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/k-mer-composition/) # It is also called "k-mer composition".
# Reference-2: iRecSpot-EF: https://www.sciencedirect.com/science/article/abs/pii/S0010482518302981
:param X:
:param seqType:
:param args:
:return:
'''
elements = utils.sequenceElements(seqType)
# print(elements)
# print(args.gGap)
# print(args.kTuple)
T = []
for x in X:
x = x[:args.terminusLength]
t = []
for i in range(1, args.kTuple + 1, 1):
v = list(itertools.product(elements, repeat=i))
# seqLength = len(x) - i + 1
for i in v:
# print(x.count(''.join(i)), end=',')
t.append(x.count(''.join(i)))
### --- ###
t = np.array(t)
# t = t.reshape(-1, 1)
# print(t.shape)
T.append(t)
#end-for
T = np.array(T)
# print(T.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
totalFeature = np.sum([4**(i) for i in range(1, args.kTuple + 1)])
else:
if seqType == 'PROT':
totalFeature = np.sum([20**(i) for i in range(1, args.kTuple + 1)])
else:
None
#end-if
save.datasetSave(T, totalFeature, 'fkmer')
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):
'''
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'DNA' or seqType == 'RNA':
p = [0] * (4 * 4) # As we are working for g11
else:
if seqType == 'PROT':
p = [0] * (20 * 20) # As we are working for g11
else:
None
# Trail: Merged
elements = utils.sequenceElements(seqType)
m = list(itertools.product(elements, repeat=2))
T = []
for x in X:
merged = []
x = x[:args.terminusLength]
for i in range(1, args.gGap + 1):
kmers = utils.kmers(x, 2 + i) # g11 --> 2, gGap (g11+gGap)
t = []
require = (args.terminusLength - (2 + 1) + 1) - (len(x) -
(2 + i) + 1)
for kmer in kmers:
d = {''.join(_): 0 for _ in m}
segment = kmer[0] + kmer[-1]
d[segment] = 1
t.append(list(d.values()))
# break
# break
# print(v)
if require > 0:
for i in range(require):
t.append(p)
# end-for
else:
None
t = np.array(t)
# print(t)
merged.append(t)
# print('------------------')
# end-for
T.append(np.concatenate((merged), axis=1))
# end-for
T = np.array(T)
# print(T.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
totalFeature = (4 * args.gGap * 4)
else:
if seqType == 'PROT':
totalFeature = (20 * args.gGap * 20)
else:
None
# end-if
save.datasetSave(T, totalFeature, 'pg11')
#end-for
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: repRNA
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'RNA':
d = {
'AA': [
2.000, 0.000, -6.600, -6.820, -18.400, -19.000, -0.900, -0.930,
0.000, 0.000, 0.023, 0.040, 0.000, 2.000, 3.180, 7.000, -0.080,
-1.270, -13.700, 0.000, -0.800, 31.000
],
'AC': [
1.000, 1.000, -10.200, -11.400, -26.200, -29.500, -2.100,
-2.240, 1.000, 0.000, 0.083, 0.140, 0.000, 1.000, 3.240, 4.800,
0.230, -1.430, -13.800, 0.000, 0.800, 32.000
],
'AG': [
1.000, 0.000, -7.600, -10.480, -19.200, -27.100, -1.700,
-2.080, 1.000, 1.000, 0.035, 0.080, 0.000, 2.000, 3.300, 8.500,
-0.040, -1.500, -14.000, 0.000, 0.500, 30.000
],
'AU': [
