Mercurial > repos > jay > pdaug_peptide_length_distribution

annotate PDAUG_ML_Models/PDAUG_ML_Models.py @ 9:dbd0c523c308 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author jay
date Wed, 12 Jan 2022 19:58:29 +0000
parents 3f9bdcf83244
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
2 import numpy as np
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
3 import sys,os
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
4 from scipy import interp
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
5 import pandas as pd
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
6
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
7 ###############################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
8 from sklearn.metrics import *
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
9 from sklearn import preprocessing
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
10 from sklearn.metrics import accuracy_score
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
11 from sklearn.metrics import precision_recall_fscore_support
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
12 from sklearn.metrics import roc_curve, auc
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
13 from sklearn.model_selection import StratifiedKFold
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
14 from sklearn.preprocessing import StandardScaler
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
15 from sklearn.preprocessing import MinMaxScaler
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
16 ###############################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
17 from sklearn.linear_model import LogisticRegression
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
18 from sklearn.naive_bayes import GaussianNB
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
19 from sklearn.neighbors import KNeighborsClassifier
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
20 from sklearn.tree import DecisionTreeClassifier
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
21 from sklearn.svm import SVC
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
22 from sklearn.ensemble import RandomForestClassifier
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
23 from sklearn.linear_model import SGDClassifier
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
24 from sklearn.ensemble import GradientBoostingClassifier
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
25 from sklearn.neural_network import MLPClassifier
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
26 ###############################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
27 from itertools import cycle
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
28 ################################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
29 from sklearn.model_selection import train_test_split
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
30
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
31
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
32
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
33 def ReturnData(TrainFile, TestMethod, TestFile=None):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
34
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
35 if (TestFile == None) and (TestMethod == 'Internal' or 'CrossVal'):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
36
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
37 df = pd.read_csv(TrainFile, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
38 clm_list = df.columns.tolist()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
39 X_train = df[clm_list[0:len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
40 y_train = df[clm_list[len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
41 X_test = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
42 y_test = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
43 return X_train, y_train, X_test, y_test
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
44
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
45 elif (TestFile is not None) and (TestMethod == 'External'):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
46
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
47 df = pd.read_csv(TrainFile, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
48 clm_list = df.columns.tolist()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
49 X_train = df[clm_list[0:len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
50 y_train = df[clm_list[len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
51 df1 = pd.read_csv(TestFile, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
52 clm_list = df1.columns.tolist()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
53 X_test = df1[clm_list[0:len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
54 y_test = df1[clm_list[len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
55 return X_train, y_train, X_test, y_test
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
56
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
57 elif (TestFile is not None) and (TestMethod == 'Predict'):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
58
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
59 df = pd.read_csv(TrainFile, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
60 clm_list = df.columns.tolist()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
61 X_train = df[clm_list[0:len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
62 y_train = df[clm_list[len(clm_list)-1]].values
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
63
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
64 df = pd.read_csv(TestFile, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
65 X_test = df
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
66 y_test = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
67 return X_train, y_train, X_train, y_train
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
68
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
69 def Fit_Model(TrainData, Test_Method, Algo, Selected_Sclaer, Workdirpath, htmlOutDir, OutFile, htmlFname, NoOfFolds=None, TestSize=None, TestData=None ):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
70
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
71 if not os.path.exists(htmlOutDir):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
72 os.makedirs(htmlOutDir)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
73
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
74 if Test_Method == 'Internal':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
75 X,y,_,_ = ReturnData(TrainData, Test_Method)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
76
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
77 mean_tpr = 0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
78 mean_fpr = np.linspace(0, 1, 100)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
79
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
80 specificity_list = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
81 sensitivity_list = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
82 precison_list = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
83 mcc_list = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
84 f1_list = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
85
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
86 folds = StratifiedKFold(n_splits=5)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
87 mean_tpr = 0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
88 mean_fpr = np.linspace(0, 1, 100)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
89
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
90 ##########################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
91 accuracy_score_l = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
92 cohen_kappa_score_l = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
93 matthews_corrcoef_l = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
94 precision_l = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
95 recall_l = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
96 f_score_l = []
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
97 ##########################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
98
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
99 folds = StratifiedKFold(n_splits=5)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
100
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
101 for i, (train, test) in enumerate(folds.split(X, y)):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
102
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
103 if Selected_Sclaer=='Min_Max':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
104 scaler = MinMaxScaler().fit(X[train])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
105 x_train = scaler.transform(X[train])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
106 x_test = scaler.transform(X[test])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
107
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
108 elif Selected_Sclaer=='Standard_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
109 scaler = preprocessing.StandardScaler().fit(X[train])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
110 x_train = scaler.transform(X[train])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
111 x_test = scaler.transform(X[test])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
112
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
113 elif Selected_Sclaer == 'No_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
114 x_train = X[train]
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
115 x_test = X[test]
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
116
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
117 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
118 print('Scalling Method option was not correctly selected...!')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
119
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
120 prob = Algo.fit(x_train, y[train]).predict_proba(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
121 predicted = Algo.fit(x_train, y[train]).predict(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
122
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
123 fpr, tpr, thresholds = roc_curve(y[test], prob[:, 1])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
124 mean_tpr += interp(mean_fpr, fpr, tpr)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
125 mean_tpr[0] = 0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
126
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
127 TN, FP, FN, TP = confusion_matrix(y[test], predicted).ravel()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
128
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
129 accuracy_score_l.append(round(accuracy_score(y[test], predicted),3))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
130 a = precision_recall_fscore_support(y[test], predicted, average='macro')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
131 precision_l.append(round(a[0],3))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
132 recall_l.append(round(a[1],3))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
133 f_score_l .append(round(a[2],3))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
134
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
135 accuracy_score_mean = round(float(sum(accuracy_score_l)/float(len(accuracy_score_l))),3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
136 precision_mean = round(float(sum(precision_l)/float(len(precision_l))),3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
137 recall_mean = round(float(sum(recall_l)/float(len(recall_l))),3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
138 f_score_mean = round(float(sum(f_score_l )/float(len(f_score_l ))),3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
139
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
140
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
141 mean_tpr /= folds.get_n_splits(X, y)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
142 mean_tpr[-1] = 1.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
143 mean_auc = auc(mean_fpr, mean_tpr)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
144
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
145 ########################################################################################################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
146 V_header = ["Algo","accuracy","precision","recall","f1","mean_auc"] #
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
147 v_values = [sys.argv[1], round(accuracy_score_mean, 3), round(precision_mean, 3), round(recall_mean, 3),round(f_score_mean, 3), round(mean_auc, 3)] #
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
148 ########################################################################################################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
149
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
150 df = pd.DataFrame([v_values], columns=V_header)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
151 df.to_csv(os.path.join(Workdirpath, OutFile), columns=V_header, sep='\t', index=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
152
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
153 ############################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
154 from plotly.subplots import make_subplots
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
155 import plotly.graph_objects as go
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
156
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
157 fig = make_subplots(
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
158 rows=1, cols=2,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
159 specs=[[{"type": "xy"}, {"type": "scatter"}],], subplot_titles=("Algorithm performance", " ROC curve (AUC Score = %0.2f" % mean_auc+')'),
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
160
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
161 )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
162
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
163 fig.add_trace( go.Bar(x=V_header[1:], y=v_values[1:],marker_color=['#F58518','#109618','#E45756','#1F77B4','#19D3F3']), row=1, col=1)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
164
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
165 print (mean_fpr, mean_tpr)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
166
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
167 fig.add_trace(go.Scatter(x=mean_fpr, y=mean_tpr), row=1, col=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
