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1 def __inputArguments():
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2
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3 import argparse
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4 parser = argparse.ArgumentParser()
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5
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6 parser.add_argument("--method", nargs='?',default ='pls',help="Name of the method on which model will build; \
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7 Available Methods are:- pls, glm , glmboost ")
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8 parser.add_argument("rdata",help="Descriptor file for model building")
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9 parser.add_argument("--getdatainfoeval",nargs='?',default='TRUE',help="Validation of the data ")
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10 parser.add_argument("--getdatainfoecho",nargs='?',default='FALSE',help="print on consol about Validity of the data ")
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11 parser.add_argument("--getdatainforesult",nargs='?',default='hide',help="print in output file about Validity of the data ")
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12 parser.add_argument("--missingfiltereval",nargs='?',default='FALSE',help="Processing step :: removal of missing value ")
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13 parser.add_argument("--missingfilterecho",nargs='?',default='FALSE',help="print Processing step :: removal of missing value ")
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14 parser.add_argument("--missingfilterresult",nargs='?',default='hide',help="print in output file about Processing step :: removal of missing value ")
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15 parser.add_argument("--missingfilterthreshc",nargs='?',default=0.20,type=float,help="info about highly missing column data")
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16 parser.add_argument("--missingfilterthreshr",nargs='?',default=0.20,type=float,help="info about highly missing row number")
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17 parser.add_argument("--pcaeval",nargs='?',default='FALSE',help="PCA of data ")
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18 parser.add_argument("--pcaecho",nargs='?',default='FALSE',help="PCA of data ")
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19 parser.add_argument("--pcaresult",nargs='?',default='hide',help="print in file about PCA of data ")
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20 parser.add_argument("--pcacomp",nargs='?',default=3,type=int,help="Number of PCA componant will be plotted ")
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21 parser.add_argument("--pcaploteval",nargs='?',default='FALSE',help="PCA plot of data ")
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22 parser.add_argument("--pcaplotecho",nargs='?',default='FALSE',help="print PCA plot of data ")
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23 parser.add_argument("--pcaplotresult",nargs='?',default='hide',help="write in output file about PCA plot of data")
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24 parser.add_argument("--pcaplotfig",nargs='?',default='TRUE',help="make figure file for integration in output file")
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25 parser.add_argument("--initialdataspliteval",nargs='?',default='TRUE',help="data splitting in test and train set ")
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26 parser.add_argument("--initialdatasplitecho",nargs='?',default='FALSE',help="print about data splitting in test and train set")
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27 parser.add_argument("--initialdatasplitresult",nargs='?',default='hide',help="write in outputfile about data splitting in test and train set")
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28 parser.add_argument("--percent",nargs='?',default=0.8,type=float,help="percent value at which data splitting is done")
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29 parser.add_argument("--nzveval",nargs='?',default='FALSE',help="remove near zero values")
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30 parser.add_argument("--nzvresult",nargs='?',default='hide',help="write in outputfile about removing near zero values")
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31 parser.add_argument("--nzvecho",nargs='?',default='FALSE',help="print about removing near zero values")
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32 parser.add_argument("--corrfiltereval",nargs='?',default='FALSE',help="remove higly correlated values")
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33 parser.add_argument("--corrfilterresult",nargs='?',default='hide',help="write in outputfile about removing highly correlated values")
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34 parser.add_argument("--corrfilterecho",nargs='?',default='FALSE',help="print about removing correlated values")
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35 parser.add_argument("--threshholdcor",nargs='?',default=0.75,type=float,help="percent value at which correlated values ommitted ")
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36 parser.add_argument("--preproceval",nargs='?',default='FALSE',help="pre proccesing")
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37 parser.add_argument("--preprocecho",nargs='?',default='FALSE',help="print about pre proccesing")
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38 parser.add_argument("--preprocresult",nargs='?',default='hide',help="write in output file about pre proccesing")
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39 parser.add_argument("--setupworkersecho",nargs='?',default='FALSE',help="print about number of processors")
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40 parser.add_argument("--setupworkersresult",nargs='?',default='tex',help="write about number of processors in output file")
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41 parser.add_argument("--numworkers",nargs='?',default=1,type=int,help="defines used processors")
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42 parser.add_argument("--setupresamplingecho",nargs='?',default='FALSE',help="print resampling rules")
