def makeintlistdic_from_allep(dir_name, run_dir):
i = 1
intlistdic = {}
len_ave_list, pi_ave_list, hyd_ave_list, len_var_list, pi_var_list, hyd_var_list = [
], [], [], [], [], []
while True:
if os.path.exists(dir_name + run_dir + str(i) + '.txt'):
len_list_ep, pi_list_ep, hyd_list_ep = [], [], []
seq_size = 0
with open(dir_name + run_dir + str(i) + '.txt') as f:
for line in f:
seq = line[:-1]
seq = GlobalDescriptor(seq)
seq.length()
len_list_ep.append(seq.descriptor[0][0])
seq.isoelectric_point()
pi_list_ep.append(seq.descriptor[0][0])
seq.hydrophobic_ratio()
hyd_list_ep.append(seq.descriptor[0][0])
seq_size += 1
len_ave_list.append(round(len(len_list_ep) / seq_size, 3))
pi_ave_list.append(round(len(pi_list_ep) / seq_size, 3))
hyd_ave_list.append(round(len(hyd_list_ep) / seq_size, 3))
len_var_list.append(round(statistics.pvariance(len_list_ep),
3))
pi_var_list.append(round(statistics.pvariance(pi_list_ep), 3))
hyd_var_list.append(round(statistics.pvariance(hyd_list_ep),
3))
i += 1
else:
break
intlistdic["len_ave"] = len_ave_list
intlistdic["pi_ave"] = pi_ave_list
intlistdic["hyd_ave"] = hyd_ave_list
intlistdic["len_var"] = len_var_list
intlistdic["pi_var"] = pi_var_list
intlistdic["hyd_var"] = hyd_var_list
# print(intlistdic, len(len_ave_list))
return intlistdic
header_list = []
# row_list.append("\n")
row_list.append("\n" + run_dir + file_name)
for line in f:
seq = line[:-1]
DesObject = PyPro.GetProDes(seq)
if do_length:
len_list.append(len(seq))
if do_pi:
glob_seq = GlobalDescriptor(seq)
glob_seq.isoelectric_point()
pi_list.append(glob_seq.descriptor[0][0])
if do_hyd:
glob_seq = GlobalDescriptor(seq)
glob_seq.hydrophobic_ratio()
hyd_list.append(glob_seq.descriptor[0][0])
if do_aacomp:
aacomp_diclist.append(DesObject.GetAAComp())
if do_ctd:
# calculate 147 CTD descriptors
# Default: False
ctd_diclist.append(DesObject.GetCTD())
if file_name == real_file:
run_dir = real_file + "/"
if not os.path.exists(dir_name + run_dir):
os.mkdir(dir_name + run_dir)
if do_length:
len_ave = makehist_from_intlist(len_list, "len", eval_dir, run_dir,
file_name)
try:
desc = GlobalDescriptor([database['Sequence'][i]])
desc.aliphatic_index()
aliphatic_array.append(desc.descriptor[0][0])
except:
aliphatic_array.append('')
database['aliphatic_index'] = aliphatic_array
print("Estimate hydrophobic_ratio_array")
#estimate hydrophobic_ratio
hydrophobic_ratio_array = []
for i in range(len(database)):
try:
desc = GlobalDescriptor([database['Sequence'][i]])
desc.hydrophobic_ratio()
hydrophobic_ratio_array.append(desc.descriptor[0][0])
except:
hydrophobic_ratio_array.append('')
database['hydrophobic_ratio'] = hydrophobic_ratio_array
print("Estimate hydrophobicity_profile_array")
#profile hydrophobicity
hydrophobicity_profile_array = []
for i in range(len(database)):
try:
desc = PeptideDescriptor([database['Sequence'][i]],
scalename='Eisenberg')
desc.calculate_profile(prof_type='H')
def exec(peptide, time_node):
file = open("../src/public/jobs/service1/service1.fasta", "w")
file.write(peptide)
file.close()
fasta = SeqIO.parse("../src/public/jobs/service1/service1.fasta", "fasta")
if(any(fasta) == False): #False when `fasta` is empty
return "error"
cantidad = 0
for record in SeqIO.parse("../src/public/jobs/service1/service1.fasta", "fasta"):
cantidad = cantidad+1
if (cantidad == 1):
properties = {}
for record in SeqIO.parse("../src/public/jobs/service1/service1.fasta", "fasta"):
properties[str(record.id)] = {}
#save properties
properties[str(record.id)]["length"] = len(record.seq)
#formula
try:
desc = GlobalDescriptor(str(record.seq))
desc.formula(amide=True)
properties[str(record.id)]["formula"] = desc.descriptor[0][0]
except:
properties[str(record.id)]["formula"] = "-"
#molecular weigth
try:
desc = GlobalDescriptor(str(record.seq))
desc.calculate_MW(amide=True)
properties[str(record.id)]["molecular_weigth"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["molecular_weigth"] = "-"
#boman_index
try:
desc = GlobalDescriptor(str(record.seq))
desc.boman_index()
properties[str(record.id)]["boman_index"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["boman_index"] = "-"
#charge
try:
desc = GlobalDescriptor(str(record.seq))
desc.calculate_charge(ph=7, amide=True)
properties[str(record.id)]["charge"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["charge"] = "-"
#charge density
try:
desc = GlobalDescriptor(str(record.seq))
desc.charge_density(ph=7, amide=True)
properties[str(record.id)]["charge_density"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["charge_density"] = "-"
#estimate isoelectric point
try:
desc = GlobalDescriptor(str(record.seq))
desc.isoelectric_point()
properties[str(record.id)]["isoelectric_point"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["isoelectric_point"] = "-"
#estimate inestability index
try:
desc = GlobalDescriptor(str(record.seq))
desc.instability_index()
properties[str(record.id)]["instability_index"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["instability_index"] = "-"