168 fig.update_yaxes(title_text="True Positive Rate", range=[0, 1], row=1, col=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
169 fig.update_xaxes(title_text="False Positive Rate", range=[0, 1], row=1, col=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
170 fig.update_yaxes(title_text="Score", range=[0, 1], row=1, col=1)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
171 fig.update_xaxes(title_text="Performance measures",row=1, col=1)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
172 fig.update_layout(height=700, showlegend=False, title="Machine ")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
173 fig.write_html(os.path.join(Workdirpath, htmlOutDir, htmlFname))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
174
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
175 ############################################################
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
176
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
177 elif Test_Method == 'External':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
178
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
179 X_train,y_train,X_test,y_test = ReturnData(TrainData, Test_Method, TestData)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
180
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
181 if Selected_Sclaer=='Min_Max':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
182 scaler = MinMaxScaler().fit(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
183 x_train = scaler.transform(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
184 x_test = scaler.transform(X_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
185
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
186 elif Selected_Sclaer=='Standard_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
187 scaler = preprocessing.StandardScaler().fit(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
188 x_train = scaler.transform(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
189 x_test = scaler.transform(X_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
190
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
191 elif Selected_Sclaer == 'No_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
192 x_train = X_train
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
193 x_test = X_test
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
194
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
195 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
196 print('Scalling Method option was not correctly selected...!')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
197
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
198 prob = Algo.fit(x_train, y_train).predict_proba(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
199 predicted = Algo.fit(x_train, y_train).predict(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
200
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
201 fpr, tpr, thresholds = roc_curve(y_test, prob[:, 1])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
202 TN, FP, FN, TP = confusion_matrix(y_test, predicted).ravel()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
203 accu_score = accuracy_score(y_test, predicted)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
204
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
205 a = precision_recall_fscore_support(y_test, predicted, average='macro')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
206
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
207 pre_score = round(a[0],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
208 recall_score= round(a[1],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
209 f_score= round(a[2],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
210
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
211 pl.plot(fpr, tpr, '--', lw=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
212 auc_score = auc(fpr, tpr)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
213
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
214 a = precision_recall_fscore_support(y_test, predicted, average='macro')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
215 pre_score = round(a[0],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
216 rec_score = round(a[1],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
217 f_score = round(a[2],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
218
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
219 V_header = ["accuracy","presision","recall","f1","mean_auc"]
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
220 v_values = [accu_score, pre_score, rec_score, f_score, auc_score]
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
221
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
222 pl.figure()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
223 pl.plot(fpr, tpr, '-', color='red',label='AUC = %0.2f' % auc_score, lw=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
224 pl.xlim([0.0, 1.0])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
225 pl.ylim([0.0, 1.05])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
226 pl.xlabel('False Positive Rate')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
227 pl.ylabel('True Positive Rate')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
228 pl.title('ROC Cureve')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
229 pl.legend(loc="lower right")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
230
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
231 df = pd.DataFrame([v_values], columns=V_header)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
232 pl.savefig(os.path.join(Workdirpath, htmlOutDir, "out.png"))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
233 df.to_csv(os.path.join(Workdirpath, OutFile), columns=V_header, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
234 pl.figure()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
235 pl.bar(V_header, v_values, color=(0.2, 0.4, 0.6, 0.6))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
236 pl.xlabel('Accuracy Perameters', fontweight='bold', color = 'orange', fontsize='17', horizontalalignment='center')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
237 pl.savefig(os.path.join(Workdirpath, htmlOutDir, "2.png"))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
238 #pl.show()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
239 HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
240
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
241 elif Test_Method == "TestSplit":
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
242
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
243 X_train,y_train,_,_ = ReturnData(TrainData, Test_Method)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
244 X_train, X_test, y_train, y_test = train_test_split(X_train, y_train, test_size=float(TestSize), random_state=0)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
245
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
246
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
247 if Selected_Sclaer=='Min_Max':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
248 scaler = MinMaxScaler().fit(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
249 x_train = scaler.transform(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
250 x_test = scaler.transform(X_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
251
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
252 elif Selected_Sclaer=='Standard_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
253 scaler = preprocessing.StandardScaler().fit(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
254 x_train = scaler.transform(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
255 x_test = scaler.transform(X_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
256
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
257 elif Selected_Sclaer == 'No_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
258 x_train = X_train
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
259 x_test = X_test
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
260
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
261 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
262 print('Scalling Method option was not correctly selected...!')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
263
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
264 prob = Algo.fit(x_train, y_train).predict_proba(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
265 predicted = Algo.fit(x_train, y_train).predict(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
266 fpr, tpr, thresholds = roc_curve(y_test, prob[:, 1])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
267 accu_score = accuracy_score(y_test, predicted)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
268
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
269 a = precision_recall_fscore_support(y_test, predicted, average='macro')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
270
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
271 pre_score = round(a[0],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
272 recall_score= round(a[1],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
273 f_score= round(a[2],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
274
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
275 pl.plot(fpr, tpr, '-', color='red',label='AUC = %0.2f' % accu_score, lw=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
276
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
277 pl.xlim([0.0, 1.0])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
278 pl.ylim([0.0, 1.05])
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
279 pl.xlabel('False Positive Rate')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
280 pl.ylabel('True Positive Rate')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
281 pl.title('ROC Cureve')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
282 pl.legend(loc="lower right")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
283 pl.savefig(os.path.join(Workdirpath, htmlOutDir, "out.png"))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
284 pl.plot(fpr, tpr, '--', lw=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
285
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
286 auc_score = auc(fpr, tpr)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
287
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
288 a = precision_recall_fscore_support(y_test, predicted, average='macro')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
289 pre_score = round(a[0],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
290 rec_score = round(a[1],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
291 f_score = round(a[2],3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
292
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
293 V_header = ["accuracy","presision","recall","f1","mean_auc"]
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
294 v_values = [accu_score, pre_score, rec_score, f_score, auc_score]
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
295 df = pd.DataFrame([v_values], columns=V_header)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
296 df.to_csv(os.path.join(Workdirpath, OutFile), columns=V_header, sep='\t')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
297 pl.figure()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
298 pl.bar(V_header, v_values, color=(0.2, 0.4, 0.6, 0.6))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
299 pl.xlabel('Accuracy Perameters', fontweight='bold', color = 'orange', fontsize='17', horizontalalignment='center')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
300 pl.savefig(os.path.join(Workdirpath, htmlOutDir, "2.png"))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
301 #pl.show()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
302 HTML_Gen(os.path.join(Workdirpath, htmlOutDir, htmlFname))
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
303
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
304 elif Test_Method == "Predict":
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
305
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
306 X_train, y_train, X_test, _ = ReturnData(TrainData, Test_Method,TestData)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
307
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
308 if Selected_Sclaer=='Min_Max':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
309 scaler = MinMaxScaler().fit(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
310 x_train = scaler.transform(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
311 x_test = scaler.transform(X_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
312
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
313 elif Selected_Sclaer=='Standard_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
314 scaler = preprocessing.StandardScaler().fit(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
315 x_train = scaler.transform(X_train)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
316 x_test = scaler.transform(X_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
317
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
318 elif Selected_Sclaer == 'No_Scaler':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
319 x_train = X_train
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
320 x_test = X_test
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
321
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
322 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
323 print('Scalling Method option was not correctly selected...!')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
324
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
325 predicted = model.fit(x_train, y_train).predict(x_test)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
326
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
327
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
328 return predicted
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
329
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
330 def SVM_Classifier(C, kernel, degree, gamma, coef0, shrinking, probability, tol, cache_size, verbose, max_iter, decision_function_shape, randomState, breakties, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
331
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
332 if randomState == None:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
333 randomState =None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
334 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
335 randomState = int(randomState)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
336
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
337
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