1.000, 0.000, -5.700, -9.380, -15.500, -26.700, -0.900, -1.100,
0.000, 0.000, 0.090, 0.140, 1.000, 1.000, 3.240, 7.100, -0.060,
-1.360, -15.400, 1.000, 1.100, 33.000
],
'CA': [
1.000, 1.000, -10.500, -10.440, -27.800, -26.900, -1.800,
-2.110, 1.000, 0.000, 0.118, 0.210, 0.000, 1.000, 3.090, 9.900,
0.110, -1.460, -14.400, 0.000, 1.000, 31.000
],
'CC': [
0.000, 2.000, -12.200, -13.390, -29.700, -32.700, -2.900,
-3.260, 2.000, 0.000, 0.349, 0.490, 0.000, 0.000, 3.320, 8.700,
-0.010, -1.780, -11.100, 0.000, 0.300, 32.000
],
'CG': [
0.000, 1.000, -8.000, -10.640, -19.400, -26.700, -2.000,
-2.360, 2.000, 1.000, 0.193, 0.350, 1.000, 1.000, 3.300,
12.100, 0.300, -1.890, -15.600, 0.000, -0.100, 27.000
],
'CU': [
0.000, 1.000, -7.600, -10.480, -19.200, -27.100, -1.700,
-2.080, 1.000, 0.000, 0.378, 0.520, 1.000, 0.000, 3.300, 8.500,
-0.040, -1.500, -14.000, 1.000, 0.500, 30.000
],
'GA': [
1.000, 0.000, -13.300, -12.440, -35.500, -32.500, -2.300,
-2.350, 1.000, 1.000, 0.048, 0.100, 1.000, 2.000, 3.380, 9.400,
0.070, -1.700, -14.200, 0.000, 1.300, 32.000
],
'GC': [
0.000, 1.000, -14.200, -14.880, -34.900, -36.900, -3.400,
-3.420, 2.000, 1.000, 0.146, 0.260, 1.000, 1.000, 3.220, 6.100,
0.070, -1.390, -16.900, 0.000, 0.000, 35.000
],
'GG': [
0.000, 0.000, -12.200, -13.390, -29.700, -32.700, -2.900,
-3.260, 2.000, 2.000, 0.065, 0.170, 2.000, 2.000, 3.320,
12.100, -0.010, -1.780, -11.100, 0.000, 0.300, 32.000
],
'GU': [
0.000, 0.000, -10.200, -11.400, -26.200, -29.500, -2.100,
-2.240, 1.000, 1.000, 0.160, 0.270, 2.000, 1.000, 3.240, 4.800,
0.230, -1.430, -13.800, 1.000, 0.800, 32.000
],
'UA': [
1.000, 0.000, -8.100, -7.690, -22.600, -20.500, -1.100, -1.330,
0.000, 0.000, 0.112, 0.210, 1.000, 1.000, 3.260, 10.700,
-0.020, -1.450, -16.000, 1.000, -0.200, 32.000
],
'UC': [
0.000, 1.000, -10.200, -12.440, -26.200, -32.500, -2.100,
-2.350, 1.000, 0.000, 0.359, 0.480, 1.000, 0.000, 3.380, 9.400,
0.070, -1.700, -14.200, 1.000, 1.300, 32.000
],
'UG': [
0.000, 0.000, -7.600, -10.440, -19.200, -26.900, -1.700,
-2.110, 1.000, 1.000, 0.224, 0.340, 1.000, 1.000, 3.090, 9.900,
0.110, -1.460, -14.400, 1.000, 1.000, 31.000
],
'UU': [
0.000, 0.000, -6.600, -6.820, -18.400, -19.000, -0.900, -0.930,
0.000, 0.000, 0.389, 0.440, 2.000, 0.000, 3.180, 7.000, -0.080,
-1.270, -13.700, 2.000, -0.800, 31.000
],
'p': [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0
], # padding
}
else:
if seqType == 'PROT' or seqType == 'DNA':
print(
CRED +
'Error: The \'Physicochemical Properties-R1\' feature is NOT applicable for PROT and DNA.'
+ CEND)
return None
else:
None
#end-if
# print(X)
X = utils.processDi(X, d, args)
# print(X.shape)
totalFeature = 0
if seqType == 'RNA':
totalFeature = 22
else:
if seqType == 'PROT' or seqType == 'DNA': None
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpR1')
#end-def
def generate(X, seqType, args):
'''
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'DNA' or seqType == 'RNA':
p = [0] * (4**args.kTuple)
