|
0
|
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("--saampling",nargs='?',default="garBage",help="Perform sampling from data")
|
|
|
29 parser.add_argument("--percent",nargs='?',default=0.8,type=float,help="percent value at which data splitting is done")
|
|
|
30 parser.add_argument("--nzveval",nargs='?',default='FALSE',help="remove near zero values")
|
|
|
31 parser.add_argument("--nzvresult",nargs='?',default='hide',help="write in outputfile about removing near zero values")
|
|
|
32 parser.add_argument("--nzvecho",nargs='?',default='FALSE',help="print about removing near zero values")
|
|
|
33 parser.add_argument("--corrfiltereval",nargs='?',default='FALSE',help="remove higly correlated values")
|
|
|
34 parser.add_argument("--corrfilterresult",nargs='?',default='hide',help="write in outputfile about removing highly correlated values")
|
|
|
35 parser.add_argument("--corrfilterecho",nargs='?',default='FALSE',help="print about removing correlated values")
|
|
|
36 parser.add_argument("--threshholdcor",nargs='?',default=0.75,type=float,help="percent value at which correlated values ommitted ")
|
|
|
37 parser.add_argument("--preproceval",nargs='?',default='FALSE',help="pre proccesing")
|
|
|
38 parser.add_argument("--preprocecho",nargs='?',default='FALSE',help="print about pre proccesing")
|
|
|
39 parser.add_argument("--preprocresult",nargs='?',default='hide',help="write in output file about pre proccesing")
|
|
|
40 parser.add_argument("--setupworkersecho",nargs='?',default='FALSE',help="print about number of processors")
|
|
|
41 parser.add_argument("--setupworkersresult",nargs='?',default='tex',help="write about number of processors in output file")
|
|
|
42 parser.add_argument("--numworkers",nargs='?',default=1,type=int,help="defines used processors")
|
|
|
43 parser.add_argument("--setupresamplingecho",nargs='?',default='FALSE',help="print resampling rules")
|
|
|
44 parser.add_argument("--setupresamplingresult",nargs='?',default='hide',help="write resampling rules in output file")
|
|
|
45 parser.add_argument("--resampname",nargs='?',default='boot632',help="choose type of resampling")
|
|
|
46 parser.add_argument("--resamplenumber",nargs='?',default=10,type=int,help="set number of resampling")
|
|
|
47 parser.add_argument("--numrepeat",nargs='?',default=3,type=int,help="set times of repeat")
|
|
|
48 parser.add_argument("--resamplenumberpercent",nargs='?',default=0.75,type=float,help="set PERCENT resampling")
|
|
|
49 parser.add_argument("--setupgridresult",nargs='?',default='hide',help="write about number of grids in output file")
|
|
|
50 parser.add_argument("--setupgridecho",nargs='?',default='FALSE',help="print about number of grids")
|
|
|
51 parser.add_argument("--setupgridsize",nargs='?',default=3,type=int,help="set number of grids")
|
|
|
52 parser.add_argument("--fitmodelresult",nargs='?',default='hide',help="write about model")
|
|
|
53 parser.add_argument("--fitmodelecho",nargs='?',default='FALSE',help="print about model")
|
|
|
54 parser.add_argument("--fitmodeleval",nargs='?',default='TRUE',help="start model building")
|
|
|
55 parser.add_argument("--modeldescrecho",nargs='?',default='FALSE',help="print model description")
|
|
|
