def generate(X, seqType, args):
'''
# Reference-1: Z-Scale (iFeature)
# Reference-2: https://pubs.acs.org/doi/suppl/10.1021/jm9700575/suppl_file/jm2481.pdf
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'PROT':
d = {
'A': [0.24, -2.32, 0.60, -0.14, 1.30], # A
'C': [0.84, -1.67, 3.71, 0.18, -2.65], # C
'D': [3.98, 0.93, 1.93, -2.46, 0.75], # D
'E': [3.11, 0.26, -0.11, -0.34, -0.25], # E
'F': [-4.22, 1.94, 1.06, 0.54, -0.62], # F
'G': [2.05, -4.06, 0.36, -0.82, -0.38], # G
'H': [2.47, 1.95, 0.26, 3.90, 0.09], # H
'I': [-3.89, -1.73, -1.71, -0.84, 0.26], # I
'K': [2.29, 0.89, -2.49, 1.49, 0.31], # K
'L': [-4.28, -1.30, -1.49, -0.72, 0.84], # L
'M': [-2.85, -0.22, 0.47, 1.94, -0.98], # M
'N': [3.05, 1.62, 1.04, -1.15, 1.61], # N
'P': [-1.66, 0.27, 1.84, 0.70, 2.00], # P
'Q': [1.75, 0.50, -1.44, -1.34, 0.66], # Q
'R': [3.52, 2.50, -3.50, 1.99, -0.17], # R
'S': [2.39, -1.07, 1.15, -1.39, 0.67], # S
'T': [0.75, -2.18, -1.12, -1.46, -0.40], # T
'V': [-2.59, -2.64, -1.54, -0.85, -0.02], # V
'W': [-4.36, 3.94, 0.59, 3.44, -1.59], # W
'Y': [-2.54, 2.44, 0.43, 0.04, -1.47], # Y
'p': [0, 0, 0, 0, 0], # p
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(
CRED +
'Error: The \'Physicochemical Properties-P4\' feature is NOT applicable for DNA/RNA.'
+ CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA': None
else:
if seqType == 'PROT':
totalFeature = 5
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpP4')
def generate(X, seqType, args):
'''
# Reference: Spider-2
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'PROT':
d = {
'A': [-0.350, -0.680, -0.677, -0.171, -0.170, 0.900, -0.476],
'C': [-0.140, -0.329, -0.359, 0.508, -0.114, -0.652, 0.476],
'D': [-0.213, -0.417, -0.281, -0.767, -0.900, -0.155, -0.635],
'E': [-0.230, -0.241, -0.058, -0.696, -0.868, 0.900, -0.582],
'F': [0.363, 0.373, 0.412, 0.646, -0.272, 0.155, 0.318],
'G': [-0.900, -0.900, -0.900, -0.342, -0.179, -0.900, -0.900],
'H': [0.384, 0.110, 0.138, -0.271, 0.195, -0.031, -0.106],
'I': [0.900, -0.066, -0.009, 0.652, -0.186, 0.155, 0.688],
'K': [-0.088, 0.066, 0.163, -0.889, 0.727, 0.279, -0.265],
'L': [0.213, -0.066, -0.009, 0.596, -0.186, 0.714, -0.053],
'M': [0.110, 0.066, 0.087, 0.337, -0.262, 0.652, -0.001],
'N': [-0.213, -0.329, -0.243, -0.674, -0.075, -0.403, -0.529],
'P': [0.247, -0.900, -0.294, 0.055, -0.010, -0.900, 0.106],
'Q': [-0.230, -0.110, -0.020, -0.464, -0.276, 0.528, -0.371],
'R': [0.105, 0.373, 0.466, -0.900, 0.900, 0.528, -0.371],
'S': [-0.337, -0.637, -0.544, -0.364, -0.265, -0.466, -0.212],
'T': [0.402, -0.417, -0.321, -0.199, -0.288, -0.403, 0.212],
'V': [0.677, -0.285, -0.232, 0.331, -0.191, -0.031, 0.900],
'W': [0.479, 0.900, 0.900, 0.900, -0.209, 0.279, 0.529],
'Y': [0.363, 0.417, 0.541, 0.188, -0.274, -0.155, 0.476],
'p': [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(
CRED +
'Error: The \'Physicochemical Properties-P5\' feature is NOT applicable for DNA/RNA.'
+ CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA': None
else:
if seqType == 'PROT':
totalFeature = 7
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpP5')
def generate(X, seqType, args):
'''
# Reference: It is a very common feature.
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'DNA':
d = {
'A': [0, 5, 5, 1],
'C': [5, 1, 0, 5],
'G': [1, 5, 5, 0],
'T': [5, 0, 1, 5],
'p': [0, 0, 0, 0], # padding
}
else:
if seqType == 'RNA':
d = {
'A': [0, 5, 5, 1],
'C': [5, 1, 0, 5],
'G': [1, 5, 5, 0],
'U': [5, 0, 1, 5],
'p': [0, 0, 0, 0], # padding
}
else:
if seqType == 'PROT':
print(CRED + 'Error: The \'Transition-Transversion\' feature is NOT applicable for PROT.' + CEND)
return None
else: None
#end-if
# print(X)
X = utils.processMono(X, d, args)
# print(X.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
totalFeature = 4
else:
if seqType == 'PROT': None
else:
None
# end-if
save.datasetSave(X, totalFeature, 'tt')
#end-def
def generate(X, seqType, args):
'''
# Reference-1: http://rosalind.info/glossary/blosum62/
# Reference-2: https://www.pnas.org/content/89/22/10915/
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'PROT':
d = {
'A': [
4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0,
0, -3, -2
],
'C': [
0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1,
-1, -1, -2, -2
],
'D': [
-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1,
-3, -4, -3
],
'E': [
-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2,
-3, -2
],
'F': [
-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2,
-1, 1, 3
],
'G': [
0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2,
-3, -2, -3
],
'H': [
-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2,
-3, -2, 2
],
'I': [
-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1,
3, -3, -1
],
'K': [
-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1,
-2, -3, -2
],
'L': [
-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1,
1, -2, -1
],
'M': [
-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1,
1, -1, -1
],
'N': [
-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3,
-4, -2
],
'P': [
-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1,
-1, -2, -4, -3
],
'Q': [
-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2,
-2, -1
],
'R': [
-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1,
-3, -3, -2
],
'S': [
1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2,
-3, -2
],
'T': [
0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5,
0, -2, -2
],
'V': [
0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0,
4, -3, -1
],
'W': [
-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3,
-2, -3, 11, 2
],
'Y': [
-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2,
-2, -1, 2, 7
],
'p': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(
CRED +
'Error: The \'BLOSUM62\' feature is NOT applicable for DNA/RNA.'
+ CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
# print(X.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
None
else:
if seqType == 'PROT':
totalFeature = 20
else:
None
# end-if
save.datasetSave(X, totalFeature, 'blosum62')
def generate(X, seqType, args):
'''
# Reference: https://www.biorxiv.org/content/10.1101/332171v2.full.pdf (Supp: Table-5)
:param X:
:param seqType:
:param args:
:return:
'''