else:
if seqType == 'PROT':
p = [0] * (20**args.kTuple)
else:
None
# print(p)
# print(len(p))
elements = utils.sequenceElements(seqType)
m = list(itertools.product(elements, repeat=args.kTuple))
terminusLength = args.terminusLength
# print(terminusLength)
T = []
for x in X:
# print(len(x))
x = x[:terminusLength]
# print(len(x))
# print('-----------------')
require = (terminusLength - args.kTuple + 1) - (len(x) - args.kTuple +
1)
# print(require)
t = []
kmers = utils.kmers(x, args.kTuple)
for kmer in kmers:
d = {''.join(i): 0 for i in m}
d[kmer] = 1
t.append(list(d.values()))
#end-for
if require > 0:
for i in range(require):
t.append(p)
#end-for
else:
None
t = np.array(t)
# print(t.shape)
T.append(t)
# print(t.shape)
#end-for
T = np.array(T)
# print(T.shape)
totalFeature = 0
if seqType == 'DNA' or seqType == 'RNA':
totalFeature = (4**args.kTuple)
else:
if seqType == 'PROT':
totalFeature = (20**args.kTuple)
else:
None
# end-if
save.datasetSave(T, totalFeature, 'pkmer')
#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')
def generate(X, seqType, args):
'''
# Reference: repRNA
:param X:
:param seqType:
:param args:
:return:
'''
if seqType == 'DNA':
d = {
'GGG': [5.7000, 5.8500, 3.0000, 13.0000, 5.8270, 5.8270, 3.3110, 3.8680, 622.4000, 103.3887, 6.0000,3.5360, ],
'GGA': [6.2000, 5.0000, 2.0000, -5.0000, 4.9907, 4.9907, 3.8190, 3.5810, 622.4000, 103.3887, 3.8000,4.7990, ],
'GGC': [8.2000, 9.1000, 3.0000, 45.0000, 9.0823, 9.0823, 1.3870, 2.4480, 622.4000, 103.3887, 10.0000,1.3090, ],
'GGT': [5.2000, 5.3000, 2.0000, 8.0000, 5.3160, 5.3160, 3.6190, 4.1560, 622.4000, 103.3887, 5.4000,3.8780, ],
'GAG': [6.6000, 6.0000, 2.0000, 8.0000, 5.9806, 5.9806, 3.2210, 3.3530, 621.4000, 103.2226, 5.4000,3.8780, ],
'GAA': [5.1000, 4.0500, 1.0000, -12.0000, 4.0633, 4.0633, 4.3850, 4.2140, 621.4000, 103.2226, 3.0000,5.2640, ],
'GAC': [5.6000, 5.5000, 2.0000, 8.0000, 5.5164, 5.5164, 3.4980, 3.9250, 621.4000, 103.2226, 5.4000,3.8780, ],
'GAT': [3.6000, 4.4500, 1.0000, 7.0000, 4.4432, 4.4432, 4.1530, 5.0870, 621.4000, 103.2226, 5.3000,3.9350, ],
'GCG': [4.3000, 5.9000, 3.0000, 25.0000, 5.8914, 5.8914, 3.2750, 4.6780, 622.4000, 103.3887, 7.5000,2.6910, ],
'GCA': [7.5000, 6.7500, 2.0000, 13.0000, 6.7553, 6.7553, 2.7540, 2.8420, 622.4000, 103.3887, 6.0000,3.5360, ],
'GCC': [8.2000, 9.1000, 3.0000, 45.0000, 9.0823, 9.0823, 1.3870, 2.4480, 622.4000, 103.3887, 10.0000, 1.3090, ],
'GCT': [6.3000, 6.9000, 2.0000, 25.0000, 6.8829, 6.8829, 2.6830, 3.5240, 622.4000, 103.3887, 7.5000,2.6910, ],
'GTG': [6.8000, 6.6500, 2.0000, 17.0000, 6.6255, 6.6255, 2.8320, 3.2390, 621.4000, 103.2226, 6.5000,3.2530, ],
'GTA': [6.4000, 5.0500, 1.0000, -6.0000, 5.0673, 5.0673, 3.7700, 3.4670, 621.4000, 103.2226, 3.7000,4.8570, ],
'GTC': [5.6000, 5.5000, 2.0000, 8.0000, 5.5164, 5.5164, 3.4980, 3.9250, 621.4000, 103.2226, 5.4000,3.8780, ],
'GTT': [1.6000, 2.6500, 1.0000, -6.0000, 2.6412, 2.6412, 5.2600, 6.2720, 621.4000, 103.2226, 3.7000,4.8570, ],