56 parser.add_argument("--modeldescrresult",nargs='?',default='hide',help="write model description in outout file")
|
|
|
57 parser.add_argument("--resamptableecho",nargs='?',default='FALSE',help="print resample table")
|
|
|
58 parser.add_argument("--resamptableresult",nargs='?',default='tex',help="write resample table in output file")
|
|
|
59 parser.add_argument("--profileplotecho",nargs='?',default='FALSE',help="print about profile plots")
|
|
|
60 parser.add_argument("--profileplotfig",nargs='?',default='TRUE',help=" profile plots")
|
|
|
61 parser.add_argument("--stopworkersecho",nargs='?',default='FALSE',help="stop workers ie processors")
|
|
|
62 parser.add_argument("--stopworkersresult",nargs='?',default='hide',help="write about workers ie processors used")
|
|
|
63 parser.add_argument("--testpredresult",nargs='?',default='tex',help="write about statistical measure")
|
|
|
64 parser.add_argument("--testpredecho",nargs='?',default='FALSE',help="print about statistical measure")
|
|
|
65 parser.add_argument("--classprobstexresult",nargs='?',default='tex',help="paste various figure of statistical measure in outputfile")
|
|
|
66 parser.add_argument("--classprobstexecho",nargs='?',default='FALSE',help="print various figure of statistical measure")
|
|
|
67 parser.add_argument("--classprobstexresult1",nargs='?',default='hide',help="create roc curve in outputfile")
|
|
|
68 parser.add_argument("--classprobstexecho1",nargs='?',default='FALSE',help="print figure of statistical measure")
|
|
|
69 parser.add_argument("--savedataecho",nargs='?',default='FALSE',help="information about completion of model building ")
|
|
|
70 parser.add_argument("--savedataresult",nargs='?',default='hide',help="write information about completion of model building in outputfile ")
|
|
|
71 parser.add_argument("--datasets", help="name of the generated datasets")
|
|
|
72 parser.add_argument("--outputmodel", help="give name for the generated model")
|
|
|
73 parser.add_argument("--outputresultpdf", help="give name for the output pdf file")
|
|
|
74
|
|
|
75 args = parser.parse_args()
|
|
|
76 return args
|
|
|
77
|
|
|
78 def generateRnwScript():
|
|
|
79
|
|
|
80 import templateLibrary
|
|
|
81 t = templateLibrary.__template4Rnw()
|
|
|
82
|
|
|
83 from string import Template
|
|
|
84 s = Template(t)
|
|
|
85
|
|
|
86 args = __inputArguments()
|
|
|
87
|
|
|
88 templt = s.safe_substitute(METHOD=args.method,
|
|
|
89 RDATA=args.rdata,
|
|
|
90 GETDATAINFOEVAL=args.getdatainfoeval,
|
|
|
91 GETDATAINFOECHO=args.getdatainfoecho,
|
|
|
92 GETDATAINFORESULT=args.getdatainforesult,
|
|
|
93 MISSINGFILTEREVAL=args.missingfiltereval,
|
|
|
94 MISSINGFILTERECHO=args.missingfilterecho,
|
|
|
95 MISSINGFILTERRESULT=args.missingfilterresult,
|
|
|
96 MISSINGFILTERTHRESHC=args.missingfilterthreshc,
|
|
|
97 MISSINGFILTERTHRESHR=args.missingfilterthreshr,
|
|
|
98 PCAEVAL=args.pcaeval,
|
|
|
99 PCAECHO=args.pcaecho,
|
|
|
100 PCARESULT=args.pcaresult,
|
|
|
101 PCACOMP=args.pcacomp,
|
|
|
102 PCAPLOTEVAL=args.pcaploteval,
|
|
|
103 PCAPLOTECHO=args.pcaplotecho,
|
|
|
104 PCAPLOTRESULT=args.pcaplotresult,
|
|
|
105 PCAPLOTFIG=args.pcaplotfig,
|
|
|
106 INITIALDATASPLITEVAL=args.initialdataspliteval,
|
|
|