# Column1 --> Acidic : D, E
# Column2 --> Basic : R, H, K
# Column3 --> Aromatic side chain : Y, F, W
# Column4 --> Aliphatic side chain: I, L, V, A, G
# Column5 --> Cyclic : P
# Column6 --> Sulfur containing : M, C
# Column7 --> Hydroxyl containing : S, T
# Column8 --> Acidic amide : Q, N
# [1, 0, 0, 0, 0, 0, 0, 0], #Acidic
# [0, 1, 0, 0, 0, 0, 0, 0], #Basic
# [0, 0, 1, 0, 0, 0, 0, 0], #Aromatic side chain
# [0, 0, 0, 1, 0, 0, 0, 0], #Aliphatic side chain
# [0, 0, 0, 0, 1, 0, 0, 0], #Cyclic
# [0, 0, 0, 0, 0, 1, 0, 0], #Sulfur containing
# [0, 0, 0, 0, 0, 0, 1, 0], #Hydroxyl containing
# [0, 0, 0, 0, 0, 0, 0, 1], #Acidic amide
# [0, 0, 0, 0, 0, 0, 0, 0], #padding
if seqType == 'PROT':
d = {
'A': [0, 0, 0, 1, 0, 0, 0, 0], #Aliphatic side chain
'C': [0, 0, 0, 0, 0, 1, 0, 0], #Sulfur containing
'D': [1, 0, 0, 0, 0, 0, 0, 0], #Acidic
'E': [1, 0, 0, 0, 0, 0, 0, 0], #Acidic
'F': [0, 0, 1, 0, 0, 0, 0, 0], #Aromatic side chain
'G': [0, 0, 0, 1, 0, 0, 0, 0], #Aliphatic side chain
'H': [0, 1, 0, 0, 0, 0, 0, 0], #Basic
'I': [0, 0, 0, 1, 0, 0, 0, 0], #Aliphatic side chain
'K': [0, 1, 0, 0, 0, 0, 0, 0], #Basic
'L': [0, 0, 0, 1, 0, 0, 0, 0], #Aliphatic side chain
'M': [0, 0, 0, 0, 0, 1, 0, 0], #Sulfur containing
'N': [0, 0, 0, 0, 0, 0, 0, 1], #Acidic amide
'P': [0, 0, 0, 0, 1, 0, 0, 0], #Cyclic
'Q': [0, 0, 0, 0, 0, 0, 0, 1], #Acidic amide
'R': [0, 1, 0, 0, 0, 0, 0, 0], #Basic
'S': [0, 0, 0, 0, 0, 0, 1, 0], #Hydroxyl containing
'T': [0, 0, 0, 0, 0, 0, 1, 0], #Hydroxyl containing
'V': [0, 0, 0, 1, 0, 0, 0, 0], #Aliphatic side chain
'W': [0, 0, 1, 0, 0, 0, 0, 0], #Aromatic side chain
'Y': [0, 0, 1, 0, 0, 0, 0, 0], #Aromatic side chain
'p': [0, 0, 0, 0, 0, 0, 0, 0], #padding
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(
CRED +
'Error: The \'Physicochemical Properties-P3\' feature is NOT applicable for DNA/RNA.'
+ CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA': None
else:
if seqType == 'PROT':
totalFeature = 8
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpP3')
def generate(X, seqType, args):
'''
# Reference: https://doi.org/10.1016/j.omtn.2019.04.025 (It is also called "identity matrix".)
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'DNA':
d = {
'A': [1, 0, 0, 0],
'C': [0, 1, 0, 0],
'G': [0, 0, 1, 0],
'T': [0, 0, 0, 1],
'p': [0, 0, 0, 0], # padding
}
else:
if seqType == 'RNA':
d = {
'A': [1, 0, 0, 0],
'C': [0, 1, 0, 0],
'G': [0, 0, 1, 0],
'U': [0, 0, 0, 1],
'p': [0, 0, 0, 0], # padding
}
else:
if seqType == 'PROT':
# Protein/Peptide One-Zero Encoding
d = {
'A': [
1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'C': [
0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'D': [
0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'E': [
0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'F': [
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'G': [
0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'H': [
0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'I': [
0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'K': [
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'L': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'M': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0
],
'N': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0
],
'P': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0,
0, 0
],
'Q': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
0, 0
],
'R': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0,
0, 0
],
'S': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
0, 0
],
'T': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0
],
'V': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
0, 0
],
'W': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 0
],
'Y': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 1
],
'p': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0
], # padding
}
else:
None
#end-if
# print(X)
X = utils.processMono(X, d, args)
