def CKSAAGP(fastas, gap = 5, **kw):
if gap < 0:
print('Error: the gap should be equal or greater than zero' + '\n\n')
return 0
if checkFasta.minSequenceLength(fastas) < gap+2:
print('Error: all the sequence length should be greater than the (gap value) + 2 = ' + str(gap+2) + '\n\n')
return 0
group = {
'alphaticr': 'GAVLMI',
'aromatic': 'FYW',
'postivecharger': 'KRH',
'negativecharger': 'DE',
'uncharger': 'STCPNQ'
}
AA = 'ARNDCQEGHILKMFPSTWYV'
groupKey = group.keys()
index = {}
for key in groupKey:
for aa in group[key]:
index[aa] = key
gPairIndex = []
for key1 in groupKey:
for key2 in groupKey:
gPairIndex.append(key1+'.'+key2)
encodings = []
header = ['#']
for g in range(gap + 1):
for p in gPairIndex:
header.append(p+'.gap'+str(g))
encodings.append(header)
for i in fastas:
name, sequence = i[0], re.sub('-', '', i[1])
code = [name]
for g in range(gap + 1):
gPair = generateGroupPairs(groupKey)
sum = 0
for p1 in range(len(sequence)):
p2 = p1 + g + 1
if p2 < len(sequence) and sequence[p1] in AA and sequence[p2] in AA:
gPair[index[sequence[p1]]+'.'+index[sequence[p2]]] = gPair[index[sequence[p1]]+'.'+index[sequence[p2]]] + 1
sum = sum + 1
if sum == 0:
for gp in gPairIndex:
code.append(0)
else:
for gp in gPairIndex:
code.append(gPair[gp] / sum)
encodings.append(code)
return encodings
def PAAC(fastas, lambdaValue=1, w=0.05, **kw):
if checkFasta.minSequenceLength(fastas) < lambdaValue + 1:
print(
'Error: all the sequence length should be larger than the lambdaValue+1: '
+ str(lambdaValue + 1) + '\n\n')
return 0
dataFile = re.sub(
'codes$', '',
os.path.split(os.path.realpath(__file__))
[0]) + r'\data\PAAC.txt' if platform.system() == 'Windows' else re.sub(
'codes$', '',
os.path.split(os.path.realpath(__file__))[0]) + '/data/PAAC.txt'
with open(dataFile) as f:
records = f.readlines()
AA = ''.join(records[0].rstrip().split()[1:])
AADict = {}
for i in range(len(AA)):
AADict[AA[i]] = i
AAProperty = []
AAPropertyNames = []
for i in range(1, len(records)):
array = records[i].rstrip().split(
) if records[i].rstrip() != '' else None
AAProperty.append([float(j) for j in array[1:]])
AAPropertyNames.append(array[0])
AAProperty1 = []
for i in AAProperty:
meanI = sum(i) / 20
fenmu = math.sqrt(sum([(j - meanI)**2 for j in i]) / 20)
AAProperty1.append([(j - meanI) / fenmu for j in i])
encodings = []
header = ['#']
for aa in AA:
header.append('Xc1.' + aa)
for n in range(1, lambdaValue + 1):
header.append('Xc2.lambda' + str(n))
encodings.append(header)
for i in fastas:
name, sequence = i[0], re.sub('-', '', i[1])
code = [name]
theta = []
for n in range(1, lambdaValue + 1):
theta.append(
sum([
Rvalue(sequence[j], sequence[j + n], AADict, AAProperty1)
for j in range(len(sequence) - n)
]) / (len(sequence) - n))
myDict = {}
for aa in AA:
myDict[aa] = sequence.count(aa) / 100
code = code + [myDict[aa] / (1 + w * sum(theta)) for aa in AA]
code = code + [(w * j) / (1 + w * sum(theta)) for j in theta]
encodings.append(code)
return encodings
def CKSAAP(fastas, gap=5, **kw):
if gap < 0:
print('Error: the gap should be equal or greater than zero' + '\n\n')
return 0
if checkFasta.minSequenceLength(fastas) < gap + 2:
print(
'Error: all the sequence length should be larger than the (gap value) + 2 = '
+ str(gap + 2) + '\n\n')
return 0
AA = 'ACDEFGHIKLMNPQRSTVWY'
encodings = []
aaPairs = []
for aa1 in AA:
for aa2 in AA:
aaPairs.append(aa1 + aa2)
header = ['#']
for g in range(gap + 1):
for aa in aaPairs:
header.append(aa + '.gap' + str(g))
encodings.append(header)
for i in fastas:
name, sequence = i[0], i[1]
code = [name]
for g in range(gap + 1):
myDict = {}
for pair in aaPairs:
myDict[pair] = 0
sum = 0
for index1 in range(len(sequence)):
index2 = index1 + gap + 1
if index1 < len(sequence) and index2 < len(
sequence
) and sequence[index1] in AA and sequence[index2] in AA:
myDict[sequence[index1] +
sequence[index2]] = myDict[sequence[index1] +
sequence[index2]] + 1
sum = sum + 1
for pair in aaPairs:
code.append(myDict[pair] / sum)
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
def NMBroto(fastas,
props=[
'CIDH920105', 'BHAR880101', 'CHAM820101', 'CHAM820102',
'CHOC760101', 'BIGC670101', 'CHAM810101', 'DAYM780201'
],
nlag=6,
**kw):
if checkFasta.minSequenceLength(fastas) < nlag + 1:
print(
'Error: all the sequence length should be larger than the nlag+1: '
+ str(nlag + 1) + '\n\n')
return 0
AA = 'ARNDCQEGHILKMFPSTWYV'
fileAAidx = re.sub('codes$', '',
os.path.split(os.path.realpath(__file__))
[0]) + r'\data\AAidx.txt' if platform.system(
) == 'Windows' else sys.path[0] + '/data/AAidx.txt'
with open(fileAAidx) as f:
records = f.readlines()[1:]
myDict = {}
for i in records:
array = i.rstrip().split('\t')
myDict[array[0]] = array[1:]
AAidx = []
AAidxName = []
for i in props:
if i in myDict:
AAidx.append(myDict[i])
AAidxName.append(i)
else:
print('"' + i + '" properties not exist.')
return None
AAidx1 = np.array([float(j) for i in AAidx for j in i])
AAidx = AAidx1.reshape((len(AAidx), 20))
pstd = np.std(AAidx, axis=1)
pmean = np.average(AAidx, axis=1)
for i in range(len(AAidx)):
for j in range(len(AAidx[i])):
AAidx[i][j] = (AAidx[i][j] - pmean[i]) / pstd[i]
index = {}
for i in range(len(AA)):
index[AA[i]] = i
encodings = []
header = ['#']
for p in props:
for n in range(1, nlag + 1):
header.append(p + '.lag' + str(n))
encodings.append(header)
for i in fastas:
name, sequence = i[0], re.sub('-', '', i[1])
code = [name]
N = len(sequence)
for prop in range(len(props)):
for n in range(1, nlag + 1):
if len(sequence) > nlag:
# if key is '-', then the value is 0
rn = sum([
AAidx[prop][index.get(sequence[j], 0)] *
AAidx[prop][index.get(sequence[j + n], 0)]
for j in range(len(sequence) - n)
]) / (N - n)
else:
rn = 'NA'
code.append(rn)
encodings.append(code)
return encodings
