def BINARY(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "BINARY" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
AA = 'ARNDCQEGHILKMFPSTWYVX'
encodings = []
header = ['#']
for i in range(1, len(fastas[0][1]) * 21 + 1):
header.append('BINARY.F' + str(i))
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for aa in sequence:
if aa == '-':
code = code + [
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0
]
break
for aa1 in AA:
tag = 1 if aa == aa1 else 0
code.append(tag)
encodings.append(code)
return encodings
def PSSM(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "PSSM" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
pssmDir = kw['path']
if pssmDir == None:
print(
'Error: please specify the directory of predicted protein disorder files by "--path" \n\n'
)
return 0
AA = 'ARNDCQEGHILKMFPSTWYV'
encodings = []
header = ['#']
for p in range(1, len(fastas[0][1]) + 1):
for aa in AA:
header.append('Pos.' + str(p) + '.' + aa)
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
if os.path.exists(pssmDir + '/' + name + '.pssm') == False:
print('Error: pssm prfile for protein ' + name +
' does not exist.')
#sys.exit(1)
proteinSeq = ''
pssmMatrix = []
continue
with open(pssmDir + '/' + name + '.pssm') as f:
records = f.readlines()[3:29]
proteinSeq = ''
pssmMatrix = []
for line in records:
if (len(line) == 1):
print("got u")
continue
array = line.strip().split()
pssmMatrix.append(array[2:22])
proteinSeq = proteinSeq + array[1]
pos = proteinSeq.find(sequence)
if pos == -1:
print('Warning: could not find the peptide in proteins.\n\n')
else:
for p in range(pos, pos + len(sequence)):
code = code + pssmMatrix[p]
encodings.append(code)
return encodings
def DisorderB(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "DisorderB" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
disDir = kw['path']
if disDir == None:
print(
'Error: please specify the directory of predicted protein disorder files by "--path"'
)
return 0
encodings = []
header = ['#']
for p in range(1, 2 * len(fastas[0][1]) + 1):
header.append('disorderB.F' + str(p))
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
if os.path.exists(disDir + '/' + name + '.dis') == False:
print(
'Error: the predicted disorder information file (.dis) for protein '
+ name + ' does not exist.')
return 0
with open(disDir + '/' + name + '.dis') as f:
records = f.readlines()
tag = 0
for i in range(len(records)):
if re.search('^-------', records[i]):
tag = i
break
records = records[tag + 1:-1]
proteinSeq = ''
disValue = []
myDict = {'D': [0, 1], 'O': [1, 0]}
for line in records:
array = line.rstrip().split() if line.rstrip() != '' else None
key = array[3] if array[3] == 'D' else 'O'
proteinSeq = proteinSeq + array[1]
disValue.append(key)
pos = proteinSeq.find(sequence)
if pos == -1:
print('Warning: could not find the peptide in proteins.\n\n')
else:
for p in range(pos, pos + len(sequence)):
code = code + myDict[disValue[p]]
encodings.append(code)
return encodings
def AAINDEX(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "AAINDEX" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
AA = 'ARNDCQEGHILKMFPSTWXYV'
fileAAindex = re.sub(
'codes$', '',
os.path.split(os.path.realpath(__file__))
[0]) + r'\data\AAINDEXwithX.txt' if platform.system(
) == 'Windows' else re.sub(
'codes$', '',
os.path.split(os.path.realpath(__file__))[0]) + '/data/AAindex.txt'
with open(fileAAindex) as f:
records = f.readlines()[1:]
AAindex = []
AAindexName = []
for i in records:
AAindex.append(i.rstrip().split()[1:] if i.rstrip() != '' else None)
AAindexName.append(i.rstrip().split()[0] if i.rstrip() != '' else None)
index = {}
for i in range(len(AA)):
index[AA[i]] = i
encodings = []
header = ['#']
for pos in range(1, len(fastas[0][1]) + 1):
for idName in AAindexName:
header.append('SeqPos.' + str(pos) + '.' + idName)
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for aa in sequence:
if aa == '-':
for j in AAindex:
code.append(0)
continue
for j in AAindex:
code.append(j[index[aa]])
encodings.append(code)
return encodings
def TA(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "TA" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
encodings = []
header = ['#']
for p in range(1, len(fastas[0][1]) + 1):
header.append('TA.F' + str(p) + '.phi')
header.append('TA.F' + str(p) + '.psi')
encodings.append(header)
disDir = kw['path']
if disDir == None:
print(
'Error: please specify the directory of predicted protein TA file by "--path"'
)
return 0
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
if os.path.exists(disDir + '/' + name + '.dis') == False:
print(
'Error: the predicted TA information file (.spXout) for protein '
+ name + ' does not exist.')
