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distance_canberraword.py
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distance_canberraword.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],[traindna,testdna,3,0,False]]
def distance_canberraword (fm_train_dna=traindna,fm_test_dna=testdna,order=3,gap=0,reverse=False):
from shogun import StringCharFeatures, StringWordFeatures, DNA
from shogun import SortWordString
from shogun import CanberraWordDistance
charfeat=StringCharFeatures(DNA)
charfeat.set_features(fm_train_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(DNA)
charfeat.set_features(fm_test_dna)
feats_test=StringWordFeatures(charfeat.get_alphabet())
feats_test.obtain_from_char(charfeat, order-1, order, gap, reverse)
feats_test = preproc.apply(feats_test)
distance=CanberraWordDistance(feats_train, feats_train)
dm_train=distance.get_distance_matrix()
distance.init(feats_train, feats_test)
dm_test=distance.get_distance_matrix()
return distance,dm_train,dm_test
if __name__=='__main__':
print('CanberraWordDistance')
distance_canberraword(*parameter_list[0])