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43 parser.add_argument("--setupresamplingresult",nargs='?',default='hide',help="write resampling rules in output file")
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44 parser.add_argument("--resamplenumber",nargs='?',default=10,type=int,help="set number of resampling")
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45 parser.add_argument("--resamplenumberpercent",nargs='?',default=0.75,type=float,help="set PERCENT resampling")
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46 parser.add_argument("--setupgridresult",nargs='?',default='hide',help="write about number of grids in output file")
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47 parser.add_argument("--setupgridecho",nargs='?',default='FALSE',help="print about number of grids")
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48 parser.add_argument("--setupgridsize",nargs='?',default=3,type=int,help="set number of grids")
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49 parser.add_argument("--fitmodelresult",nargs='?',default='hide',help="write about model")
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50 parser.add_argument("--fitmodelecho",nargs='?',default='FALSE',help="print about model")
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51 parser.add_argument("--fitmodeleval",nargs='?',default='TRUE',help="start model building")
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52 parser.add_argument("--modeldescrecho",nargs='?',default='FALSE',help="print model description")
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53 parser.add_argument("--modeldescrresult",nargs='?',default='hide',help="write model description in outout file")
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54 parser.add_argument("--resamptableecho",nargs='?',default='FALSE',help="print resample table")
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55 parser.add_argument("--resamptableresult",nargs='?',default='tex',help="write resample table in output file")
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56 parser.add_argument("--profileplotecho",nargs='?',default='FALSE',help="print about profile plots")
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57 parser.add_argument("--profileplotfig",nargs='?',default='TRUE',help=" profile plots")
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58 parser.add_argument("--stopworkersecho",nargs='?',default='FALSE',help="stop workers ie processors")
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59 parser.add_argument("--stopworkersresult",nargs='?',default='hide',help="write about workers ie processors used")
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60 parser.add_argument("--testpredresult",nargs='?',default='tex',help="write about statistical measure")
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61 parser.add_argument("--testpredecho",nargs='?',default='FALSE',help="print about statistical measure")
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62 parser.add_argument("--classprobstexresult",nargs='?',default='tex',help="paste various figure of statistical measure in outputfile")
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63 parser.add_argument("--classprobstexecho",nargs='?',default='FALSE',help="print various figure of statistical measure")
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64 parser.add_argument("--savedataecho",nargs='?',default='FALSE',help="information about completion of model building ")
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65 parser.add_argument("--savedataresult",nargs='?',default='hide',help="write information about completion of model building in outputfile ")
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66 parser.add_argument("--outputmodel", help="give name for the generated model")
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67 parser.add_argument("--outputresultpdf", help="give name for the output pdf file")
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68
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69 args = parser.parse_args()
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70 return args
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71
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72 def generateRnwScript():
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73
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74 import templateLibrary
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75 t = templateLibrary.__template4Rnw()
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76
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77 from string import Template
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78 s = Template(t)
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79
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80 args = __inputArguments()
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81
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82 templt = s.safe_substitute(METHOD=args.method,
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83 RDATA=args.rdata,
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84 GETDATAINFOEVAL=args.getdatainfoeval,
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85 GETDATAINFOECHO=args.getdatainfoecho,
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86 GETDATAINFORESULT=args.getdatainforesult,
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87 MISSINGFILTEREVAL=args.missingfiltereval,
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88 MISSINGFILTERECHO=args.missingfilterecho,
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89 MISSINGFILTERRESULT=args.missingfilterresult,
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90 MISSINGFILTERTHRESHC=args.missingfilterthreshc,
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91 MISSINGFILTERTHRESHR=args.missingfilterthreshr,
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92 PCAEVAL=args.pcaeval,
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93 PCAECHO=args.pcaecho,
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94 PCARESULT=args.pcaresult,
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95 PCACOMP=args.pcacomp,
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96 PCAPLOTEVAL=args.pcaploteval,
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97 PCAPLOTECHO=args.pcaplotecho,