'AGG': [4.7000, 5.0500, 2.0000, 8.0000, 5.0523, 5.0523, 3.7820, 4.4450, 622.4000, 103.3887, 5.4000,3.8780, ],
'AGA': [6.5000, 4.9000, 1.0000, -9.0000, 4.8884, 4.8884, 3.8790, 3.4100, 622.4000, 103.3887, 3.3000,5.0890, ],
'AGC': [6.3000, 6.9000, 2.0000, 25.0000, 6.8829, 6.8829, 2.6830, 3.5240, 622.4000, 103.3887, 7.5000,2.6910, ],
'AGT': [2.0000, 3.9000, 1.0000, 11.0000, 3.9232, 3.9232, 4.4710, 6.0330, 622.4000, 103.3887, 5.8000,3.6500, ],
'AAG': [4.2000, 4.7000, 1.0000, 6.0000, 4.6992, 4.6992, 3.9950, 4.7360, 621.4000, 103.2226, 5.2000,3.9920, ],
'AAA': [0.1000, 0.0500, 0.0000, -36.0000, 0.0633, 0.0633, 6.8820, 7.1760, 621.4000, 103.2226, 0.0000,7.0450, ],
'AAC': [1.6000, 2.6500, 1.0000, -6.0000, 2.6412, 2.6412, 5.2600, 6.2720, 621.4000, 103.2226, 3.7000,4.8570, ],
'AAT': [0.0000, 0.3500, 0.0000, -30.0000, 0.3500, 0.3500, 6.6980, 7.2370, 621.4000, 103.2226, 0.7000,6.6240, ],
'ACG': [5.2000, 5.3000, 2.0000, 8.0000, 5.3055, 5.3055, 3.6250, 4.1560, 622.4000, 103.3887, 5.4000,3.8780, ],
'ACA': [5.8000, 5.5000, 1.0000, 6.0000, 5.4903, 5.4903, 3.5160, 3.8100, 622.4000, 103.3887, 5.2000,3.9920, ],
'ACC': [5.2000, 5.3000, 2.0000, 8.0000, 5.3160, 5.3160, 3.6190, 4.1560, 622.4000, 103.3887, 5.4000,3.8780, ],
'ACT': [2.0000, 3.9000, 1.0000, 11.0000, 3.9232, 3.9232, 4.4710, 6.0330, 622.4000, 103.3887, 5.8000,3.6500, ],
'ATG': [8.7000, 7.7000, 1.0000, 18.0000, 7.7171, 7.7171, 2.1850, 2.1690, 621.4000, 103.2226, 6.7000,3.1400, ],
'ATA': [9.7000, 6.2500, 0.0000, -13.0000, 6.2734, 6.2734, 3.0470, 1.6130, 621.4000, 103.2226, 2.8000,5.3810, ],
'ATC': [3.6000, 4.4500, 1.0000, 7.0000, 4.4432, 4.4432, 4.1530, 5.0870, 621.4000, 103.2226, 5.3000,3.9350, ],
'ATT': [0.0000, 0.3500, 0.0000, -30.0000, 0.3500, 0.3500, 6.6980, 7.2370, 621.4000, 103.2226, 0.7000,6.6240, ],
'CGG': [3.0000, 3.8500, 3.0000, 2.0000, 3.8690, 3.8690, 4.5020, 5.4400, 622.4000, 103.3887, 4.7000,4.2790, ],
'CGA': [5.8000, 7.0500, 2.0000, 31.0000, 7.0720, 7.0720, 2.5700, 3.8100, 622.4000, 103.3887, 8.3000,2.2450, ],
'CGC': [4.3000, 5.9000, 3.0000, 25.0000, 5.8914, 5.8914, 3.2750, 4.6780, 622.4000, 103.3887, 7.5000,2.6910, ],
'CGT': [5.2000, 5.3000, 2.0000, 8.0000, 5.3055, 5.3055, 3.6250, 4.1560, 622.4000, 103.3887, 5.4000,3.8780, ],
'CAG': [9.6000, 6.9000, 2.0000, -2.0000, 6.8996, 6.8996, 2.6710, 1.6680, 621.4000, 103.2226, 4.2000,4.5670, ],
'CAA': [6.2000, 4.7500, 1.0000, -9.0000, 4.7618, 4.7618, 3.9580, 3.5810, 621.4000, 103.2226, 3.3000,5.0890, ],
'CAC': [6.8000, 6.6500, 2.0000, 17.0000, 6.6255, 6.6255, 2.8320, 3.2390, 621.4000, 103.2226, 6.5000,3.2530, ],
'CAT': [8.7000, 7.7000, 1.0000, 18.0000, 7.7171, 7.7171, 2.1850, 2.1690, 621.4000, 103.2226, 6.7000,3.1400, ],
'CCG': [3.0000, 3.8500, 3.0000, 2.0000, 3.8690, 3.8690, 4.5020, 5.4400, 622.4000, 103.3887, 4.7000,4.2790, ],
'CCA': [0.7000, 3.0500, 2.0000, 8.0000, 3.0587, 3.0587, 5.0000, 6.8130, 622.4000, 103.3887, 5.4000,3.8780, ],
