def CTD_feature_extractor(self, protein_sequence):
value_list = []
features_list = ["_Polarizability", "_SolventAccessibility", "_SecondaryStr",
"_Charge", "_Polarity", "_NormalizedVDWV", "_Hydrophobicity"]
ctd_features = CTD.CalculateCTD(protein_sequence)
for feature_keys in ctd_features.keys():
value = ctd_features.get(feature_keys)
if value > 1:
value = round((value/100), 3)
value_list.append(value)
return np.array(value_list, dtype=np.float32)
def generate_features(sequence):
seq = str(sequence)
feature = CTD.CalculateCTD(seq)
feature_all = []
count = 0
for key in sorted(feature.keys()):
feature_all.append(feature[key])
count = count + 1
if count == 147:
feature_numpy = np.array(feature_all)
# print(feature_numpy)
return feature_numpy
def feature_generation(input_file):
global feature_file, feature
# feature_file = open(os.path.expanduser("C:/Users/Rayin/Google Drive/Tier_2_MOE2014/5_Journal/Plos_One/Data/feature/feature.csv"), 'w')
input_file = pd.DataFrame(input_file)
input_file = input_file['seq']
count = 0
for row in range(0, len(input_file)):
seq = str(input_file.loc[row])
feature = CTD.CalculateCTD(seq)
if row == 0:
write_header()
for key in sorted(feature.keys()):
feature_value = feature[key]
count = count + 1
if count == 147:
count = 0
write_to_csv = str(feature_value) + '\n'
else:
write_to_csv = str(feature_value) + ','
#write_to_csv = str(feature_value) + ','
feature_file.write(write_to_csv)
feature_file.close()
res[i + '+' + i] = round(dict1[i] + dict2[i], 3)
res[i + '*' + i] = round(dict1[i] * dict2[i], 3)
return res
if __name__ == '__main__':
from PyBioMed.PyDNA import PyDNAac
DNA_des = PyDNAac.GetTCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC',
phyche_index=['Dnase I', 'Nucleosome', 'MW-kg'])
print DNA_des
from PyBioMed.PyProtein import CTD
protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
protein_des = CTD.CalculateCTD(protein)
from PyBioMed.PyMolecule import moe
from rdkit import Chem
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
m = Chem.MolFromSmiles(smis[3])
mol_des = moe.GetMOE(m)
mol_mol_interaction1 = CalculateInteraction1(mol_des, mol_des)
print mol_mol_interaction1
mol_mol_interaction2 = CalculateInteraction2(mol_des, mol_des)
print mol_mol_interaction2
mol_mol_interaction3 = CalculateInteraction3(mol_des, mol_des)
print mol_mol_interaction3
def test_pyinteration():
from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction1
from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction2
from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction3
from PyBioMed.PyDNA import PyDNAac
print '...............................................................'
print 'testing the DNA descriptors'
DNA_des = PyDNAac.GetTCC('GACTGAACTGCACTTTGGTTTCATATTATTTGCTC',
phyche_index=['Dnase I', 'Nucleosome', 'MW-kg'])
print DNA_des
print '...............................................................'
print 'testing the protein descriptors'
from PyBioMed.PyProtein import CTD
protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
protein_des = CTD.CalculateCTD(protein)
print '...............................................................'
print 'testing the molecular descriptors'
from PyBioMed.PyMolecule import moe
from rdkit import Chem
smis = ['CCCC', 'CCCCC', 'CCCCCC', 'CC(N)C(=O)O', 'CC(N)C(=O)[O-].[Na+]']
m = Chem.MolFromSmiles(smis[3])
mol_des = moe.GetMOE(m)
print '...............................................................'
print 'testing the Interaction type 1 module'
mol_mol_interaction1 = CalculateInteraction1(mol_des, mol_des)
print mol_mol_interaction1
pro_mol_interaction1 = CalculateInteraction1(mol_des, protein_des)
print pro_mol_interaction1
DNA_mol_interaction1 = CalculateInteraction1(DNA_des, mol_des)
print DNA_mol_interaction1
print '...............................................................'
print 'testing the Interaction type 2 module'
mol_mol_interaction2 = CalculateInteraction2(mol_des, mol_des)
print mol_mol_interaction2
pro_mol_interaction2 = CalculateInteraction2(mol_des, protein_des)
print pro_mol_interaction2
DNA_mol_interaction2 = CalculateInteraction2(DNA_des, mol_des)
print DNA_mol_interaction2
print '...............................................................'
