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preprocessor_sortwordstring.py
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preprocessor_sortwordstring.py
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#!/usr/bin/env python
from tools.load import LoadMatrix
lm=LoadMatrix()
traindna = lm.load_dna('../data/fm_train_dna.dat')
testdna = lm.load_dna('../data/fm_test_dna.dat')
parameter_list = [[traindna,testdna,3,0,False,False],[traindna,testdna,3,0,False,False]]
def preprocessor_sortwordstring (fm_train_dna=traindna,fm_test_dna=testdna,order=3,gap=0,reverse=False,use_sign=False):
from shogun import CommWordStringKernel
from shogun import StringCharFeatures, StringWordFeatures, DNA
from shogun import SortWordString
charfeat=StringCharFeatures(fm_train_dna, DNA)
feats_train=StringWordFeatures(charfeat.get_alphabet())
feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse)
preproc = SortWordString()
preproc.fit(feats_train)
feats_train = preproc.apply(feats_train)
charfeat=StringCharFeatures(fm_test_dna, DNA)
feats_test=StringWordFeatures(charfeat.get_alphabet())
feats_test.obtain_from_char(charfeat, order-1, order, gap, reverse)
feats_test = preproc.apply(feats_test)
kernel=CommWordStringKernel(feats_train, feats_train, use_sign)
km_train=kernel.get_kernel_matrix()
kernel.init(feats_train, feats_test)
km_test=kernel.get_kernel_matrix()
return km_train,km_test,kernel
if __name__=='__main__':
print('CommWordString')
preprocessor_sortwordstring(*parameter_list[0])