338 if cache_size == None:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
339 cache_size =None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
340 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
341 cache_size = float(cache_size)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
342
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
343
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
344 if probability or shrinking == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
345 probability, shrinking = True, True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
346 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
347 probability, shrinking = False, False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
348
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
349
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
350 if verbose == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
351 verbose = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
352 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
353 verbose = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
354
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
355
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
356 if breakties == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
357 breakties = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
358 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
359 breakties = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
360
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
361
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
362
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
363
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
364 pera={
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
365
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
366 'C':float(C),
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
367 'kernel':kernel,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
368 'degree':int(degree), #3
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
369 'gamma':gamma, #default=scale
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
370 'coef0':float(coef0), #default=0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
371 'shrinking':shrinking, #P
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
372 'probability':probability,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
373 'tol':float(tol), #default=1e-3
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
374 'cache_size':cache_size,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
375 'verbose':verbose,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
376 'max_iter':int(max_iter),#default=-1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
377 'decision_function_shape':decision_function_shape,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
378 'random_state':randomState,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
379 'break_ties':breakties
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
380 }
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
381
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
382
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
383 model = SVC(**pera )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
384
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
385 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
386
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
387
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
388 def SGD_Classifier( loss, penalty, alpha, l1_ratio, fit_intercept, max_iter, tol, shuffle, verbose, epsilon, n_jobs, random_state, learning_rate, eta0, power_t, early_stopping, validation_fraction, n_iter_no_change, warm_start, average, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
389
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
390 if n_jobs == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
391 n_jobs =None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
392 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
393 n_jobs = int(n_jobs)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
394
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
395 if random_state == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
396 random_state =None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
397 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
398 random_state = int(random_state)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
399
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
400 if fit_intercept == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
401 fit_intercept = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
402 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
403 fit_intercept = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
404
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
405 if shuffle == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
406 shuffle = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
407 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
408 shuffle = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
409
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
410 if early_stopping == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
411 early_stopping = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
412 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
413 early_stopping = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
414
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
415 if warm_start == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
416 warm_start = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
417 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
418 warm_start = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
419
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
420 if average == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
421 average = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
422 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
423 average = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
424
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
425 pera = {"loss":loss,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
426 "penalty":penalty,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
427 "alpha":float(alpha),#0.0001
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
428 "l1_ratio":float(l1_ratio),#0.15
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
429 "fit_intercept":fit_intercept,#true
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
430 "max_iter":int(max_iter),#default=1000
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
431 "tol":float(tol),#default=1e-3
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
432 "shuffle":shuffle,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
433 "verbose":int(verbose), #default=0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
434 "epsilon":float(epsilon), #default=0.1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
435 "n_jobs":n_jobs, #default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
436 "random_state":random_state, #default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
437 "learning_rate":learning_rate,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
438 "eta0":float(eta0), #default=0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
439 "power_t":float(power_t), #default=0.5
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
440 "early_stopping":early_stopping,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
441 "validation_fraction":float(validation_fraction), #default=0.1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
442 "n_iter_no_change":int(n_iter_no_change), #default=5
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
443 "warm_start":warm_start,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
444 "average":average}
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
445
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
446 model = SGDClassifier(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
447
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
448 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
449
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
450
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
451 def DT_Classifier(criterion, splitter, max_depth, min_samples_split, min_samples_leaf, min_weight_fraction_leaf, random_state, max_leaf_nodes, min_impurity_decrease, min_impurity_split, presort, ccpalpha, max_features, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
452
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
453 if max_depth == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
454 max_depth =None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
455 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
456 max_depth = int(max_depth)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
457
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
458 if '.' in min_samples_split:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
459 min_samples_split = float(min_samples_split)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
460 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
461 min_samples_split = int(min_samples_split)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
462
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
463 if '.' in min_samples_leaf:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
464 min_samples_split = float(min_samples_leaf)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
465 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
466 min_samples_leaf = int(min_samples_leaf)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
467
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
468 if max_features == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
469 max_features = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
470 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
471 if '.' in max_features:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
472 max_features = float(max_features)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
473 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
474 max_features = int(max_features)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
475
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
476 if random_state == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
477 random_state = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
478 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
479 random_state = int(random_state)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
480
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
481
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
482 if max_leaf_nodes == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
483 max_leaf_nodes = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
484 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
485 max_leaf_nodes = int(max_leaf_nodes)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
486
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
487
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
488 pera = {"criterion":criterion,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
489 "splitter":splitter,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
490 "max_depth":max_depth,#int, default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
491 "min_samples_split":int(min_samples_split),#default=2
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
492 "min_samples_leaf":int(min_samples_leaf), #default=1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
493 "min_weight_fraction_leaf":float(min_weight_fraction_leaf),#default=0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
494 "random_state":random_state, #default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
495 "max_leaf_nodes":max_leaf_nodes, #default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
496 "min_impurity_decrease":float(min_impurity_decrease),#float, default=0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
497 "min_impurity_split":float(min_impurity_split), #float, default=1e-7
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
498 "presort":presort,#default=deprecated
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
499 'ccp_alpha':float(ccpalpha),#non-negative float, default=0.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
500 'max_features': max_features}#int, float or {"auto", "sqrt", "log2"}, default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
501
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
502 model = DecisionTreeClassifier(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
503
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
504 #Fit_Model('GBC.tsv', 'Internal', model, 'Min_Max', os.getcwd(), os.path.join(os.getcwd(),'report_dir'), 'out.tsv', 'out.html', NoOfFolds=3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
505 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
506
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
507
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
508 def GB_Classifier(loss, learning_rate, n_estimators, subsample, criterion, min_samples_split, min_samples_leaf, min_weight_fraction_leaf, max_depth, min_impurity_decrease,min_impurity_split, init, random_state, verbose, max_leaf_nodes, warm_start, presort, validation_fraction, n_iter_no_change, tol, ccpalpha, max_features, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
509
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
510 if '.' in min_samples_split:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
511 min_samples_split = float(min_samples_split)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
512 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
513 min_samples_split = int(min_samples_split)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
514
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
515 if '.' in min_samples_leaf:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
516 min_samples_split = float(min_samples_leaf)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
517 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
518 min_samples_leaf = int(min_samples_leaf)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
519
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
520 if max_features == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
521 max_features = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
522 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
523 if '.' in max_features:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
524 max_features = float(max_features)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