#estimate aromaticity
try:
desc = GlobalDescriptor(str(record.seq))
desc.aromaticity()
properties[str(record.id)]["aromaticity"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["aromaticity"] = "-"
#estimate aliphatic_index
try:
desc = GlobalDescriptor(str(record.seq))
desc.aliphatic_index()
properties[str(record.id)]["aliphatic_index"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["aliphatic_index"] = "-"
#estimate hydrophobic_ratio
try:
desc = GlobalDescriptor(str(record.seq))
desc.hydrophobic_ratio()
properties[str(record.id)]["hydrophobic_ratio"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["hydrophobic_ratio"] = "-"
#profile hydrophobicity
try:
desc = PeptideDescriptor(str(record.seq), scalename='Eisenberg')
desc.calculate_profile(prof_type='H')
properties[str(record.id)]["hydrophobicity_profile"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["hydrophobicity_profile"] = "-"
#profile hydrophobic
try:
desc = PeptideDescriptor(str(record.seq), scalename='Eisenberg')
desc.calculate_profile(prof_type='uH')
properties[str(record.id)]["hydrophobic_profile"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["hydrophobic_profile"] = "-"
#moment
try:
desc = PeptideDescriptor(str(record.seq), scalename='Eisenberg')
desc.calculate_moment()
properties[str(record.id)]["calculate_moment"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["calculate_moment"] = "-"
try:
os.mkdir("../src/public/jobs/service1/"+time_node)
except:
print("Error")
#generate plot profile
plot_profile(str(record.seq), scalename='eisenberg', filename= "../src/public/jobs/service1/"+time_node+"/profile.png")
#generate helical wheel
helical_wheel(str(record.seq), colorcoding='charge', lineweights=False, filename= "../src/public/jobs/service1/"+time_node+"/helical.png")
return(properties)
if (cantidad > 1):
properties = {}
for record in SeqIO.parse("../src/public/jobs/service1/service1.fasta", "fasta"):
properties[str(record.id)] = {}
properties[str(record.id)]["length"] = len(record.seq)
#formula
try:
desc = GlobalDescriptor(str(record.seq))
desc.formula(amide=True)
properties[str(record.id)]["formula"] = desc.descriptor[0][0]
except:
properties[str(record.id)]["formula"] = "-"
#molecular weigth
try:
desc = GlobalDescriptor(str(record.seq))
desc.calculate_MW(amide=True)
properties[str(record.id)]["molecular_weigth"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["molecular_weigth"] = "-"
#boman_index
try:
desc = GlobalDescriptor(str(record.seq))
desc.boman_index()
properties[str(record.id)]["boman_index"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["boman_index"] = "-"
#charge
try:
desc = GlobalDescriptor(str(record.seq))
desc.calculate_charge(ph=7, amide=True)
properties[str(record.id)]["charge"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["charge"] = "-"
#charge density
try:
desc = GlobalDescriptor(str(record.seq))
desc.charge_density(ph=7, amide=True)
properties[str(record.id)]["charge_density"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["charge_density"] = "-"
#estimate isoelectric point
try:
desc = GlobalDescriptor(str(record.seq))
desc.isoelectric_point()
properties[str(record.id)]["isoelectric_point"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["isoelectric_point"] = "-"
#estimate inestability index
try:
desc = GlobalDescriptor(str(record.seq))
desc.instability_index()
properties[str(record.id)]["instability_index"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["instability_index"] = "-"
#estimate aromaticity
try:
desc = GlobalDescriptor(str(record.seq))
desc.aromaticity()
properties[str(record.id)]["aromaticity"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["aromaticity"] = "-"
#estimate aliphatic_index
try:
desc = GlobalDescriptor(str(record.seq))
desc.aliphatic_index()
properties[str(record.id)]["aliphatic_index"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["aliphatic_index"] = "-"
#estimate hydrophobic_ratio
try:
desc = GlobalDescriptor(str(record.seq))
desc.hydrophobic_ratio()
properties[str(record.id)]["hydrophobic_ratio"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["hydrophobic_ratio"] = "-"
#profile hydrophobicity
try:
desc = PeptideDescriptor(str(record.seq), scalename='Eisenberg')
desc.calculate_profile(prof_type='H')
properties[str(record.id)]["hydrophobicity_profile"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["hydrophobicity_profile"] = "-"
#profile hydrophobic
try:
desc = PeptideDescriptor(str(record.seq), scalename='Eisenberg')
desc.calculate_profile(prof_type='uH')
properties[str(record.id)]["hydrophobic_profile"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["hydrophobic_profile"] = "-"
#moment
try:
desc = PeptideDescriptor(str(record.seq), scalename='Eisenberg')
desc.calculate_moment()
properties[str(record.id)]["calculate_moment"] = float("%.4f" % desc.descriptor[0][0])
except:
properties[str(record.id)]["calculate_moment"] = "-"
return(properties)