return 0
with open(disDir + '/' + name + '.spXout') as f:
records = f.readlines()[1:]
proteinSeq = ''
asaValue = []
for line in records:
array = line.strip().split() if line.strip() != '' else None
proteinSeq = proteinSeq + array[1]
asaValue.append(array[3:5])
pos = proteinSeq.find(sequence)
if pos == -1:
print('Warning: could not find the peptide in proteins.\n\n')
else:
for p in range(pos, pos + len(sequence)):
code.append(asaValue[p][0])
code.append(asaValue[p][1])
encodings.append(code)
return encodings
def ZSCALE(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "ZSCALE" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
zscale = {
'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
'-': [0.00, 0.00, 0.00, 0.00, 0.00], # -
}
encodings = []
header = ['#']
for p in range(1, len(fastas[0][1]) + 1):
for z in ('1', '2', '3', '4', '5'):
header.append('Pos' + str(p) + '.ZSCALE' + z)
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for aa in sequence:
code = code + zscale[aa]
encodings.append(code)
return encodings
def EGAAC(fastas, window=5, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "EGAAC" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
if window < 1:
print('Error: the sliding window should be greater than zero' + '\n\n')
return 0
group = {
'alphaticr': 'GAVLMI',
'aromatic': 'FYW',
'postivecharger': 'KRH',
'negativecharger': 'DE',
'uncharger': 'STCPNQ'
}
groupKey = group.keys()
encodings = []
header = ['#']
for w in range(1, len(fastas[0][1]) - window + 2):
for g in groupKey:
header.append('SW.' + str(w) + '.' + g)
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for j in range(len(sequence)):
if j + window <= len(sequence):
count = Counter(sequence[j:j + window])
myDict = {}
for key in groupKey:
for aa in group[key]:
myDict[key] = myDict.get(key, 0) + count[aa]
for key in groupKey:
code.append(myDict[key] / window)
encodings.append(code)
return encodings
def BLOSUM62(fastas, **kw):
if checkFasta.checkFasta(fastas) == False:
print('Error: for "BLOSUM62" encoding, the input fasta sequences should be with equal length. \n\n')
return 0
blosum62 = {
'A': [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0], # A
'R': [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3], # R
'N': [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3], # N
'D': [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3], # D
'C': [0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1], # C
'Q': [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2], # Q
'E': [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2], # E
'G': [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3], # G
'H': [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3], # H
'I': [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3], # I
'L': [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1], # L
'K': [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2], # K
'M': [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1], # M
'F': [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1], # F
'P': [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2], # P
'S': [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2], # S
'T': [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0], # T
'W': [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3], # W
'Y': [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1], # Y
'V': [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4], # V
'-': [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], # -
}
encodings = []
header = ['#']
for i in range(1, len(fastas[0][1]) * 20 + 1):
header.append('blosum62.F'+str(i))
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for aa in sequence:
code = code + blosum62[aa]
encodings.append(code)
return encodings
def EAAC(fastas, window=5, **kw):
if checkFasta.checkFasta(fastas) == False:
print(
'Error: for "EAAC" encoding, the input fasta sequences should be with equal length. \n\n'
)
return 0
if window < 1:
print('Error: the sliding window should be greater than zero' + '\n\n')
return 0
if checkFasta.minSequenceLength(fastas) < window:
print(
'Error: all the sequence length should be larger than the sliding window :'
+ str(window) + '\n\n')
return 0
AA = kw['order'] if kw['order'] != None else 'ACDEFGHIKLMNPQRSTVWY'
#AA = 'ARNDCQEGHILKMFPSTWYV'
encodings = []
header = ['#']
for w in range(1, len(fastas[0][1]) - window + 2):
for aa in AA:
header.append('SW.' + str(w) + '.' + aa)
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for j in range(len(sequence)):
if j < len(sequence) and j + window <= len(sequence):
count = Counter(re.sub('-', '', sequence[j:j + window]))
for key in count:
count[key] = count[key] / len(
re.sub('-', '', sequence[j:j + window]))
for aa in AA:
code.append(count[aa])
encodings.append(code)
return encodings