525 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
526 max_features = int(max_features)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
527
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
528 if random_state == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
529 random_state = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
530 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
531 random_state = int(random_state)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
532
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
533 if max_leaf_nodes == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
534 max_leaf_nodes = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
535 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
536 max_leaf_nodes = int(max_leaf_nodes)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
537
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
538 if warm_start == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
539 warm_start = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
540 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
541 warm_start = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
542
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
543
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
544 if n_iter_no_change == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
545 n_iter_no_change = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
546 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
547 n_iter_no_change = int(n_iter_no_change)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
548
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
549
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
550 if init == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
551 init = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
552 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
553 init = init
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
554
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
555
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
556 pera = {"loss":loss,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
557 "learning_rate":float(learning_rate),
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
558 "n_estimators":int(n_estimators), #int (default=100)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
559 "subsample":float(subsample), #float, optional (default=1.0)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
560 "criterion":criterion,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
561 "min_samples_split":min_samples_split, #int, float, optional (default=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
562 "min_samples_leaf":min_samples_leaf, #int, float, optional (default=1)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
563 "min_weight_fraction_leaf":float(min_weight_fraction_leaf), #float, optional (default=0.)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
564 "max_depth":int(max_depth), #integer, optional (default=3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
565 "min_impurity_decrease":float(min_impurity_decrease),#float, optional (default=0.)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
566 "min_impurity_split":float(min_impurity_split), #float, (default=1e-7)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
567 "init":init, #estimator or zero, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
568 "random_state":random_state, #int, RandomState instance or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
569 "verbose":int(verbose), #int, default: 0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
570 "max_features": max_features,#int, float, string or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
571 "max_leaf_nodes":max_leaf_nodes, #int or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
572 "warm_start":warm_start, #bool, default: False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
573 "presort":presort, #deprecated, default=deprecated
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
574 "validation_fraction":float(validation_fraction), #float, optional, default 0.1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
575 "n_iter_no_change":n_iter_no_change, #int, default None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
576 "tol":float(tol),#default 1e-4
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
577 "ccp_alpha":float(ccpalpha)} #non-negative float, optional (default=0.0)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
578
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
579
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
580 model = GradientBoostingClassifier(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
581
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
582 #Fit_Model('GBC.tsv', 'Internal', model, 'Min_Max', os.getcwd(), os.path.join(os.getcwd(),'report_dir'), 'out.tsv', 'out.html', NoOfFolds=3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
583 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
584
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
585
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
586 def RF_Classifier( n_estimators, criterion, max_depth, min_samples_split, min_samples_leaf, min_weight_fraction_leaf, max_features, max_leaf_nodes, min_impurity_decrease, min_impurity_split, bootstrap, oob_score, n_jobs, random_state, verbose, warm_start, ccp_alpha, max_samples, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
587
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
588 if max_depth == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
589 max_depth = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
590 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
591 max_depth = int(max_depth)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
592
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
593 if '.' in min_samples_split:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
594 min_samples_split = float(min_samples_split)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
595 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
596 min_samples_split = int(min_samples_split)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
597
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
598 if '.' in min_samples_leaf:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
599 min_samples_split = float(min_samples_leaf)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
600 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
601 min_samples_leaf = int(min_samples_leaf)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
602
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
603 if max_features == 'auto':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
604 max_features = 'auto'
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
605 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
606 if '.' in max_features:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
607 max_features = float(max_features)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
608 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
609 max_features = int(max_features)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
610
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
611 if max_leaf_nodes == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
612 max_leaf_nodes = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
613 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
614 max_leaf_nodes = int(max_leaf_nodes)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
615
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
616 if bootstrap == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
617 bootstrap = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
618 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
619 bootstrap = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
620
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
621 if oob_score == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
622 oob_score = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
623 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
624 oob_score = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
625
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
626 if n_jobs == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
627 n_jobs = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
628 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
629 n_jobs = int(n_jobs)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
630
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
631 if random_state == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
632 random_state = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
633 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
634 random_state = int(random_state)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
635
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
636 if warm_start == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
637 warm_start = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
638 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
639 warm_start = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
640
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
641 if max_samples == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
642 max_samples = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
643 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
644 if '.' in max_samples:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
645 max_samples = float(max_samples)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
646 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
647 max_samples = int(max_samples)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
648
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
649
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
650 pera = {
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
651 "n_estimators":int(n_estimators), #integer, optional (default=100)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
652 "criterion":criterion, #string, optional (default='gini')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
653 "max_depth":max_depth, #integer #or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
654 "min_samples_split":min_samples_split,# int, float, optional (default=2)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
655 "min_samples_leaf":min_samples_leaf, #int, float, optional (default=1)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
656 "min_weight_fraction_leaf":float(min_weight_fraction_leaf),#float, optional (default=0.)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
657 "max_features":max_features, #int, float, string or None, optional (default='auto')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
658 "max_leaf_nodes":max_leaf_nodes, #int or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
659 "min_impurity_decrease":float(min_impurity_decrease), #float, optional (default=0.)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
660 "min_impurity_split":float(min_samples_split), #float, (default=1e-7)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
661 "bootstrap":bootstrap, #boolean, optional (default=True)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
662 "oob_score":oob_score, #bool (default=False)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
663 "n_jobs":n_jobs, #int or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
664 "random_state":random_state, #int, RandomState instance or None, optional (default=None)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
665 "verbose":int(verbose), #int, optional (default=0)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
666 "warm_start":warm_start,#bool, optional (default=False)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
667 "ccp_alpha":float(ccp_alpha),#non-negative float, optional (default=0.0)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
668 "max_samples": max_samples #int or float, default=None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
669 }
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
670
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
671 model = RandomForestClassifier(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
672 #Fit_Model('GBC.tsv', 'Internal', model, 'Min_Max', os.getcwd(), os.path.join(os.getcwd(),'report_dir'), 'out.tsv', 'out.html', NoOfFolds=3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
673 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
674
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
675
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
676 def LR_Classifier(penalty, dual, tol, C, fit_intercept, intercept_scaling, random_state, solver, max_iter, multi_class, verbose, warm_start, n_jobs, l1_ratio, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
677
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
678 if dual == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
679 dual = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
680 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
681 dual = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
682
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
683 if fit_intercept == "true":
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
684 fit_intercept = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
685 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
686 fit_intercept = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
687
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
688 if random_state == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
689 random_state = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
690 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
691 random_state = int(random_state)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
692
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
693 if warm_start == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
694 warm_start = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
695 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
696 warm_start = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
697
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
698 if n_jobs == "none":
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
699 n_jobs = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
700 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
701 n_jobs = int(n_jobs)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
702
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
703 if l1_ratio == "none":
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
