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Nfeature_DNA.py
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Nfeature_DNA.py
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# -*- coding: utf-8 -*-
"""
Created on Fri Aug 7 12:42:37 2020
@author: Megha Mathur
"""
import argparse
import warnings
import os
from argparse import RawTextHelpFormatter
warnings.filterwarnings('ignore')
parser = argparse.ArgumentParser(description='NFDNA....Please provide following arguments to proceed',formatter_class=RawTextHelpFormatter)
nf_path = os.path.dirname(__file__)
## Read Arguments from command
parser.add_argument("-i", "--input", type=str,required=True,help="Input: Enter DNA sequence in FASTA format")
parser.add_argument("-o", "--output", type=str,help="Output File name")
parser.add_argument("-ft", "--feature",required=True,type=str,
help="Select among various features and include _NT,_CT,_REST,_SPLIT after feature name for N-Terminal,C-Terminal,Reamining of N-terminal and C-Terminal and for splitted sequence respectively.\n"
"\n"
"ALL_COMP : all composition based features\n"
"ALL_CORR : all correlation based features\n"
"ALL_BIN: all binary profile based features\n"
"CDK : kmer composition\n"
"RDK : Reverse Compliment kmer composition\n"
"DAC : Dinucleotide based auto correlation\n"
"DCC : Dinucleotide based cross correlation\n"
"DACC : Dinucleotide based auto cross correlation\n"
"TAC : Trinucleotide based auto correlation\n"
"TCC : Trinucleotide based cross correlation\n"
"TACC : Trinucleotide based auto cross correlation\n"
"PDNC : Pseudo dinucleotide composition\n"
"PKNC : Pseudo k-tuple nucleotide composition\n"
"PC_PDNC : parallel correlation pseudo dinucleotide composition\n"
"PC_PTNC : parallel correlation pseudo trinucleotide composition\n"
"SC_PDNC : Serial correlation pseudo dinucleotide composition\n"
"SC_PTNC : Serial correlation pseudo trinucleotide composition\n"
"NMBAC : Normalized Moreau–Broto autocorrelation\n"
"MAC : Moran autocorrelation\n"
"GAC : Geary autocorrelation\n"
"NRI : Nucleotide repeat index\n"
"ES : Sequence level entropy of whole sequence\n"
"EN : Nucleotide level entropy of whole sequence\n"
"DDN : Distance Distribution of whole sequence\n"
"BPD : Binary profile dinucleotide\n"
"BPM : Binary profile Monotide\n"
"BPT : binary profile trinucleotide\n"
"BP_TP : Trinucleotide properties\n"
"BP_DP : Dinucleotide properties")
parser.add_argument("-k","--kvalue",type=int, help="Enter the k value and by default it is set to 2")
parser.add_argument("-n","--nvalue",type=int, help="Enter the n value")
parser.add_argument("-c","--cvalue",type=int, help="Enter the c value")
parser.add_argument("-s","--split",type=int, help="Enter the split value")
parser.add_argument("-or","--order",type=int, help="Enter the order value and by default it is set to 1")
parser.add_argument("-p", "--property",type=str,nargs='+',help=" Refer the property list of dipeptides and enter property names having space in between")
parser.add_argument("-l","--lagvalue",type=int, help="Enter the lag value and its default value is 2")
parser.add_argument("-w","--wvalue",type=float, help="Enter the w value and its default value is 0.05")
parser.add_argument("-lm","--lmvalue",type=int, help="Enter the lamada value and its default value is 1")
parser.add_argument("-path","--pythonpath",type=str, help="Enter the python environment path")
args = parser.parse_args()
sequence = args.input
feature = args.feature
feature=feature.upper()
f_list=['ALL_COMP','ALL_CORR','ALL_BIN','CDK','CDK_NT','RDK_NT','RDK_CT','RDK_REST','RDK_SPLIT','CDK_CT','CDK_REST','CDK_SPLIT','RDK','NRI','NRI_NT','NRI_CT','NRI_REST','NRI_SPLIT','DDN','DDN_NT','DDN_CT','DDN_REST','DDN_SPLIT','ES','ES_NT','ES_CT','ES_REST','ES_SPLIT','EN','EN_NT','EN_CT','EN_REST','EN_SPLIT','BPM','BPM_NT','BPM_CT','BPM_REST','BPM_SPLIT','BPD','BPD_NT','BPD_CT','BPD_REST','BPD_SPLIT','BPT','BPT_NT','BPT_CT','BPT_REST','BPT_SPLIT','BP_DP','BP_DP_NT','BP_DP_CT','BP_DP_REST','BP_DP_SPLIT','BP_TP_NT','BP_TP_CT','BP_TP_REST','BP_TP','BP_TP_SPLIT','DAC','DAC_NT','DAC_CT','DAC_REST','DAC_SPLIT','DACC','DACC_NT','DACC_CT','DACC_REST','DACC_SPLIT','DCC','DCC_NT','DCC_CT','DCC_REST','DCC_SPLIT','TAC','TAC_NT','TAC_CT','TAC_REST','TAC_SPLIT','TACC','TACC_NT','TACC_CT','TACC_REST','TACC_SPLIT','TCC','TCC_NT','TCC_CT','TCC_REST','TCC_SPLIT','MAC','MAC_NT','MAC_CT','MAC_REST','MAC_SPLIT','GAC','GAC_NT','GAC_CT','GAC_REST','GAC_SPLIT','NMBAC','NMBAC_NT','NMBAC_CT','NMBAC_REST','NMBAC_SPLIT','PDNC','PDNC_NT','PDNC_CT','PDNC_REST','PDNC_SPLIT','PKNC','PKNC_NT','PKNC_CT','PKNC_REST','PKNC_SPLIT','PC_PDNC','PC_PDNC_NT','PC_PDNC_CT','PC_PDNC_REST','PC_PDNC_SPLIT','PC_PTNC','PC_PTNC_NT','PC_PTNC_CT','PC_PTNC_REST','PC_PTNC_SPLIT','SC_PDNC','SC_PDNC_NT','SC_PDNC_CT','SC_PDNC_REST','SC_PDNC_SPLIT','SC_PTNC','SC_PTNC_NT','SC_PTNC_CT','SC_PTNC_REST','SC_PTNC_SPLIT']
