Mercurial > repos > deepakjadmin > caret_reg_tool2

comparison modelBuilding.py @ 0:b82c88293260 draft

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author deepakjadmin
date Fri, 22 Jan 2016 14:16:12 -0500
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-1:000000000000 0:b82c88293260
1 def __inputArguments():
2
3 import argparse
4 parser = argparse.ArgumentParser()
5
6 parser.add_argument("--method", nargs='?',default ='pls',help="Name of the method on which model will build; \
7 Available Methods are:- pls, glm , glmboost ")
8 parser.add_argument("rdata",help="Descriptor file for model building")
9 parser.add_argument("--getdatainfoeval",nargs='?',default='TRUE',help="Validation of the data ")
10 parser.add_argument("--getdatainfoecho",nargs='?',default='FALSE',help="print on consol about Validity of the data ")
11 parser.add_argument("--getdatainforesult",nargs='?',default='hide',help="print in output file about Validity of the data ")
12 parser.add_argument("--missingfiltereval",nargs='?',default='FALSE',help="Processing step :: removal of missing value ")
13 parser.add_argument("--missingfilterecho",nargs='?',default='FALSE',help="print Processing step :: removal of missing value ")
14 parser.add_argument("--missingfilterresult",nargs='?',default='hide',help="print in output file about Processing step :: removal of missing value ")
15 parser.add_argument("--missingfilterthreshc",nargs='?',default=0.20,type=float,help="info about highly missing column data")
16 parser.add_argument("--missingfilterthreshr",nargs='?',default=0.20,type=float,help="info about highly missing row number")
17 parser.add_argument("--pcaeval",nargs='?',default='FALSE',help="PCA of data ")
18 parser.add_argument("--pcaecho",nargs='?',default='FALSE',help="PCA of data ")
19 parser.add_argument("--pcaresult",nargs='?',default='hide',help="print in file about PCA of data ")
20 parser.add_argument("--pcacomp",nargs='?',default=3,type=int,help="Number of PCA componant will be plotted ")
21 parser.add_argument("--pcaploteval",nargs='?',default='FALSE',help="PCA plot of data ")
22 parser.add_argument("--pcaplotecho",nargs='?',default='FALSE',help="print PCA plot of data ")
23 parser.add_argument("--pcaplotresult",nargs='?',default='hide',help="write in output file about PCA plot of data")
24 parser.add_argument("--pcaplotfig",nargs='?',default='TRUE',help="make figure file for integration in output file")
25 parser.add_argument("--initialdataspliteval",nargs='?',default='TRUE',help="data splitting in test and train set ")
26 parser.add_argument("--initialdatasplitecho",nargs='?',default='FALSE',help="print about data splitting in test and train set")
27 parser.add_argument("--initialdatasplitresult",nargs='?',default='hide',help="write in outputfile about data splitting in test and train set")
28 parser.add_argument("--percent",nargs='?',default=0.8,type=float,help="percent value at which data splitting is done")
29 parser.add_argument("--nzveval",nargs='?',default='FALSE',help="remove near zero values")
30 parser.add_argument("--nzvresult",nargs='?',default='hide',help="write in outputfile about removing near zero values")
31 parser.add_argument("--nzvecho",nargs='?',default='FALSE',help="print about removing near zero values")
32 parser.add_argument("--corrfiltereval",nargs='?',default='FALSE',help="remove higly correlated values")
33 parser.add_argument("--corrfilterresult",nargs='?',default='hide',help="write in outputfile about removing highly correlated values")