704 l1_ratio = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
705 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
706 l1_ratio =float(l1_ratio)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
707
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
708 pera = {
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
709 "penalty":penalty, #l2
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
710 "dual":dual, #false
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
711 "tol":float(tol), #1e-4
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
712 "C":float(C), #1.0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
713 "fit_intercept":fit_intercept, #True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
714 "intercept_scaling":float(intercept_scaling), #1
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
715 "random_state":random_state, #None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
716 "solver":solver, #lbfgs
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
717 "max_iter":int(max_iter), #100
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
718 "multi_class":multi_class, #auto
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
719 "verbose":int(verbose), #0
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
720 "warm_start":warm_start,#False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
721 "n_jobs":n_jobs, #None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
722 "l1_ratio":l1_ratio} #None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
723
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
724 model = LogisticRegression(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
725
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
726 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
727
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
728
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
729 def KN_Classifier(n_neighbors, weights, algorithm, leaf_size, p, metric, metric_params, n_jobs, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
730
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
731 if n_jobs == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
732 n_jobs = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
733 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
734 n_jobs = int(n_jobs)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
735
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
736 pera = {
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
737 "n_neighbors":int(n_neighbors),#int5
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
738 "weights":weights,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
739 "algorithm":algorithm,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
740 "leaf_size":int(leaf_size), #int30
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
741 "p":int(p), #int2
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
742 "metric":metric, #minkowski
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
743 "n_jobs":n_jobs} #none
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
744
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
745 model = KNeighborsClassifier(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
746
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
747 #Fit_Model('GBC.tsv', 'Internal', model, 'Min_Max', os.getcwd(), os.path.join(os.getcwd(),'report_dir'), 'out.tsv', 'out.html', NoOfFolds=3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
748 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
749
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
750 def GNB_Classifier( var_smoothing, TrainFile, TestMethod, SelectedSclaer, NFolds, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
751
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
752 pera = {
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
753 "var_smoothing":float(var_smoothing)} #
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
754
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
755 model = GaussianNB(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
756
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
757 #Fit_Model('GBC.tsv', 'Internal', model, 'Min_Max', os.getcwd(), os.path.join(os.getcwd(),'report_dir'), 'out.tsv', 'out.html', NoOfFolds=3)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
758 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=int(NFolds), TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
759
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
760
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
761 def MLP_Classifier(hidden_layer_sizes, activation,solver,alpha,batch_size,learning_rate,learning_rate_init,power_t,max_iter,shuffle,random_state,tol,verbose,warm_start,momentum,nesterovs_momentum,early_stopping,validation_fraction,beta_1,beta_2,epsilon,n_iter_no_change,max_fun,TrainFile, TestMethod, SelectedSclaer, NFolds, Testspt, TestFile, OutFile, htmlOutDir, htmlFname, Workdirpath):
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
762
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
763 if shuffle == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
764 shuffle = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
765 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
766 shuffle = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
767
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
768 if nesterovs_momentum == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
769 nesterovs_momentum = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
770 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
771 nesterovs_momentum = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
772
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
773 if early_stopping == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
774 early_stopping = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
775 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
776 early_stopping = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
777
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
778 if random_state == 'none':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
779 random_state = None
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
780 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
781 random_state = int(random_state)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
782
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
783 if verbose == 'false':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
784 verbose = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
785 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
786 verbose = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
787
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
788 if warm_start == 'true':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
789 warm_start = True
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
790 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
791 warm_start = False
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
792
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
793 pera ={
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
794 'hidden_layer_sizes':hidden_layer_sizes, #=(100,),
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
795 'activation':activation, #='relu',
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
796 'solver':solver, #='adam',
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
797 'alpha':alpha, #=0.0001,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
798 'batch_size':batch_size, #='auto',
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
799 'learning_rate':learning_rate, #='constant',
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
800 'learning_rate_init':learning_rate_init, #=0.001,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
801 'power_t':power_t, #=0.5,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
802 'max_iter':max_iter, #=200,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
803 'shuffle':shuffle, #=True,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
804 'random_state':random_state, #=None,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
805 'tol':tol, #=0.0001,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
806 'verbose':verbose, #=False,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
807 'warm_start':warm_start, #=False,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
808 'momentum':momentum, #=0.9,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
809 'nesterovs_momentum':nesterovs_momentum, #=True,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
810 'early_stopping':early_stopping, #=False,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
811 'validation_fraction':validation_fraction, #=0.1,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
812 'beta_1':beta_1, #=0.9,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
813 'beta_2':beta_2, #=0.999,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
814 'epsilon':epsilon, #=1e-08,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
815 'n_iter_no_change':n_iter_no_change, #=10,
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
816 'max_fun':max_fun #=15000
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
817 }
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
818
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
819 model = MLPClassifier(**pera)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
820
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
821 Fit_Model(TrainData=TrainFile, Test_Method=TestMethod, Algo=model, Selected_Sclaer=SelectedSclaer, Workdirpath=Workdirpath, htmlOutDir=htmlOutDir, OutFile=OutFile, htmlFname=htmlFname, NoOfFolds=NFolds, TestSize=Testspt, TestData=TestFile)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
822
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
823
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
824 if __name__=="__main__":
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
825
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
826 import argparse
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
827
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
828 parser = argparse.ArgumentParser(description='Deployment tool')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
829 subparsers = parser.add_subparsers()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
830
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
831 svmc = subparsers.add_parser('SVMC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
832 svmc.add_argument("--C", required=False, default=1.0, help="Regularization parameter. The strength of the regularization is inversely proportional to C. Must be strictly positive. The penalty is a squared l2 penalty.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
833 svmc.add_argument("--kernel", required=False, default='rbf', help="Specifies the kernel type to be used in the algorithm. It must be one of 'linear', 'poly', 'rbf', 'sigmoid', 'precomputed' or a callable. If none is given, 'rbf' will be used. If a callable is given it is used to pre-compute the kernel matrix from data matrices; that matrix should be an array of shape (n_samples, n_samples).")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
834 svmc.add_argument("--degree", required=False, default=3, help="Degree of the polynomial kernel function ('poly'). Ignored by all other kernels.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
835 svmc.add_argument("--gamma", required=False, default='scale', help="Kernel coefficient for 'rbf', 'poly' and 'sigmoid'. if gamma='scale' (default) is passed then it uses 1 / (n_features * X.var()) as value of gamma, if 'auto', uses 1 / n_features.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
836 svmc.add_argument("--coef0", required=False, default=0.0, help="Independent term in kernel function. It is only significant in 'poly' and 'sigmoid'.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
837 svmc.add_argument("--shrinking", required=False, default=True, help="Whether to use the shrinking heuristic.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
838 svmc.add_argument("--probability", required=False, default=True, help="Whether to enable probability estimates. This must be enabled prior to calling fit, will slow down that method as it internally uses 5-fold cross-validation, and predict_proba may be inconsistent with predict")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
839 svmc.add_argument("--tol", required=False, default=0.001, help="Tolerance for stopping criterion.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
840 svmc.add_argument("--cache_size", required=False, default=200, help="Specify the size of the kernel cache (in MB).")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
841 svmc.add_argument("--verbose", required=False, default=False, help="Enable verbose output. Note that this setting takes advantage of a per-process runtime setting in libsvm that, if enabled, may not work properly in a multithreaded context.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
842 svmc.add_argument("--max_iter", required=False, default=-1, help="Hard limit on iterations within solver, or -1 for no limit.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
843 svmc.add_argument("--decision_function_shape", required=False, default='ovr', help="Whether to return a one-vs-rest ('ovr') decision function of shape (n_samples, n_classes) as all other classifiers, or the original one-vs-one ('ovo') decision function of libsvm which has shape (n_samples, n_classes * (n_classes - 1) / 2). However, one-vs-one ('ovo') is always used as multi-class strategy.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
844 svmc.add_argument("--randomState", required=False, default=None, help="The seed of the pseudo random number generator used when shuffling the data for probability estimates. If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
845 svmc.add_argument("--breakties", required=False, default=False, help="If true, decision_function_shape='ovr', and number of classes > 2, predict will break ties according to the confidence values of decision_function; otherwise the first class among the tied classes is returned. Please note that breaking ties comes at a relatively high computational cost compared to a simple predict." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
846 svmc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
847 svmc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
848 svmc.add_argument("--SelectedSclaer", required=True, help="'Min_Max','Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
849 svmc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