if feature not in f_list:
print("No Such Feature Exists")
exit()
if(args.output==None):
out="Output.csv"
else:
out=args.output
if(args.pythonpath==None):
path='python'
else:
path=args.pythonpath
# Calling each features
if feature == 'CDK':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
a = path+" "+nf_path+"/Data/K_Mer.py "+"-i "+sequence+" -k "+k+" -or "+order+" -o "+out
os.system(a)
if feature == 'RDK':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
a = path+" "+nf_path+"/Data/RDK.py "+"-i "+sequence+" -k "+k+" -o "+out
os.system(a)
if feature == 'ALL_COMP':
if args.wvalue == None:
w = str(0.05)
else:
w = float(args.wvalue)
w=str(w)
if args.lmvalue == None:
lm = str(1)
else:
lm = int(args.lmvalue)
lm=str(lm)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
file = open(out,'w')
file.close()
a = path+" "+nf_path+"/Data/K_Mer.py "+"-i "+sequence+" -k "+k+" -or "+order+" -o "+out
b= path+" "+nf_path+"/Data/NRI.py "+"-i "+sequence+" -o "+out
c = path+" "+nf_path+"/Data/DDON.py "+"-i "+sequence+" -o "+out
d= path+" "+nf_path+"/Data/RDK.py "+"-i "+sequence+" -k "+k+" -o "+out
e = path+" "+nf_path+"/Data/ENT.py "+"-i "+sequence+" -o "+out
f = path+" "+nf_path+"/Data/ENT_NL.py "+"-i "+sequence+" -o "+out
k1 = path+" "+nf_path+"/Data/psednc.py "+"-i "+sequence+" -w "+w+" -k "+k+" -lm "+lm+" -o "+out
l = path+" "+nf_path+"/Data/pseknc.py "+"-i "+sequence+" -w "+w+" -k "+k+" -lm "+lm+" -o "+out
os.system(a)
os.system(b)
os.system(c)
os.system(d)
os.system(e)
os.system(f)
os.system(k1)
os.system(l)
if feature == 'ALL_BIN':
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop=args.property
if args.order == None:
order = str(1)
else:
order = int(args.order)
order=str(order)
file = open(out,'w')
file.close()
a = path+" "+nf_path+"/Data/BinaryProfile_monotide.py "+"-i "+sequence+" -o "+out
b= path+" "+nf_path+"/Data/BinaryProfile_dinucleotide.py "+"-i "+sequence+" -o "+out
c = path+" "+nf_path+"/Data/BinaryProfile_trinucleotide.py "+"-i "+sequence+" -o "+out
d = path+" "+nf_path+"/Data/dinucleotide_prop.py "+"-i "+sequence+" -or "+order+" -o "+out+" -p"
e = path+" "+nf_path+"/Data/trinucleotide_prop.py "+"-i "+sequence+" -or "+order+" -o "+out+" -p"
for i in prop:
j='"'+i+'"'
d=d+" "+j
e=e+" "+j
os.system(a)
os.system(b)
os.system(c)
os.system(d)
os.system(e)
if feature == 'ALL_CORR':
if args.wvalue == None:
w = str(0.05)
else:
w = float(args.wvalue)
w=str(w)
if args.lmvalue == None:
lm = str(1)
else:
lm = int(args.lmvalue)
lm=str(lm)
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop=args.property
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
file = open(out,'w')
file.close()
a = path+" "+nf_path+"/Data/DAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
b = path+" "+nf_path+"/Data/TAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
c = path+" "+nf_path+"/Data/MAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -k "+k+" -p"
d = path+" "+nf_path+"/Data/GAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -k "+k+" -p"
e = path+" "+nf_path+"/Data/NMBAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -k "+k+" -p"
f = path+" "+nf_path+"/Data/DCC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
g = path+" "+nf_path+"/Data/TCC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
h = path+" "+nf_path+"/Data/DACC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
j1 = path+" "+nf_path+"/Data/TACC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
m = path+" "+nf_path+"/Data/pcpsednc.py "+"-i "+sequence+" -w "+w+" -k "+k+" -o "+out+" -lm "+lm+" -p"
n = path+" "+nf_path+"/Data/pcpsetnc.py "+"-i "+sequence+" -w "+w+" -k "+str(3)+" -lm "+lm+" -o "+out+" -p"
q = path+" "+nf_path+"/Data/scpsednc.py "+"-i "+sequence+" -w "+w+" -k "+k+" -lm "+lm+" -o "+out+" -p"
