import sys
from modlamp.descriptors import PeptideDescriptor, GlobalDescriptor
database = pd.read_csv(sys.argv[1])
path_output = sys.argv[2]
print("Estimate formula")
#get formula for each sequence
formula_array = []
for i in range(len(database)):
try:
desc = GlobalDescriptor([database['Sequence'][i]])
desc.formula(amide=True)
for v in desc.descriptor:
formula_array.append(v[0])
except:
formula_array.append('')
database['formula'] = formula_array
print("Estimate molecular_weigth")
#get MW for each sequence
molecular_weigth_array = []
for i in range(len(database)):
try:
desc = GlobalDescriptor([database['Sequence'][i]])
desc.calculate_MW(amide=True)
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)