 |
| 93 fname = results.inputname | |
| 94 input_file = open(fname,'rU') | |
| 95 input_lines = input_file.readlines() | |
| 96 input_file.close() | |
| 97 table_lines = [] | |
| 98 for x in input_lines: | |
| 99 first_column = x.split('\t')[0] | |
| 100 table_lines.append(first_column) | |
| 101 | |
| 102 | |
| 103 | |
| 104 FileTimeStamp = strftime("%Y%m%d%H%M%S", gmtime()) | |
| 105 LastMetaInt = 0 | |
| 106 if results.lastmeta and not results.lastmeta == "None": | |
| 107 LastMetaInt = int(results.lastmeta) - 1 | |
| 108 | |
| 109 StratifyValueInt = 0 | |
| 110 if results.stratify_value and not results.stratify_value == "None": | |
| 111 StratifyValueInt = int(results.stratify_value) - 2 | |
| 112 | |
| 113 LabelValueInt = 0 | |
| 114 if results.label_value and not results.label_value == "None": | |
| 115 LabelValueInt = int(results.label_value) - 1 | |
| 116 | |
| 117 stratify_string = "" | |
| 118 q = '"' | |
| 119 if not results.stratify_value == '1': | |
| 120 stratify_string = " --stratify " + q + table_lines[StratifyValueInt] + q + " " | |
| 121 | |
| 122 if results.MParameter == "features": | |
| 123 TBTargets = list() | |
| 124 TableTargets = results.targets.split(',') | |
| 125 for t in TableTargets: | |
| 126 tb_entry = int(t) + LastMetaInt | |
| 127 TBTargets.append(int(tb_entry)) | |
| 128 | |
| 129 | |
| 11 | 130 OutTargetsFile = tempfile.NamedTemporaryFile('w', delete=False ) |
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131 TempTargetsFileName = OutTargetsFile.name |
| 0 | 132 indx = -1 |
| 133 for c in table_lines: | |
| 134 indx+=1 | |
| 135 if indx in TBTargets: | |
| 136 OutputString = table_lines[indx] + "\n" | |
| 137 OutTargetsFile.write(OutputString) | |
| 138 OutTargetsFile.close() | |
| 139 os_command = "python " + \ | |
| 4 | 140 root_dir + \ |
| 8 | 141 "/MicroPITA.py "+\ |
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142 "--lastmeta " + table_lines[LastMetaInt]+ " " +\ |
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143 "--feature_method " + results.feature_method + " " + \ |
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144 "--target " + TempTargetsFileName + " " +\ |
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145 "-m " + results.MParameter + " " + \ |
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146 "-n " + results.NSamples + " " +\ |
| 0 | 147 stratify_string + " " +\ |
| 148 results.inputname + " " +\ | |
| 149 results.outputname | |
| 150 #print os_command | |
| 151 os.system(os_command) | |
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152 argsx = shlex.split(os_command) #Split the command |
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153 try: |
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154 subprocess.check_call(argsx , shell=False) |
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155 except: |
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156 print "The call to micropita failed=============" |
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157 sys.exit(0) |
| 0 | 158 |
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159 |
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160 |
| 0 | 161 if results.MParameter == "representative"\ |
| 162 or results.MParameter == "diverse"\ | |
| 163 or results.MParameter == "extreme": | |
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164 os_command = "python " + \ |
| 4 | 165 root_dir + \ |
| 8 | 166 "/MicroPITA.py "+\ |
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167 "--lastmeta " + table_lines[LastMetaInt]+ " " +\ |
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168 "-m " + results.MParameter + " " + \ |
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169 "-n " + results.NSamples + " " +\ |
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170 stratify_string + " " + \ |
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171 results.inputname + " " +\ |
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172 results.outputname |
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173 argsx = shlex.split(os_command) #Split the command |
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174 try: |
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175 ###os.system(os_command) |
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176 subprocess.check_call(argsx , shell=False) |
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177 except: |
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178 print "The call to micropita failed=============" |
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179 sys.exit(0) |
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180 |
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181 |
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182 |
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183 |
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184 if results.MParameter == "distinct"\ |
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185 or results.MParameter == "discriminant": |
| 0 | 186 os_command = "python " + \ |
| 4 | 187 root_dir + \ |
| 8 | 188 "/MicroPITA.py "+\ |
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189 "--lastmeta " + table_lines[LastMetaInt]+ " " +\ |
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190 "--label " + table_lines[LastMetaInt]+ " " +\ |
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191 "-m " + results.MParameter + " " + \ |
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192 "-n " + results.NSamples + " " +\ |
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193 stratify_string + " " + \ |
| 0 | 194 results.inputname + " " +\ |
| 195 results.outputname | |
| 196 #print os_command | |
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197 argsx = shlex.split(os_command) #Split the command |
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198 try: |
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199 subprocess.check_call(argsx , shell=False) |
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200 except: |
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201 print "The call to micropita failed=============" |
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202 sys.exit(0) |