850 svmc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
851 svmc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.csv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
852 svmc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
853 svmc.add_argument("--htmlFname", required=False, default='Out.html', help="HTML out file")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
854 svmc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
855
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
856 sgdc = subparsers.add_parser('SGDC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
857 sgdc.add_argument("--loss", required=False, default='log', help="The loss function to be used. Defaults to 'hinge', which gives a linear SVM. The possible options are 'hinge', 'log', 'modified_huber', 'squared_hinge', 'perceptron', or a regression loss: 'squared_loss', 'huber', 'epsilon_insensitive', or squared_epsilon_insensitive'.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
858 sgdc.add_argument("--penalty", required=False, default='l2', help="The penalty (aka regularization term) to be used. Defaults to 'l2' which is the standard regularizer for linear SVM models. 'l1' and 'elasticnet' might bring sparsity to the model (feature selection) not achievable with 'l2'.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
859 sgdc.add_argument("--alpha", required=False, default=0.0001, help="Constant that multiplies the regularization term. Defaults to 0.0001. Also used to compute learning_rate when set to 'optimal'.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
860 sgdc.add_argument("--l1_ratio", required=False, default=0.15, help="The Elastic Net mixing parameter, with 0 <= l1_ratio <= 1. l1_ratio=0 corresponds to L2 penalty, l1_ratio=1 to L1. Defaults to 0.15.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
861 sgdc.add_argument("--fit_intercept", required=False, default=True, help="Whether the intercept should be estimated or not. If False, the data is assumed to be already centered. Defaults to True.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
862 sgdc.add_argument("--max_iter", required=False, default=1000, help="The maximum number of passes over the training data (aka epochs). It only impacts the behavior in the fit method, and not the partial_fit method.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
863 sgdc.add_argument("--tol", required=False, default=0.001, help="The stopping criterion. If it is not None, the iterations will stop when (loss > best_loss - tol) for n_iter_no_change consecutive epochs.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
864 sgdc.add_argument("--shuffle", required=False, default=True, help="Whether or not the training data should be shuffled after each epoch. Defaults to True.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
865 sgdc.add_argument("--verbose", required=False, default=0, help="The verbosity level.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
866 sgdc.add_argument("--epsilon", required=False, default=0.1, help="Epsilon in the epsilon-insensitive loss functions; only if loss is 'huber', 'epsilon_insensitive', or 'squared_epsilon_insensitive'. For 'huber', determines the threshold at which it becomes less important to get the prediction exactly right. For epsilon-insensitive, any differences between the current prediction and the correct label are ignored if they are less than this threshold.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
867 sgdc.add_argument("--n_jobs", required=False, default='none', help="The number of CPUs to use to do the OVA (One Versus All, for multi-class problems) computation. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
868 sgdc.add_argument("--random_state", required=False, default='none', help="The seed of the pseudo random number generator to use when shuffling the data. If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
869 sgdc.add_argument("--learning_rate", required=False, default='optimal', help="The learning rate schedule:")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
870 sgdc.add_argument("--eta0", required=False, default=0.0, help="eta = eta0")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
871 sgdc.add_argument("--power_t", required=False, default=0.5, help="eta = 1.0 / (alpha * (t + t0)) where t0 is chosen by a heuristic proposed by Leon Bottou.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
872 sgdc.add_argument("--early_stopping", required=False, default=False, help="MinMaxScaler")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
873 sgdc.add_argument("--validation_fraction", required=False, default=0.1, help="The proportion of training data to set aside as validation set for early stopping. Must be between 0 and 1. Only used if early_stopping is True.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
874 sgdc.add_argument("--n_iter_no_change", required=False, default=5, help="Number of iterations with no improvement to wait before early stopping.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
875 sgdc.add_argument("--warm_start", required=False, default=False, help="When set to True, reuse the solution of the previous call to fit as initialization, otherwise, just erase the previous solution.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
876 sgdc.add_argument("--average", required=False, default=False, help="MinMaxScaler")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
877 sgdc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
878 sgdc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
879 sgdc.add_argument("--SelectedSclaer", required=True, help="'Min_Max','Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
880 sgdc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
881 sgdc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
882 sgdc.add_argument("--OutFile", required=False, default='Out.csv', help="float, Max=1.0")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
883 sgdc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
884 sgdc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
885 sgdc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
886
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
887 dtc = subparsers.add_parser('DTC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
888 dtc.add_argument("--criterion", required=False, default='gini', help="The function to measure the quality of a split. Supported criteria are 'gini' for the Gini impurity and 'entropy' for the information gain.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
889 dtc.add_argument("--splitter", required=False, default='best', help="The strategy used to choose the split at each node. Supported strategies are 'best' to choose the best split and 'random' to choose the best random split." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
890 dtc.add_argument("--max_depth", required=False, default='none', help="The maximum depth of the tree. If None, then nodes are expanded until all leaves are pure or until all leaves contain less than min_samples_split samples.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
891 dtc.add_argument("--min_samples_split", required=False, default='2', help="The minimum number of samples required to split an internal node: If int, then consider min_samples_split as the minimum number. If float, then min_samples_split is a fraction and ceil(min_samples_split * n_samples) are the minimum number of samples for each split.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
892 dtc.add_argument("--min_samples_leaf", required=False, default='1', help="The minimum number of samples required to be at a leaf node. A split point at any depth will only be considered if it leaves at least min_samples_leaf training samples in each of the left and right branches. This may have the effect of smoothing the model, especially in regression.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
893 dtc.add_argument("--min_weight_fraction_leaf", required=False, default=0.0, help="The minimum weighted fraction of the sum total of weights (of all the input samples) required to be at a leaf node. Samples have equal weight when sample_weight is not provided.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
894 dtc.add_argument("--random_state", required=False, default='none', help="If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
895 dtc.add_argument("--max_leaf_nodes", required=False, default='none', help="A node will be split if this split induces a decrease of the impurity greater than or equal to this value. The weighted impurity decrease equation is the following")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
896 dtc.add_argument("--min_impurity_decrease", required=False, default=0.0, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
897 dtc.add_argument("--min_impurity_split", required=False, default=1e-09, help="Threshold for early stopping in tree growth. A node will split if its impurity is above the threshold, otherwise it is a leaf.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
898 dtc.add_argument("--presort", required=False, default='deprecate', help="This parameter is deprecated and will be removed in v0.24.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
899 dtc.add_argument("--ccpalpha", required=False, default=0.0, help="Complexity parameter used for Minimal Cost-Complexity Pruning. The subtree with the largest cost complexity that is smaller than ccp_alpha will be chosen. By default, no pruning is performed. See Minimal Cost-Complexity Pruning for details.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
900 dtc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
901 dtc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
902 dtc.add_argument("--max_features", required=False, default='none')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
903 dtc.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
904 dtc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
905 dtc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
906 dtc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
907 dtc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
908 dtc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
909 dtc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
910
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
911 gbc = subparsers.add_parser('GBC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
912 gbc.add_argument("--loss", required=False, default='deviance', help="loss function to be optimized. 'deviance' refers to deviance (= logistic regression) for classification with probabilistic outputs. For loss 'exponential' gradient boosting recovers the AdaBoost algorithm.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
913 gbc.add_argument("--learning_rate", required=False, default=0.1, help="learning rate shrinks the contribution of each tree by learning_rate. There is a trade-off between learning_rate and n_estimators.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
914 gbc.add_argument("--n_estimators", required=False, default=100, help="The number of boosting stages to perform. Gradient boosting is fairly robust to over-fitting so a large number usually results in better performance.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
915 gbc.add_argument("--subsample", required=False, default=1.0, help="The fraction of samples to be used for fitting the individual base learners. If smaller than 1.0 this results in Stochastic Gradient Boosting. subsample interacts with the parameter n_estimators. Choosing subsample < 1.0 leads to a reduction of variance and an increase in bias.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
916 gbc.add_argument("--criterion", required=False,default='friedman_mse', help="The function to measure the quality of a split. Supported criteria are 'friedman_mse' for the mean squared error with improvement score by Friedman, 'mse' for mean squared error, and 'mae' for the mean absolute error. The default value of 'friedman_mse' is generally the best as it can provide a better approximation in some cases.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
917 gbc.add_argument("--min_samples_split", required=False, default='2', help="The minimum number of samples required to split an internal node: If int, then consider min_samples_split as the minimum number. If float, then min_samples_split is a fraction and ceil(min_samples_split * n_samples) are the minimum number of samples for each split.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
918 gbc.add_argument("--min_samples_leaf", required=False, default='1', help="The minimum number of samples required to be at a leaf node. A split point at any depth will only be considered if it leaves at least min_samples_leaf training samples in each of the left and right branches. This may have the effect of smoothing the model, especially in regression.If int, then consider min_samples_leaf as the minimum number. If float, then min_samples_leaf is a fraction and ceil(min_samples_leaf * n_samples) are the minimum number of samples for each node.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
919 gbc.add_argument("--min_weight_fraction_leaf", required=False, default=0, help="The minimum weighted fraction of the sum total of weights (of all the input samples) required to be at a leaf node. Samples have equal weight when sample_weight is not provided.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
920 gbc.add_argument("--max_depth", required=False, default=3, help="maximum depth of the individual regression estimators. The maximum depth limits the number of nodes in the tree. Tune this parameter for best performance; the best value depends on the interaction of the input variables.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
921 gbc.add_argument("--min_impurity_decrease", required=False, default=0.0, help="A node will be split if this split induces a decrease of the impurity greater than or equal to this value. The weighted impurity decrease equation is the following: 'N_t / N * (impurity - N_t_R / N_t * right_impurity - N_t_L / N_t * left_impurity'), where N is the total number of samples, N_t is the number of samples at the current node, N_t_L is the number of samples in the left child, and N_t_R is the number of samples in the right child. N, N_t, N_t_R and N_t_L all refer to the weighted sum, if sample_weight is passed. New in version 0.19.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
922 gbc.add_argument("--min_impurity_split", required=False, default=0.00000007, help="Threshold for early stopping in tree growth. A node will split if its impurity is above the threshold, otherwise it is a leaf.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
