Carlos-Francisco Méndez-Cruz / lcg-bioinfoI-bionlp

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Carlos-Francisco Méndez-Cruz
2d7bab8b 1 parent 37f5d386

Training and testing binding thrombin dataset

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...@@ -33,18 +33,18 @@ __author__ = 'CMendezC' ...@@ -33,18 +33,18 @@ __author__ = 'CMendezC'
33 # Execution: 33 # Execution:
34 34
35 # python training-validation-binding-thrombin.py 35 # python training-validation-binding-thrombin.py
36 -# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/binding-thrombin-dataset 36 +# --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset
37 # --inputTrainingData thrombin.data 37 # --inputTrainingData thrombin.data
38 # --inputTestingData Thrombin.testset 38 # --inputTestingData Thrombin.testset
39 # --inputTestingClasses Thrombin.testset.class 39 # --inputTestingClasses Thrombin.testset.class
40 -# --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/binding-thrombin-dataset/models 40 +# --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models
41 # --outputModelFile SVM-model.mod 41 # --outputModelFile SVM-model.mod
42 -# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/binding-thrombin-dataset/reports 42 +# --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports
43 # --outputReportFile SVM.txt 43 # --outputReportFile SVM.txt
44 # --classifier SVM 44 # --classifier SVM
45 45
46 # source activate python3 46 # source activate python3
47 -# python training-validation-binding-thrombin.py --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/binding-thrombin-dataset/models --outputModelFile SVM-model.mod --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/binding-thrombin-dataset/reports --outputReportFile SVM.txt --classifier SVM 47 +# python training-validation-binding-thrombin.py --inputPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset --inputTrainingData thrombin.data --inputTestingData Thrombin.testset --inputTestingClasses Thrombin.testset.class --outputModelPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/models --outputModelFile SVM-model.mod --outputReportPath /home/compu2/bionlp/lcg-bioinfoI-bionlp/clasificacion-automatica/binding-thrombin-dataset/reports --outputReportFile SVM.txt --classifier SVM
48 48
49 ########################################################### 49 ###########################################################
50 # MAIN PROGRAM # 50 # MAIN PROGRAM #
...@@ -116,7 +116,7 @@ if __name__ == "__main__": ...@@ -116,7 +116,7 @@ if __name__ == "__main__":
116 for line in iFile: 116 for line in iFile:
117 line = line.strip('\r\n') 117 line = line.strip('\r\n')
118 listLine = line.split(',') 118 listLine = line.split(',')
119 - testingData.append(listLine) 119 + testingData.append(listLine[1:])
120 testingMatrix = csr_matrix(testingData, dtype='double') 120 testingMatrix = csr_matrix(testingData, dtype='double')
121 with open(os.path.join(args.inputPath, args.inputTestingClasses), encoding='utf8', mode='r') \ 121 with open(os.path.join(args.inputPath, args.inputTestingClasses), encoding='utf8', mode='r') \
122 as iFile: 122 as iFile:
......