print 'testing the Interaction type 3 module'
mol_mol_interaction3 = CalculateInteraction3(mol_des, mol_des)
print mol_mol_interaction3
def test_pyprotein():
AAC = eval(modulelists[0])
AC = eval(modulelists[1])
CTD = eval(modulelists[2])
QSO = eval(modulelists[3])
PAAC = eval(modulelists[4])
GPFU = eval(modulelists[5])
GSS = eval(modulelists[6])
print '...............................................................'
print "testing the GetSubSeq module"
ProteinSequence = 'ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS'
temp = GSS.GetSubSequence(ProteinSequence, ToAA='D', window=5)
print temp
print '...............................................................'
print "testing the AAComposition module"
temp = AAC.CalculateAAComposition(ProteinSequence)
print temp
temp = AAC.CalculateDipeptideComposition(ProteinSequence)
temp = AAC.GetSpectrumDict(ProteinSequence)
temp = AAC.CalculateAADipeptideComposition(ProteinSequence)
print '...............................................................'
print "testing the Autocorrelation module"
temp = AC.CalculateNormalizedMoreauBrotoAuto(ProteinSequence,
[AC._ResidueASA],
['ResidueASA'])
print temp
temp = AC.CalculateMoranAuto(ProteinSequence, [AC._ResidueASA],
['ResidueASA'])
print temp
temp = AC.CalculateGearyAuto(ProteinSequence, [AC._ResidueASA],
['ResidueASA'])
print temp
temp = AC.CalculateAutoTotal(ProteinSequence)
print '...............................................................'
print "testing the CTD module"
temp = CTD.CalculateC(ProteinSequence)
print temp
temp = CTD.CalculateT(ProteinSequence)
print temp
temp = CTD.CalculateD(ProteinSequence)
print temp
temp = CTD.CalculateCTD(ProteinSequence)
print temp
print '...............................................................'
print "testing the QuasiSequenceOrder module"
temp = QSO.GetSequenceOrderCouplingNumberTotal(ProteinSequence, maxlag=30)
print temp
temp = QSO.GetQuasiSequenceOrder(ProteinSequence, maxlag=30, weight=0.1)
print temp
print '...............................................................'
print "testing the PseudoAAC module"
temp = PAAC.GetAPseudoAAC(ProteinSequence, lamda=10, weight=0.5)
print temp
temp = PAAC._GetPseudoAAC(ProteinSequence, lamda=10, weight=0.05)
print temp
print '...............................................................'
print "Tested successfully!"
def test_pyinteration():
from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction1
from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction2
from PyBioMed.PyInteraction.PyInteraction import CalculateInteraction3
from PyBioMed.PyDNA import PyDNAac
print("...............................................................")
print("testing the DNA descriptors")
DNA_des = PyDNAac.GetTCC(
"GACTGAACTGCACTTTGGTTTCATATTATTTGCTC",
phyche_index=["Dnase I", "Nucleosome", "MW-kg"],
)
print(DNA_des)
print("...............................................................")
print("testing the protein descriptors")
from PyBioMed.PyProtein import CTD
protein = "ADGCGVGEGTGQGPMCNCMCMKWVYADEDAADLESDSFADEDASLESDSFPWSNQRVFCSFADEDAS"
protein_des = CTD.CalculateCTD(protein)
print("...............................................................")
print("testing the molecular descriptors")
from PyBioMed.PyMolecule import moe
from rdkit import Chem
smis = ["CCCC", "CCCCC", "CCCCCC", "CC(N)C(=O)O", "CC(N)C(=O)[O-].[Na+]"]
m = Chem.MolFromSmiles(smis[3])
mol_des = moe.GetMOE(m)
print("...............................................................")
print("testing the Interaction type 1 module")
mol_mol_interaction1 = CalculateInteraction1(mol_des, mol_des)
print(mol_mol_interaction1)
pro_mol_interaction1 = CalculateInteraction1(mol_des, protein_des)
print(pro_mol_interaction1)
DNA_mol_interaction1 = CalculateInteraction1(DNA_des, mol_des)
print(DNA_mol_interaction1)
print("...............................................................")
print("testing the Interaction type 2 module")
mol_mol_interaction2 = CalculateInteraction2(mol_des, mol_des)
print(mol_mol_interaction2)
pro_mol_interaction2 = CalculateInteraction2(mol_des, protein_des)
print(pro_mol_interaction2)
DNA_mol_interaction2 = CalculateInteraction2(DNA_des, mol_des)
print(DNA_mol_interaction2)
print("...............................................................")
print("testing the Interaction type 3 module")
mol_mol_interaction3 = CalculateInteraction3(mol_des, mol_des)
print(mol_mol_interaction3)