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98 PCAPLOTRESULT=args.pcaplotresult,
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99 PCAPLOTFIG=args.pcaplotfig,
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100 INITIALDATASPLITEVAL=args.initialdataspliteval,
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101 INITIALDATASPLITECHO=args.initialdatasplitecho,
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102 INITIALDATASPLITRESULT=args.initialdatasplitresult,
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103 PERCENT=args.percent,
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104 NZVEVAL=args.nzveval,
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105 NZVRESULT=args.nzvresult,
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106 NZVECHO=args.nzvecho,
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107 CORRFILTEREVAL=args.corrfiltereval,
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108 CORRFILTERRESULT=args.corrfilterresult,
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109 CORRFILTERECHO=args.corrfilterecho,
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110 THRESHHOLDCOR=args.threshholdcor,
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111 PREPROCEVAL=args.preproceval,
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112 PREPROCECHO=args.preprocecho,
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113 PREPROCRESULT=args.preprocresult,
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114 SETUPWORKERSECHO=args.setupworkersecho,
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115 SETUPWORKERSRESULT=args.setupworkersresult,
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116 NUMWORKERS=args.numworkers,
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117 SETUPRESAMPLINGECHO=args.setupresamplingecho,
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118 SETUPRESAMPLINGRESULT=args.setupresamplingresult,
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119 RESAMPLENUMBER=args.resamplenumber,
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120 RESAMPLENUMBERPERCENT=args.resamplenumberpercent,
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121 SETUPGRIDRESULT=args.setupgridresult,
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122 SETUPGRIDECHO=args.setupgridecho,
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123 SETUPGRIDSIZE=args.setupgridsize,
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124 FITMODELRESULT=args.fitmodelresult,
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125 FITMODELECHO=args.fitmodelecho,
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126 FITMODELEVAL=args.fitmodeleval,
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127 MODELDESCRECHO=args.modeldescrecho,
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128 MODELDESCRRESULT=args.modeldescrresult,
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129 RESAMPTABLEECHO=args.resamptableecho,
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130 RESAMPTABLERESULT=args.resamptableresult,
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131 PROFILEPLOTECHO=args.profileplotecho,
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132 PROFILEPLOTFIG=args.profileplotfig,
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133 STOPWORKERSECHO=args.stopworkersecho,
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134 STOPWORKERSRESULT=args.stopworkersresult,
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135 TESTPREDRESULT=args.testpredresult,
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136 TESTPREDECHO=args.testpredecho,
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137 CLASSPROBSTEXRESULT=args.classprobstexresult,
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138 CLASSPROBSTEXECHO=args.classprobstexecho,
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139 SAVEDATAECHO=args.savedataecho,
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140 SAVEDATARESULT=args.savedataresult )
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141
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142
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143 f = open('result-doc.Rnw','w')
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144 f.write(templt)
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145 f.close()
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146
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147 def modelBuilding():
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148
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149 import os
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150 os.system('R CMD Sweave result-doc.Rnw > cmd.log.1 2>&1')
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151 os.system('pdflatex result-doc.tex > cmd.log.2 2>&1')
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152 os.system('pdflatex result-doc.tex > cmd.log.2 2>&1')
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153 # os.system('pdflatex result-doc.tex 2>&1 | tee cmd.log.2')
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154 args = __inputArguments()
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155
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156 from string import Template
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157 s1 = Template('cp $METHOD-Fit.RData $OUTPUTMODEL')
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158 s2 = Template('cp result-doc.pdf $OUTPUTRESULTPDF')
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159
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160 cmd1 = s1.safe_substitute(METHOD=args.method, OUTPUTMODEL=args.outputmodel)
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161 cmd2 = s2.safe_substitute(OUTPUTRESULTPDF=args.outputresultpdf)
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162
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163 os.system(cmd1)
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164 os.system(cmd2)
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165
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166
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167 if __name__ == "__main__" :
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168
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169 generateRnwScript()
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170 modelBuilding()
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