# print(X.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
totalFeature = 4
else:
if seqType == 'PROT':
totalFeature = 20
else:
None
# end-if
save.datasetSave(X, totalFeature, 'bpf')
#end-def
def generate(X, seqType, args):
'''
# Reference: https://doi.org/10.1093/bioinformatics/bty451 (Supp: Table S2)
:param X:
:param seqType:
:param args:
:return:
'''
# Column1 --> Aromatic: {F, Y, W, H}
# Column2 --> Negative: {D, E}
# Column3 --> Positive: {K, H, R}
# Column4 --> Polar: {N, Q, S, D, E, C, T, K, R, H, Y, W}
# Column5 --> Hydrophobic: {A, G, C, T, I, V, L, K, H, F, Y, W, M}
# Column6 --> Aliphatic: {I, V, L}
# Column7 --> Tiny: {A, S, G, C}
# Column8 --> Charged: {K, H, R, D, E}
# Column9 --> Small: {P, N, D, T, C, A, G, S, V}
# Column10 --> Proline: {P}
if seqType == 'PROT':
d = {
'A': [0, 0, 0, 0, 1, 0, 1, 0, 1, 0],
'R': [0, 0, 1, 1, 0, 0, 0, 1, 0, 0],
'N': [0, 0, 0, 1, 0, 0, 0, 0, 1, 0],
'D': [0, 1, 0, 1, 0, 0, 0, 1, 1, 0],
'C': [0, 0, 0, 1, 1, 0, 1, 0, 1, 0],
'Q': [0, 0, 0, 1, 0, 0, 0, 0, 0, 0],
'E': [0, 1, 0, 1, 0, 0, 0, 1, 0, 0],
'G': [0, 0, 0, 0, 1, 0, 1, 0, 1, 0],
'H': [1, 0, 1, 1, 1, 0, 0, 1, 0, 0],
'I': [0, 0, 0, 0, 1, 1, 0, 0, 0, 0],
'L': [0, 0, 0, 0, 1, 1, 0, 0, 0, 0],
'K': [0, 0, 1, 1, 1, 0, 0, 1, 0, 0],
'M': [0, 0, 0, 0, 1, 0, 0, 0, 0, 0],
'F': [1, 0, 0, 0, 1, 0, 0, 0, 0, 0],
'P': [0, 0, 0, 0, 0, 0, 0, 0, 1, 1],
'S': [0, 0, 0, 1, 0, 0, 1, 0, 1, 0],
'T': [0, 0, 0, 1, 1, 0, 0, 0, 1, 0],
'W': [1, 0, 0, 1, 1, 0, 0, 0, 0, 0],
'Y': [1, 0, 0, 1, 1, 0, 0, 0, 0, 0],
'V': [0, 0, 0, 0, 1, 1, 0, 0, 1, 0],
'p': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(CRED+'Error: The \'Physicochemical Properties-P1\' feature is NOT applicable for DNA/RNA.'+CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA': None
else:
if seqType == 'PROT':
totalFeature = 10
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpP1')
def generate(X, seqType, args):
'''
# Reference-1: http://rosalind.info/glossary/pam250/
# Reference-2: http://profs.scienze.univr.it/~liptak/ALBioinfo/2011_2012/files/pam1.pdf (M.O. Dayhoff et al.)
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'PROT':
d = {
'A': [
2, -2, 0, 0, -3, 1, -1, -1, -1, -2, -1, 0, 1, 0, -2, 1, 1, 0,
-6, -3
],
'C': [
-2, 12, -5, -5, -4, -3, -3, -2, -5, -6, -5, -4, -3, -5, -4, 0,
-2, -2, -8, 0
],
'D': [
0, -5, 4, 3, -6, 1, 1, -2, 0, -4, -3, 2, -1, 2, -1, 0, 0, -2,
-7, -4
],
'E': [
0, -5, 3, 4, -5, 0, 1, -2, 0, -3, -2, 1, -1, 2, -1, 0, 0, -2,
-7, -4
],
'F': [
-3, -4, -6, -5, 9, -5, -2, 1, -5, 2, 0, -3, -5, -5, -4, -3, -3,
-1, 0, 7
],
'G': [
1, -3, 1, 0, -5, 5, -2, -3, -2, -4, -3, 0, 0, -1, -3, 1, 0, -1,
-7, -5
],
'H': [
-1, -3, 1, 1, -2, -2, 6, -2, 0, -2, -2, 2, 0, 3, 2, -1, -1, -2,
-3, 0
],
'I': [
-1, -2, -2, -2, 1, -3, -2, 5, -2, 2, 2, -2, -2, -2, -2, -1, 0,
4, -5, -1
],
'K': [
-1, -5, 0, 0, -5, -2, 0, -2, 5, -3, 0, 1, -1, 1, 3, 0, 0, -2,
-3, -4
],
'L': [
-2, -6, -4, -3, 2, -4, -2, 2, -3, 6, 4, -3, -3, -2, -3, -3, -2,
2, -2, -1
],
'M': [
-1, -5, -3, -2, 0, -3, -2, 2, 0, 4, 6, -2, -2, -1, 0, -2, -1,
2, -4, -2
],
'N': [
0, -4, 2, 1, -3, 0, 2, -2, 1, -3, -2, 2, 0, 1, 0, 1, 0, -2, -4,
-2
],
'P': [
1, -3, -1, -1, -5, 0, 0, -2, -1, -3, -2, 0, 6, 0, 0, 1, 0, -1,
-6, -5
],
'Q': [
0, -5, 2, 2, -5, -1, 3, -2, 1, -2, -1, 1, 0, 4, 1, -1, -1, -2,
-5, -4
],
'R': [
-2, -4, -1, -1, -4, -3, 2, -2, 3, -3, 0, 0, 0, 1, 6, 0, -1, -2,
2, -4
],
'S': [
1, 0, 0, 0, -3, 1, -1, -1, 0, -3, -2, 1, 1, -1, 0, 2, 1, -1,
-2, -3
],
'T': [
1, -2, 0, 0, -3, 0, -1, 0, 0, -2, -1, 0, 0, -1, -1, 1, 3, 0,
-5, -3
],
'V': [
0, -2, -2, -2, -1, -1, -2, 4, -2, 2, 2, -2, -1, -2, -2, -1, 0,
4, -6, -2
],
'W': [
-6, -8, -7, -7, 0, -7, -3, -5, -3, -2, -4, -4, -6, -5, 2, -2,