34 parser.add_argument("--corrfilterecho",nargs='?',default='FALSE',help="print about removing correlated values")
35 parser.add_argument("--threshholdcor",nargs='?',default=0.75,type=float,help="percent value at which correlated values ommitted ")
36 parser.add_argument("--preproceval",nargs='?',default='FALSE',help="pre proccesing")
37 parser.add_argument("--preprocecho",nargs='?',default='FALSE',help="print about pre proccesing")
38 parser.add_argument("--preprocresult",nargs='?',default='hide',help="write in output file about pre proccesing")
39 parser.add_argument("--setupworkersecho",nargs='?',default='FALSE',help="print about number of processors")
40 parser.add_argument("--setupworkersresult",nargs='?',default='tex',help="write about number of processors in output file")
41 parser.add_argument("--numworkers",nargs='?',default=1,type=int,help="defines used processors")
42 parser.add_argument("--setupresamplingecho",nargs='?',default='FALSE',help="print resampling rules")
43 parser.add_argument("--setupresamplingresult",nargs='?',default='hide',help="write resampling rules in output file")
44 parser.add_argument("--resamplenumber",nargs='?',default=10,type=int,help="set number of resampling")
45 parser.add_argument("--resamplenumberpercent",nargs='?',default=0.75,type=float,help="set PERCENT resampling")
46 parser.add_argument("--setupgridresult",nargs='?',default='hide',help="write about number of grids in output file")
47 parser.add_argument("--setupgridecho",nargs='?',default='FALSE',help="print about number of grids")
48 parser.add_argument("--setupgridsize",nargs='?',default=3,type=int,help="set number of grids")
49 parser.add_argument("--fitmodelresult",nargs='?',default='hide',help="write about model")
50 parser.add_argument("--fitmodelecho",nargs='?',default='FALSE',help="print about model")
51 parser.add_argument("--fitmodeleval",nargs='?',default='TRUE',help="start model building")
52 parser.add_argument("--modeldescrecho",nargs='?',default='FALSE',help="print model description")
53 parser.add_argument("--modeldescrresult",nargs='?',default='hide',help="write model description in outout file")
54 parser.add_argument("--resamptableecho",nargs='?',default='FALSE',help="print resample table")
55 parser.add_argument("--resamptableresult",nargs='?',default='tex',help="write resample table in output file")
56 parser.add_argument("--profileplotecho",nargs='?',default='FALSE',help="print about profile plots")
57 parser.add_argument("--profileplotfig",nargs='?',default='TRUE',help=" profile plots")
58 parser.add_argument("--stopworkersecho",nargs='?',default='FALSE',help="stop workers ie processors")
59 parser.add_argument("--stopworkersresult",nargs='?',default='hide',help="write about workers ie processors used")
60 parser.add_argument("--testpredresult",nargs='?',default='tex',help="write about statistical measure")
61 parser.add_argument("--testpredecho",nargs='?',default='FALSE',help="print about statistical measure")
62 parser.add_argument("--classprobstexresult",nargs='?',default='tex',help="paste various figure of statistical measure in outputfile")
63 parser.add_argument("--classprobstexecho",nargs='?',default='FALSE',help="print various figure of statistical measure")
64 parser.add_argument("--savedataecho",nargs='?',default='FALSE',help="information about completion of model building ")
65 parser.add_argument("--savedataresult",nargs='?',default='hide',help="write information about completion of model building in outputfile ")
66 parser.add_argument("--outputmodel", help="give name for the generated model")
