def getMatrix(dirname):
pssmList = os.listdir(dirname)
pssmList.sort(key=lambda x: eval(x[:]))
m = len(pssmList)
reMatrix = np.zeros((m, 1000))
for i in range(m):
matrix = readToMatrix(dirname + '/' + pssmList[i], 'psfm')
matrix = autoNorm(matrix, 'psfm')
binaryMatrix = [ # A R N D C Q E G H I L K M F P S T W Y V
[
-1.56, -1.67, -0.97, -0.27, -0.93, -0.78, -0.2, -0.08, 0.21,
-0.48
], # a
[0.22, 1.27, 1.37, 1.87, -1.7, 0.46, 0.92, -0.39, 0.23, 0.93], # r
[1.14, -0.07, -0.12, 0.81, 0.18, 0.37, -0.09, 1.23, 1.1,
-1.73], # n
[0.58, -0.22, -1.58, 0.81, -0.92, 0.15, -1.52, 0.47, 0.76,
0.7], # d
[0.12, -0.89, 0.45, -1.05, -0.71, 2.41, 1.52, -0.69, 1.13,
1.1], # c
[-0.47, 0.24, 0.07, 1.1, 1.1, 0.59, 0.84, -0.71, -0.03,
-2.33], # q
[-1.45, 0.19, -1.61, 1.17, -1.31, 0.4, 0.04, 0.38, -0.35,
-0.12], # e
[1.46, -1.96, -0.23, -0.16, 0.1, -0.11, 1.32, 2.36, -1.66,
0.46], # g
[-0.41, 0.52, -0.28, 0.28, 1.61, 1.01, -1.85, 0.47, 1.13,
1.63], # h
[-0.73, -0.16, 1.79, -0.77, -0.54, 0.03, -0.83, 0.51, 0.66,
-1.78], # i
[-1.04, 0.0, -0.24, -1.1, -0.55, -2.05, 0.96, -0.76, 0.45,
0.93], # l
[-0.34, 0.82, -0.23, 1.7, 1.54, -1.62, 1.15, -0.08, -0.48,
0.6], # k
[-1.4, 0.18, -0.42, -0.73, 2.0, 1.52, 0.26, 0.11, -1.27,
0.27], # m
[-0.21, 0.98, -0.36, -1.43, 0.22, -0.81, 0.67, 1.1, 1.71,
-0.44], # f
[2.06, -0.33, -1.15, -0.75, 0.88, -0.45, 0.3, -2.3, 0.74,
-0.28], # p
[
0.81, -1.08, 0.16, 0.42, -0.21, -0.43, -1.89, -1.15, -0.97,
-0.23
], # s
[0.26, -0.7, 1.21, 0.63, -0.1, 0.21, 0.24, -1.15, -0.56,
0.19], # t
[0.3, 2.1, -0.72, -1.57, -1.16, 0.57, -0.48, -0.4, -2.3,
-0.6], # w
[1.38, 1.48, 0.8, -0.56, 0.0, -0.68, -0.31, 1.03, -0.05,
0.53], # y
[-0.74, -0.71, 2.04, -0.4, 0.5, -0.81, -1.07, 0.06, -0.46, 0.65],
] # v 20*10
binaryMatrix = autoNormTenFactor(np.array(binaryMatrix))
WHmatrix = np.dot(matrix, binaryMatrix) # L*10
reMatrix[i, :] = getACC(WHmatrix, 10)
print(reMatrix.shape)
return reMatrix
def getMatrix(dirname):
pssmList = os.listdir(dirname)
pssmList.sort(key=lambda x: eval(x[:]))
m = len(pssmList)
reMatrix = np.zeros((m, 400*3))
for i in range(m):
matrix = readToMatrix(dirname + '/' + pssmList[i], 'pssm')
matrix = autoNorm(matrix, 'pssm')
reMatrix[i, :] = np.hstack(getEDT(matrix,3))
print(reMatrix.shape)
return reMatrix