-5, -6, 17, 0
],
'Y': [
-3, 0, -4, -4, 7, -5, 0, -1, -4, -1, -2, -2, -5, -4, -4, -3,
-3, -2, 0, 10
],
'p': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(
CRED +
'Error: The \'PAM250\' feature is NOT applicable for DNA/RNA.'
+ CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
# print(X.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
None
else:
if seqType == 'PROT':
totalFeature = 20
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pam250')
def generate(X, seqType, args):
'''
# Reference: https://doi.org/10.1093/bioinformatics/bty451 (Supp: Table S3)
:param X:
:param seqType:
:param args:
:return:
'''
### Group-1:
# Column1 --> Hydrophobicity: {A, C, F, G, H, I, L, M, N, P, Q, S, T, V, W, Y}
# Column2 --> Normalized Van der Waals volume: {C, F, I, L, M, V, W}
# Column3 --> Polarity: {A, C, D, G, P, S, T}
# Column4 --> Polarizibility: {C, F, I, L, M, V, W, Y}
# Column5 --> Charge: {A, D, G, S, T}
# Column6 --> Secondary structures: {D, G, N, P, S}
# Column7 --> Solvent accessibility: {A, C, F, G, I, L, V, W}
### Group-2:
# Column8 --> Hydrophobicity: {D, E}
# Column9 --> Normalized Van der Waals volume: {A, G, H, P, S, T, Y}
# Column10 --> Polarity: {E, I, L, N, Q, V}
# Column11 --> Polarizibility: {A, G, P, S, T}
# Column12 --> Charge: {C, E, I, L, N, P, Q, V}
# Column13 --> Secondary structures: {A, E, H, K, L, M, Q, R}
# Column14 --> Solvent accessibility: {H, M, P, S, T, Y}
### Group-3:
# Column15 --> Hydrophobicity: {K, R}
# Column16 --> Normalized Van der Waals volume: {D, E, K, N, Q, R}
# Column17 --> Polarity: {F, H, K, M, R, W, Y}
# Column18 --> Polarizibility: {D, E, H, K, N, Q, R}
# Column19 --> Charge: {F, H, K, M, R, W, Y}
# Column20 --> Secondary structures: {C, F, I, T, V, W, Y}
# Column21 --> Solvent accessibility: {D, E, K, N, R, Q}
if seqType == 'PROT':
d = {
'A':
[1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0],
'R':
[0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1],
'N':
[1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1],
'D':
[0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1],
'C':
[1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0],
'Q':
[1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1],
'E':
[0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1],
'G':
[1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0],
'H':
[1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 0],
'I':
[1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0],
'L':
[1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0],
'K':
[0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1],
'M': [
1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0
],
'F': [
1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0
],
'P': [
1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0
],
'S': [
1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0
],
'T': [
1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0
],
'W': [
1, 0, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0
],
'Y': [
1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0
],
'V': [
1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 0, 0
],
'p': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
],
}
else:
if seqType == 'DNA' or seqType == 'RNA':
print(
CRED +
'Error: The \'Physicochemical Properties-P2\' feature is NOT applicable for DNA/RNA.'
+ CEND)
return None
else:
return None
#end-if
X = utils.processMono(X, d, args)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA': None
else:
if seqType == 'PROT':
totalFeature = 21
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpP2')