67 parser.add_argument("--outputresultpdf", help="give name for the output pdf file")
68
69 args = parser.parse_args()
70 return args
71
72 def generateRnwScript():
73
74 import templateLibrary
75 t = templateLibrary.__template4Rnw()
76
77 from string import Template
78 s = Template(t)
79
80 args = __inputArguments()
81
82 templt = s.safe_substitute(METHOD=args.method,
83 RDATA=args.rdata,
84 GETDATAINFOEVAL=args.getdatainfoeval,
85 GETDATAINFOECHO=args.getdatainfoecho,
86 GETDATAINFORESULT=args.getdatainforesult,
87 MISSINGFILTEREVAL=args.missingfiltereval,
88 MISSINGFILTERECHO=args.missingfilterecho,
89 MISSINGFILTERRESULT=args.missingfilterresult,
90 MISSINGFILTERTHRESHC=args.missingfilterthreshc,
91 MISSINGFILTERTHRESHR=args.missingfilterthreshr,
92 PCAEVAL=args.pcaeval,
93 PCAECHO=args.pcaecho,
94 PCARESULT=args.pcaresult,
95 PCACOMP=args.pcacomp,
96 PCAPLOTEVAL=args.pcaploteval,
97 PCAPLOTECHO=args.pcaplotecho,
98 PCAPLOTRESULT=args.pcaplotresult,
99 PCAPLOTFIG=args.pcaplotfig,
100 INITIALDATASPLITEVAL=args.initialdataspliteval,
101 INITIALDATASPLITECHO=args.initialdatasplitecho,
102 INITIALDATASPLITRESULT=args.initialdatasplitresult,
103 PERCENT=args.percent,
104 NZVEVAL=args.nzveval,
105 NZVRESULT=args.nzvresult,
106 NZVECHO=args.nzvecho,
107 CORRFILTEREVAL=args.corrfiltereval,
108 CORRFILTERRESULT=args.corrfilterresult,
109 CORRFILTERECHO=args.corrfilterecho,
110 THRESHHOLDCOR=args.threshholdcor,
111 PREPROCEVAL=args.preproceval,
112 PREPROCECHO=args.preprocecho,
113 PREPROCRESULT=args.preprocresult,
114 SETUPWORKERSECHO=args.setupworkersecho,
115 SETUPWORKERSRESULT=args.setupworkersresult,
116 NUMWORKERS=args.numworkers,
117 SETUPRESAMPLINGECHO=args.setupresamplingecho,
118 SETUPRESAMPLINGRESULT=args.setupresamplingresult,
119 RESAMPLENUMBER=args.resamplenumber,
120 RESAMPLENUMBERPERCENT=args.resamplenumberpercent,
121 SETUPGRIDRESULT=args.setupgridresult,
122 SETUPGRIDECHO=args.setupgridecho,
123 SETUPGRIDSIZE=args.setupgridsize,
124 FITMODELRESULT=args.fitmodelresult,
125 FITMODELECHO=args.fitmodelecho,
126 FITMODELEVAL=args.fitmodeleval,
127 MODELDESCRECHO=args.modeldescrecho,
128 MODELDESCRRESULT=args.modeldescrresult,
129 RESAMPTABLEECHO=args.resamptableecho,
130 RESAMPTABLERESULT=args.resamptableresult,
131 PROFILEPLOTECHO=args.profileplotecho,
132 PROFILEPLOTFIG=args.profileplotfig,
133 STOPWORKERSECHO=args.stopworkersecho,
134 STOPWORKERSRESULT=args.stopworkersresult,
135 TESTPREDRESULT=args.testpredresult,
136 TESTPREDECHO=args.testpredecho,
137 CLASSPROBSTEXRESULT=args.classprobstexresult,
138 CLASSPROBSTEXECHO=args.classprobstexecho,
139 SAVEDATAECHO=args.savedataecho,
140 SAVEDATARESULT=args.savedataresult )
141
142
143 f = open('result-doc.Rnw','w')
144 f.write(templt)
145 f.close()
146
147 def modelBuilding():
148
149 import os
150 os.system('R CMD Sweave result-doc.Rnw > cmd.log.1 2>&1')
151 os.system('pdflatex result-doc.tex > cmd.log.2 2>&1')
152 os.system('pdflatex result-doc.tex > cmd.log.2 2>&1')
153 # os.system('pdflatex result-doc.tex 2>&1 | tee cmd.log.2')
154 args = __inputArguments()
155
156 from string import Template
157 s1 = Template('cp $METHOD-Fit.RData $OUTPUTMODEL')
158 s2 = Template('cp result-doc.pdf $OUTPUTRESULTPDF')
159
160 cmd1 = s1.safe_substitute(METHOD=args.method, OUTPUTMODEL=args.outputmodel)
161 cmd2 = s2.safe_substitute(OUTPUTRESULTPDF=args.outputresultpdf)
162
163 os.system(cmd1)
164 os.system(cmd2)
165
166
167 if __name__ == "__main__" :
168
169 generateRnwScript()
170 modelBuilding()