r = path+" "+nf_path+"/Data/scpsetnc.py "+"-i "+sequence+" -w "+w+" -k "+str(3)+" -lm "+lm+" -o "+out+" -p"
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
b=b+" "+j
c=c+" "+j
d=d+" "+j
e=e+" "+j
f=f+" "+j
g=g+" "+j
h=h+" "+j
j1=j1+" "+j
m=m+" "+j
n=n+" "+j
q=q+" "+j
r=r+" "+j
os.system(a)
os.system(b)
os.system(c)
os.system(d)
os.system(e)
os.system(f)
os.system(g)
os.system(h)
os.system(j1)
os.system(m)
os.system(n)
os.system(q)
os.system(r)
if feature == 'CDK_NT':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.nvalue==None:
n = str(len(sequence))
else:
n=str(args.nvalue)
b = path+" "+nf_path+"/Data/3_end.py "+"-i "+sequence+" -k "+k+" -n "+n+" -or "+order+" -o "+out
os.system(b)
if feature == 'RDK_NT':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.nvalue==None:
n = str(len(sequence))
else:
n=str(args.nvalue)
b = path+" "+nf_path+"/Data/RDK_NT.py "+"-i "+sequence+" -k "+k+" -n "+n+" -or "+order+" -o "+out
os.system(b)
if feature == 'RDK_CT':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.cvalue==None:
n = str(len(sequence))
else:
n=str(args.cvalue)
b = path+" "+nf_path+"/Data/RDK_CT.py "+"-i "+sequence+" -k "+k+" -c "+n+" -or "+order+" -o "+out
os.system(b)
if feature == 'RDK_REST':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
b = path+" "+nf_path+"/Data/RDK_REST.py "+"-i "+sequence+" -k "+k+" -n "+n+" -c "+m+" -or "+order+" -o "+out
os.system(b)
if feature == 'RDK_SPLIT':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if args.order == None:
order = str(1)
else:
order = str(args.order)
e = path+" "+nf_path+"/Data/RDK_SPLIT.py "+"-i "+sequence+" -k "+k+" -s "+s+" -or "+order+" -o "+out
os.system(e)
if feature == 'CDK_CT':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.cvalue==None:
n = str(len(sequence))
else:
n=str(args.cvalue)
b = path+" "+nf_path+"/Data/5_end.py "+"-i "+sequence+" -k "+k+" -c "+n+" -or "+order+" -o "+out
os.system(b)
if feature == 'CDK_REST':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.order == None:
order = str(1)
else:
order = str(args.order)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
b = path+" "+nf_path+"/Data/rest.py "+"-i "+sequence+" -k "+k+" -n "+n+" -c "+m+" -or "+order+" -o "+out
os.system(b)
if feature == 'CDK_SPLIT':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if args.order == None:
order = str(1)
else:
order = str(args.order)
e = path+" "+nf_path+"/Data/split.py "+"-i "+sequence+" -k "+k+" -s "+s+" -or "+order+" -o "+out
os.system(e)
if feature == 'DAC':
file = open(out,'w')
file.close()
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DAC_NT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(2)
else:
n=str(args.nvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DAC_NT.py "+"-i "+sequence+" -n "+n+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DAC_CT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.cvalue==None:
m = str(2)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DAC_CT.py "+"-i "+sequence+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DAC_REST':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DAC_REST.py "+"-i "+sequence+" -n "+n+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DAC_SPLIT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DAC_SPLIT.py "+"-i "+sequence+" -s "+s+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DCC':
file = open(out,'w')
file.close()
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DCC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DCC_NT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(2)
else:
n=str(args.nvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DCC_NT.py "+"-i "+sequence+" -n "+n+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DCC_CT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.cvalue==None:
m = str(2)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DCC_CT.py "+"-i "+sequence+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DCC_REST':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DCC_REST.py "+"-i "+sequence+" -n "+n+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DCC_SPLIT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DCC_SPLIT.py "+"-i "+sequence+" -s "+s+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DACC':
file = open(out,'w')
file.close()
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop=args.property