'CCC': [5.7000, 5.8500, 3.0000, 13.0000, 5.8270, 5.8270, 3.3110, 3.8680, 622.4000, 103.3887, 6.0000,3.5360, ],
'CCT': [4.7000, 5.0500, 2.0000, 8.0000, 5.0523, 5.0523, 3.7820, 4.4450, 622.4000, 103.3887, 5.4000,3.8780, ],
'CTG': [9.6000, 6.9000, 2.0000, -2.0000, 6.8996, 6.8996, 2.6710, 1.6680, 621.4000, 103.2226, 4.2000,4.5670, ],
'CTA': [7.8000, 5.0000, 1.0000, -18.0000, 5.0030, 5.0030, 3.8130, 2.6730, 621.4000, 103.2226, 2.2000,5.7340, ],
'CTC': [6.6000, 6.0000, 2.0000, 8.0000, 5.9806, 5.9806, 3.2210, 3.3530, 621.4000, 103.2226, 5.4000,3.8780, ],
'CTT': [4.2000, 4.7000, 1.0000, 6.0000, 4.6992, 4.6992, 3.9950, 4.7360, 621.4000, 103.2226, 5.2000,3.9920, ],
'TGG': [0.7000, 3.0500, 2.0000, 8.0000, 3.0587, 3.0587, 5.0000, 6.8130, 622.4000, 103.3887, 5.4000,3.8780, ],
'TGA': [10.0000, 7.7000, 1.0000, 8.0000, 7.7000, 7.7000, 10.0000, 1.4470, 622.4000, 103.3887, 5.4000,3.8780, ],
'TGC': [7.5000, 6.7500, 2.0000, 13.0000, 6.7553, 6.7553, 2.7540, 2.8420, 622.4000, 103.3887, 6.0000,3.5360, ],
'TGT': [5.8000, 5.5000, 1.0000, 6.0000, 5.4903, 5.4903, 3.5160, 3.8100, 622.4000, 103.3887, 5.2000,3.9920, ],
'TAG': [7.8000, 5.0000, 1.0000, -18.0000, 5.0030, 5.0030, 3.8130, 2.6730, 621.4000, 103.2226, 2.2000,5.7340, ],
'TAA': [7.3000, 4.6500, 0.0000, -20.0000, 4.6709, 4.6709, 4.0130, 2.9550, 621.4000, 103.2226, 2.0000,5.8520, ],
'TAC': [6.4000, 5.0500, 1.0000, -6.0000, 5.0673, 5.0673, 3.7700, 3.4670, 621.4000, 103.2226, 3.7000,4.8570, ],
'TAT': [9.7000, 6.2500, 0.0000, -13.0000, 6.2734, 6.2734, 3.0470, 1.6130, 621.4000, 103.2226, 2.8000,5.3810, ],
'TCG': [5.8000, 7.0500, 2.0000, 31.0000, 7.0720, 7.0720, 2.5700, 3.8100, 622.4000, 103.3887, 8.3000,2.2450, ],
'TCA': [10.0000, 7.7000, 1.0000, 8.0000, 7.7000, 7.7000, 2.1970, 1.4470, 622.4000, 103.3887, 5.4000,3.8780, ],
'TCC': [6.2000, 5.0000, 2.0000, -5.0000, 4.9907, 4.9907, 3.8190, 3.5810, 622.4000, 103.3887, 3.8000,4.7990, ],
'TCT': [6.5000, 4.9000, 1.0000, -9.0000, 4.8884, 4.8884, 3.8790, 3.4100, 622.4000, 103.3887, 3.3000,5.0890, ],
'TTG': [6.2000, 4.7500, 1.0000, -9.0000, 4.7618, 4.7618, 3.9580, 3.5810, 621.4000, 103.2226, 3.3000,5.0890, ],
'TTA': [7.3000, 4.6500, 0.0000, -20.0000, 4.6709, 4.6709, 4.0130, 2.9550, 621.4000, 103.2226, 2.0000,5.8520, ],
'TTC': [5.1000, 4.0500, 1.0000, -12.0000, 4.0633, 4.0633, 4.3850, 4.2140, 621.4000, 103.2226, 3.0000,5.2640, ],
'TTT': [0.1000, 0.0500, 0.0000, -36.0000, 0.0633, 0.0633, 0.1000, 7.1760, 621.4000, 103.2226, 0.0000,7.0450, ],
'p' : [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # padding
}
else:
if seqType == 'PROT' or seqType == 'RNA':
print(CRED + 'Error: The \'Physicochemical Properties-D2\' feature is NOT applicable for PROT and RNA.' + CEND)
return None
else: None
#end-if
# print(X)
X = utils.processTri(X, d, args)
# print(X.shape)
totalFeature = 0
if seqType == 'DNA':
totalFeature = 12
else:
if seqType == 'PROT' or seqType == 'RNA': None
else:
None
# end-if
save.datasetSave(X, totalFeature, 'pcpD2')
#end-def