923 gbc.add_argument("--init", required=False,default='none', help="An estimator object that is used to compute the initial predictions. init has to provide fit and predict_proba. If 'zero', the initial raw predictions are set to zero. By default, a DummyEstimator predicting the classes priors is used.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
924 gbc.add_argument("--random_state", required=False, default='none', help="If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
925 gbc.add_argument("--max_features", required=False, default='none', help="The number of features to consider when looking for the best split: If int, then consider max_features features at each split. If float, then max_features is a fraction and int(max_features * n_features) features are considered at each split.If 'auto', then max_features=sqrt(n_features). If 'sqrt', then max_features=sqrt(n_features). If 'log2', then max_features=log2(n_features). If None, then max_features=n_features. Choosing max_features < n_features leads to a reduction of variance and an increase in bias. Note: the search for a split does not stop until at least one valid partition of the node samples is found, even if it requires to effectively inspect more than max_features features.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
926 gbc.add_argument("--verbose",required=False, default=0, help="Enable verbose output. If 1 then it prints progress and performance once in a while (the more trees the lower the frequency). If greater than 1 then it prints progress and performance for every tree.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
927 gbc.add_argument("--max_leaf_nodes", required=False, default=4, help="Grow trees with max_leaf_nodes in best-first fashion. Best nodes are defined as relative reduction in impurity. If None then unlimited number of leaf nodes.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
928 gbc.add_argument("--warm_start", required=False, default='false', help="When set to True, reuse the solution of the previous call to fit and add more estimators to the ensemble, otherwise, just erase the previous solution." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
929 gbc.add_argument("--presort", required=False,default='auto', help="This parameter is deprecated and will be removed in v0.24.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
930 gbc.add_argument("--validation_fraction", required=False, default=0.1, help="The proportion of training data to set aside as validation set for early stopping. Must be between 0 and 1. Only used if n_iter_no_change is set to an integer.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
931 gbc.add_argument("--n_iter_no_change", required=False, default=10, help="n_iter_no_change is used to decide if early stopping will be used to terminate training when validation score is not improving. By default it is set to None to disable early stopping. If set to a number, it will set aside validation_fraction size of the training data as validation and terminate training when validation score is not improving in all of the previous n_iter_no_change numbers of iterations. The split is stratified.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
932 gbc.add_argument("--tol", required=False, default=0.0001, help="Tolerance for the early stopping. When the loss is not improving by at least tol for n_iter_no_change iterations (if set to a number), the training stops.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
933 gbc.add_argument("--ccpalpha", required=False, default=0.0, help="Complexity parameter used for Minimal Cost-Complexity Pruning. The subtree with the largest cost complexity that is smaller than ccp_alpha will be chosen. By default, no pruning is performed. See Minimal Cost-Complexity Pruning for details.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
934 gbc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
935 gbc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
936 gbc.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
937 gbc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
938 gbc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
939 gbc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
940 gbc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
941 gbc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
942 gbc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
943
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
944 rfc = subparsers.add_parser('RFC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
945 rfc.add_argument("--n_estimators", required=False, default=100, help="The number of trees in the forest.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
946 rfc.add_argument("--criterion", required=False, default='gini', help="The function to measure the quality of a split. Supported criteria are 'gini' for the Gini impurity and 'entropy' for the information gain. Note: this parameter is tree-specific." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
947 rfc.add_argument("--max_depth", required=False, default='none', help="The maximum depth of the tree. If None, then nodes are expanded until all leaves are pure or until all leaves contain less than min_samples_split samples.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
948 rfc.add_argument("--min_samples_split", required=False, default='2', help="The minimum number of samples required to split an internal node: If int, then consider min_samples_split as the minimum number. If float, then min_samples_split is a fraction and ceil(min_samples_split * n_samples) are the minimum number of samples for each split.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
949 rfc.add_argument("--min_samples_leaf", required=False, default='1', help="The minimum number of samples required to be at a leaf node. A split point at any depth will only be considered if it leaves at least min_samples_leaf training samples in each of the left and right branches. This may have the effect of smoothing the model, especially in regression.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
950 rfc.add_argument("--min_weight_fraction_leaf", required=False, default=0.0, help="The minimum weighted fraction of the sum total of weights (of all the input samples) required to be at a leaf node. Samples have equal weight when sample_weight is not provided.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
951 rfc.add_argument("--max_features", required=False, default='auto', help="The number of features to consider when looking for the best split:")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
952 rfc.add_argument("--max_leaf_nodes", required=False, default='none', help="Grow trees with max_leaf_nodes in best-first fashion. Best nodes are defined as relative reduction in impurity. If None then unlimited number of leaf nodes.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
953 rfc.add_argument("--min_impurity_decrease", required=False, default=0.0, help="A node will be split if this split induces a decrease of the impurity greater than or equal to this value. The weighted impurity decrease equation is the following: N_t / N * (impurity - N_t_R / N_t * right_impurity - N_t_L / N_t * left_impurity) where N is the total number of samples, N_t is the number of samples at the current node, N_t_L is the number of samples in the left child, and N_t_R is the number of samples in the right child. N, N_t, N_t_R and N_t_L all refer to the weighted sum, if sample_weight is passed. New in version 0.19.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
954 rfc.add_argument("--min_impurity_split", required=False, default=1e-7, help="Threshold for early stopping in tree growth. A node will split if its impurity is above the threshold, otherwise it is a leaf.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
955 rfc.add_argument("--bootstrap", required=False, default='true', help="Whether bootstrap samples are used when building trees. If False, the whole datset is used to build each tree.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
956 rfc.add_argument("--oob_score", required=False, default='false', help="Whether to use out-of-bag samples to estimate the generalization accuracy.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
957 rfc.add_argument("--n_jobs", required=False, default=-1, help="The number of jobs to run in parallel. fit, predict, decision_path and apply are all parallelized over the trees. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
958 rfc.add_argument("--random_state", required=False, default='none', help="Controls both the randomness of the bootstrapping of the samples used when building trees (if bootstrap=True) and the sampling of the features to consider when looking for the best split at each node (if max_features < n_features). See Glossary for details.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
959 rfc.add_argument("--verbose", required=False, default=0, help="Controls the verbosity when fitting and predicting." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
960 rfc.add_argument("--max_samples", required=False, default='none', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
961 rfc.add_argument("--ccp_alpha", required=False, default=0.0, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
962 rfc.add_argument("--warm_start", required=False, default='false', help="When set to True, reuse the solution of the previous call to fit and add more estimators to the ensemble, otherwise, just fit a whole new forest. See the Glossary.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
963 rfc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
964 rfc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
965 rfc.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
966 rfc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
967 rfc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
968 rfc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
969 rfc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
970 rfc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
971 rfc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
972
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
973 lrc = subparsers.add_parser('LRC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
974 lrc.add_argument("--penalty", required=False, default='l2', help="Used to specify the norm used in the penalization. The 'newton-cg', 'sag' and 'lbfgs' solvers support only l2 penalties. 'elasticnet' is only supported by the 'saga' solver. If 'none' (not supported by the liblinear solver), no regularization is applied." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
975 lrc.add_argument("--dual", required=False, default='false', help="Dual or primal formulation. Dual formulation is only implemented for l2 penalty with liblinear solver. Prefer dual=False when n_samples > n_features.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
976 lrc.add_argument("--tol", required=False, default=0.0001, help="Tolerance for stopping criteria.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
977 lrc.add_argument("--C", required=False, default=1.0, help="Inverse of regularization strength; must be a positive float. Like in support vector machines, smaller values specify stronger regularization." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
978 lrc.add_argument("--fit_intercept", required=False, default='true', help="Specifies if a constant (a.k.a. bias or intercept) should be added to the decision function." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
979 lrc.add_argument("--intercept_scaling", required=False, default=1, help="Useful only when the solver 'liblinear' is used and self.fit_intercept is set to True. In this case, x becomes [x, self.intercept_scaling], i.e. a 'synthetic' feature with constant value equal to intercept_scaling is appended to the instance vector. The intercept becomes intercept_scaling * synthetic_feature_weight." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
980 lrc.add_argument("--random_state", required=False, default=10, help="The seed of the pseudo random number generator to use when shuffling the data. If int, random_state is the seed used by the random number generator; If RandomState instance, random_state is the random number generator; If None, the random number generator is the RandomState instance used by np.random. Used when solver == 'sag' or 'liblinear'.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
981 lrc.add_argument("--solver", required=False, default='lbfgs', help="Algorithm to use in the optimization problem. For small datasets, 'liblinear' is a good choice, whereas 'sag' and 'saga' are faster for large ones. For multiclass problems, only 'newton-cg', 'sag', 'saga' and 'lbfgs' handle multinomial loss; 'liblinear' is limited to one-versus-rest schemes. 'newton-cg', 'lbfgs', 'sag' and 'saga' handle L2 or no penalty 'liblinear' and 'saga' also handle L1 penalty 'saga' also supports 'elasticnet' penalty 'liblinear' does not support setting penalty='none' Note that 'sag' and 'saga' fast convergence is only guaranteed on features with approximately the same scale. You can preprocess the data with a scaler from sklearn.preprocessing. New in version 0.17: Stochastic Average Gradient descent solver.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
982 lrc.add_argument("--max_iter", required=False, default=100, help="Maximum number of iterations taken for the solvers to converge."),
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
983 lrc.add_argument("--multi_class", required=False, default='auto', help="If the option chosen is 'ovr', then a binary problem is fit for each label. For 'multinomial' the loss minimised is the multinomial loss fit across the entire probability distribution, even when the data is binary. 'multinomial' is unavailable when solver='liblinear'. 'auto' selects 'ovr' if the data is binary, or if solver='liblinear', and otherwise selects 'multinomial'. New in version 0.18: Stochastic Average Gradient descent solver for 'multinomial' case.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
984 lrc.add_argument("--verbose", required=False, default=0, help="For the liblinear and lbfgs solvers set verbose to any positive number for verbosity.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
985 lrc.add_argument("--warm_start", required=False, default='false', help="When set to True, reuse the solution of the previous call to fit as initialization, otherwise, just erase the previous solution. Useless for liblinear solver. See the Glossary. New in version 0.17: warm_start to support lbfgs, newton-cg, sag, saga solvers.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