a = path+" "+nf_path+"/Data/DACC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DACC_NT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(2)
else:
n=str(args.nvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DACC_NT.py "+"-i "+sequence+" -n "+n+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DACC_CT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.cvalue==None:
m = str(2)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DACC_CT.py "+"-i "+sequence+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DACC_REST':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DACC_REST.py "+"-i "+sequence+" -n "+n+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'DACC_SPLIT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/DACC_SPLIT.py "+"-i "+sequence+" -s "+s+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TAC':
file = open(out,'w')
file.close()
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop=args.property
a = path+" "+nf_path+"/Data/TAC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TAC_NT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(2)
else:
n=str(args.nvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TAC_NT.py "+"-i "+sequence+" -n "+n+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TAC_CT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.cvalue==None:
m = str(2)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TAC_CT.py "+"-i "+sequence+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TAC_REST':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TAC_REST.py "+"-i "+sequence+" -n "+n+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TAC_SPLIT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TAC_SPLIT.py "+"-i "+sequence+" -s "+s+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TACC':
file = open(out,'w')
file.close()
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop=args.property
a = path+" "+nf_path+"/Data/TACC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TACC_NT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(2)
else:
n=str(args.nvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TACC_NT.py "+"-i "+sequence+" -n "+n+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TACC_CT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.cvalue==None:
m = str(2)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TACC_CT.py "+"-i "+sequence+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TACC_REST':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TACC_REST.py "+"-i "+sequence+" -n "+n+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TACC_SPLIT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TACC_SPLIT.py "+"-i "+sequence+" -s "+s+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TCC':
file = open(out,'w')
file.close()
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop=args.property
a = path+" "+nf_path+"/Data/TCC.py "+"-i "+sequence+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TCC_NT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(2)
else:
n=str(args.nvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TCC_NT.py "+"-i "+sequence+" -n "+n+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TCC_CT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.cvalue==None:
m = str(2)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TCC_CT.py "+"-i "+sequence+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TCC_REST':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.nvalue==None:
n = str(0)
else:
n=str(args.nvalue)
if args.cvalue==None:
m = str(0)
else:
m=str(args.cvalue)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TCC_REST.py "+"-i "+sequence+" -n "+n+" -c "+m+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'TCC_SPLIT':
if args.lagvalue == None:
lag = str(2)
else:
lag = str(args.lagvalue)
if args.split==None:
s=str(1)
else:
s=str(args.split)
if(args.property==None):
print("Invalid number of Arguments.Enter property name in the format -p propertyname")
exit()
else:
prop= args.property
a = path+" "+nf_path+"/Data/TCC_SPLIT.py "+"-i "+sequence+" -s "+s+" -l "+lag+" -o "+out+" -p "
for i in prop:
i=i.lower()
j='"'+i+'"'
a=a+" "+j
os.system(a)
if feature == 'GAC':
file = open(out,'w')
file.close()
if args.kvalue==None:
k=str(2)
else:
k=str(args.kvalue)
if args.lagvalue == None:
lag = str(2)