107 INITIALDATASPLITECHO=args.initialdatasplitecho,
|
|
|
108 INITIALDATASPLITRESULT=args.initialdatasplitresult,
|
|
|
109 SAAMPLING=args.saampling,
|
|
|
110 PERCENT=args.percent,
|
|
|
111 NZVEVAL=args.nzveval,
|
|
|
112 NZVRESULT=args.nzvresult,
|
|
|
113 NZVECHO=args.nzvecho,
|
|
|
114 CORRFILTEREVAL=args.corrfiltereval,
|
|
|
115 CORRFILTERRESULT=args.corrfilterresult,
|
|
|
116 CORRFILTERECHO=args.corrfilterecho,
|
|
|
117 THRESHHOLDCOR=args.threshholdcor,
|
|
|
118 PREPROCEVAL=args.preproceval,
|
|
|
119 PREPROCECHO=args.preprocecho,
|
|
|
120 PREPROCRESULT=args.preprocresult,
|
|
|
121 SETUPWORKERSECHO=args.setupworkersecho,
|
|
|
122 SETUPWORKERSRESULT=args.setupworkersresult,
|
|
|
123 NUMWORKERS=args.numworkers,
|
|
|
124 SETUPRESAMPLINGECHO=args.setupresamplingecho,
|
|
|
125 SETUPRESAMPLINGRESULT=args.setupresamplingresult,
|
|
|
126 RESAMPNAME=args.resampname,
|
|
|
127 RESAMPLENUMBER=args.resamplenumber,
|
|
|
128 NUMREPEAT=args.numrepeat,
|
|
|
129 RESAMPLENUMBERPERCENT=args.resamplenumberpercent,
|
|
|
130 SETUPGRIDRESULT=args.setupgridresult,
|
|
|
131 SETUPGRIDECHO=args.setupgridecho,
|
|
|
132 SETUPGRIDSIZE=args.setupgridsize,
|
|
|
133 FITMODELRESULT=args.fitmodelresult,
|
|
|
134 FITMODELECHO=args.fitmodelecho,
|
|
|
135 FITMODELEVAL=args.fitmodeleval,
|
|
|
136 MODELDESCRECHO=args.modeldescrecho,
|
|
|
137 MODELDESCRRESULT=args.modeldescrresult,
|
|
|
138 RESAMPTABLEECHO=args.resamptableecho,
|
|
|
139 RESAMPTABLERESULT=args.resamptableresult,
|
|
|
140 PROFILEPLOTECHO=args.profileplotecho,
|
|
|
141 PROFILEPLOTFIG=args.profileplotfig,
|
|
|
142 STOPWORKERSECHO=args.stopworkersecho,
|
|
|
143 STOPWORKERSRESULT=args.stopworkersresult,
|
|
|
144 TESTPREDRESULT=args.testpredresult,
|
|
|
145 TESTPREDECHO=args.testpredecho,
|
|
|
146 CLASSPROBSTEXRESULT=args.classprobstexresult,
|
|
|
147 CLASSPROBSTEXECHO=args.classprobstexecho,
|
|
|
148 CLASSPROBSTEXRESULT1=args.classprobstexresult1,
|
|
|
149 CLASSPROBSTEXECHO1=args.classprobstexecho1,
|
|
|
150 SAVEDATAECHO=args.savedataecho,
|
|
|
151 SAVEDATARESULT=args.savedataresult )
|
|
|
152
|
|
|
153
|
|
|
154 f = open('result-doc.Rnw','w')
|
|
|
155 f.write(templt)
|
|
|
156 f.close()
|
|
|
157
|
|
|
158 def modelBuilding():
|
|
|
159
|
|
|
160 import os
|
|
|
161 os.system('R CMD Sweave result-doc.Rnw > cmd.log.1 2>&1')
|
|
|
162 os.system('pdflatex result-doc.tex > cmd.log.2 2>&1')
|
|
|
163 os.system('pdflatex result-doc.tex > cmd.log.2 2>&1')
|
|
|
164 # os.system('pdflatex result-doc.tex 2>&1 | tee cmd.log.2')
|
|
|
165 args = __inputArguments()
|
|
|
166
|
|
|
167 from string import Template
|
|
|
168 s1 = Template('cp $METHOD-Fit.RData $OUTPUTMODEL')
|
|
|
169 s2 = Template('cp result-doc.pdf $OUTPUTRESULTPDF')
|
|
|
170 s3 = Template('cp datasets.RData $DATASETS')
|
|
|
171
|
|
|
172 cmd1 = s1.safe_substitute(METHOD=args.method, OUTPUTMODEL=args.outputmodel)
|
|
|
173 cmd2 = s2.safe_substitute(OUTPUTRESULTPDF=args.outputresultpdf)
|
|
|
174 cmd3 = s3.safe_substitute(DATASETS=args.datasets)
|
|
|
175
|
|
|
176 os.system(cmd1)
|
|
|
177 os.system(cmd2)
|
|
|
178 os.system(cmd3)
|
|
|
179
|
|
|
180 if __name__ == "__main__" :
|
|
|
181
|
|
|
182 generateRnwScript()
|
|
|
183 modelBuilding()
|