986 lrc.add_argument("--n_jobs", required=False, default='none', help="Number of CPU cores used when parallelizing over classes if multi_class='ovr'. This parameter is ignored when the solver is set to 'liblinear' regardless of whether 'multi_class' is specified or not. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
987 lrc.add_argument("--l1_ratio", required=False, default='none', help="The Elastic-Net mixing parameter, with 0 <= l1_ratio <= 1. Only used if penalty='elasticnet'. Setting 'l1_ratio=0 is equivalent to using penalty='l2', while setting l1_ratio=1 is equivalent to using penalty='l1'. For 0 < l1_ratio <1, the penalty is a combination of L1 and L2.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
988 lrc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
989 lrc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
990 lrc.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
991 lrc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
992 lrc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
993 lrc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
994 lrc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
995 lrc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
996 lrc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
997
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
998 knc = subparsers.add_parser('KNC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
999 knc.add_argument("--n_neighbors", required=False, default=5, help="Number of neighbors to use by default for kneighbors queries.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1000 knc.add_argument("--weights",required=False, default='uniform', help="weight function used in prediction. Possible values: 'uniform' : uniform weights. All points in each neighborhood are weighted equally. 'distance' : weight points by the inverse of their distance. in this case, closer neighbors of a query point will have a greater influence than neighbors which are further away. [callable] : a user-defined function which accepts an array of distances, and returns an array of the same shape containing the weights.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1001 knc.add_argument("--algorithm", required=False, default='auto', help="Algorithm used to compute the nearest neighbors:'ball_tree' will use BallTree 'kd_tree' will use KDTree 'brute' will use a brute-force search. 'auto' will attempt to decide the most appropriate algorithm based on the values passed to fit method. Note: fitting on sparse input will override the setting of this parameter, using brute force." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1002 knc.add_argument("--leaf_size", required=False, default=30, help="Leaf size passed to BallTree or KDTree. This can affect the speed of the construction and query, as well as the memory required to store the tree. The optimal value depends on the nature of the problem.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1003 knc.add_argument("--p", required=False, default=2, help="Power parameter for the Minkowski metric. When p = 1, this is equivalent to using manhattan_distance (l1), and euclidean_distance (l2) for p = 2. For arbitrary p, minkowski_distance (l_p) is used." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1004 knc.add_argument("--metric", required=False, default='minkowski', help="the distance metric to use for the tree. The default metric is minkowski, and with p=2 is equivalent to the standard Euclidean metric. See the documentation of the DistanceMetric class for a list of available metrics. If metric is 'precomputed', X is assumed to be a distance matrix and must be square during fit. X may be a Glossary, in which case only 'nonzero' elements may be considered neighbors.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1005 knc.add_argument("--metric_params", required=False, default=None, help="Additional keyword arguments for the metric function." )
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1006 knc.add_argument("--n_jobs", required=False, default='none', help="The number of parallel jobs to run for neighbors search. None means 1 unless in a joblib.parallel_backend context. -1 means using all processors. See Glossary for more details. Doesn't affect fit method.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1007 knc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1008 knc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1009 knc.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1010 knc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1011 knc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1012 knc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1013 knc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1014 knc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1015 knc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1016
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1017 gnbc = subparsers.add_parser('GNBC')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1018 #gnbc.add_argument("--priors", required=False, default=None, help="Prior probabilities of the classes. If specified the priors are not adjusted according to the data.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1019 gnbc.add_argument("--var_smoothing", required=False, default=1e-09, help="Portion of the largest variance of all features that is added to variances for calculation stability.")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1020 gnbc.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1021 gnbc.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1022 gnbc.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1023 gnbc.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1024 gnbc.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1025 gnbc.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1026 gnbc.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1027 gnbc.add_argument("--htmlFname", required=False, default='Out.html', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1028 gnbc.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1029
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1030 MLP = subparsers.add_parser('MLP')
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1031 MLP.add_argument("--hidden_layer_sizes", required=False, default=(100,), help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1032 MLP.add_argument("--activation", required=False, default='relu', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1033 MLP.add_argument("--solver", required=False, default='adam', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1034 MLP.add_argument("--alpha", required=False, default=0.0001 , help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1035 MLP.add_argument("--batch_size", required=False, default='auto', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1036 MLP.add_argument("--learning_rate", required=False, default='constant', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1037 MLP.add_argument("--learning_rate_init", required=False, default=0.001, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1038 MLP.add_argument("--power_t", required=False, default=0.5, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1039 MLP.add_argument("--max_iter", required=False, default=200, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1040 MLP.add_argument("--shuffle", required=False, default='true', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1041 MLP.add_argument("--random_state", required=False, default='none', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1042 MLP.add_argument("--tol", required=False, default=0.0001, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1043 MLP.add_argument("--verbose", required=False, default='false', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1044 MLP.add_argument("--warm_start", required=False, default='false', help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1045 MLP.add_argument("--momentum", required=False, default=0.9, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1046 MLP.add_argument("--nesterovs_momentum", required=False, default='true' ,help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1047 MLP.add_argument("--early_stopping", required=False, default='false' ,help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1048 MLP.add_argument("--validation_fraction", required=False, default=0.1 ,help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1049 MLP.add_argument("--beta_1", required=False, default=0.9, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1050 MLP.add_argument("--beta_2", required=False , default=0.999, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1051 MLP.add_argument("--epsilon", required=False, default=1e-08, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1052 MLP.add_argument("--n_iter_no_change", required=False, default=10, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1053 MLP.add_argument("--max_fun", required=False, default=15000, help="")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1054 MLP.add_argument("--TrainFile", required=True, default=None, help="Positive negative dataset Ex. 'Train.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1055 MLP.add_argument("--TestMethod", required=True, default=None, help="Internal','CrossVal', 'External', 'Predict'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1056 MLP.add_argument("--SelectedSclaer", required=True, help="'Min_Max',Standard_Scaler','No_Scaler'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1057 MLP.add_argument("--NFolds", required=False, default=5, help="int, Max=10")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1058 MLP.add_argument("--Testspt", required=False, default=0.2, help="float, Max=1.0")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1059 MLP.add_argument("--TestFile", required=False, default=None, help="Test data, 'Test.csv'")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1060 MLP.add_argument("--OutFile", required=False, default='Out.csv', help="Out.tsv")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1061 MLP.add_argument("--htmlOutDir", required=False, default=os.path.join(os.getcwd(),'report_dir'), help="HTML Out Dir")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1062 MLP.add_argument("--htmlFname", required=False, help="HTML out file", default="jai.html")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1063 MLP.add_argument("--Workdirpath", required=False, default=os.getcwd(), help="Working Directory Path")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1064
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1065 args = parser.parse_args()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1066
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1067 if sys.argv[1] == 'SVMC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1068 SVM_Classifier(args.C, args.kernel, args.degree, args.gamma, args.coef0, args.shrinking, args.probability, args.tol, args.cache_size, args.verbose, args.max_iter, args.decision_function_shape, args.randomState, args.breakties, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1069 elif sys.argv[1] == 'SGDC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1070 SGD_Classifier( args.loss, args.penalty, args.alpha, args.l1_ratio, args.fit_intercept, args.max_iter, args.tol, args.shuffle, args.verbose, args.epsilon, args.n_jobs, args.random_state, args.learning_rate, args.eta0, args.power_t, args.early_stopping, args.validation_fraction, args.n_iter_no_change, args.warm_start, args.average, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1071 elif sys.argv[1] == 'DTC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1072 DT_Classifier(args.criterion, args.splitter, args.max_depth, args.min_samples_split, args.min_samples_leaf, args.min_weight_fraction_leaf, args.random_state, args.max_leaf_nodes, args.min_impurity_decrease, args.min_impurity_split, args.presort, args.ccpalpha, args.max_features, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1073 elif sys.argv[1] == 'GBC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1074 GB_Classifier(args.loss, args.learning_rate, args.n_estimators, args.subsample, args.criterion, args.min_samples_split, args.min_samples_leaf, args.min_weight_fraction_leaf, args.max_depth, args.min_impurity_decrease, args.min_impurity_split, args.init, args.random_state, args.verbose, args.max_leaf_nodes, args.warm_start, args.presort, args.validation_fraction, args.n_iter_no_change, args.tol, args.ccpalpha, args.max_features, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1075 elif sys.argv[1] == 'RFC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1076 RF_Classifier( args.n_estimators, args.criterion, args.max_depth, args.min_samples_split, args.min_samples_leaf, args.min_weight_fraction_leaf, args.max_features, args.max_leaf_nodes, args.min_impurity_decrease, args.min_impurity_split, args.bootstrap, args.oob_score, args.n_jobs, args.random_state, args.verbose, args.warm_start, args.ccp_alpha, args.max_samples, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1077 elif sys.argv[1] == 'LRC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1078 LR_Classifier(args.penalty, args.dual, args.tol, args.C, args.fit_intercept, args.intercept_scaling, args.random_state, args.solver, args.max_iter, args.multi_class, args.verbose, args.warm_start, args.n_jobs, args.l1_ratio, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1079 elif sys.argv[1] == 'KNC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1080 KN_Classifier(args.n_neighbors, args.weights, args.algorithm, args.leaf_size, args.p, args.metric, args.metric_params, args.n_jobs, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1081 elif sys.argv[1] == 'GNBC':
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1082 GNB_Classifier( args.var_smoothing, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1083 elif sys.argv[1] == 'MLP' :
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1084 MLP_Classifier(args.hidden_layer_sizes, args.activation, args.solver, args.alpha, args.batch_size, args.learning_rate, args.learning_rate_init, args.power_t, args.max_iter, args.shuffle, args.random_state, args.tol, args.verbose, args.warm_start, args.momentum, args.nesterovs_momentum, args.early_stopping, args.validation_fraction, args.beta_1, args.beta_2, args.epsilon, args.n_iter_no_change, args.max_fun, args.TrainFile, args.TestMethod, args.SelectedSclaer, args.NFolds, args.Testspt, args.TestFile, args.OutFile, args.htmlOutDir, args.htmlFname, args.Workdirpath)
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1085 else:
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1086 print ("option not correct")
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1087 exit()
3f9bdcf83244 "planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
diff changeset
1088