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handlemore.py
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handlemore.py
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# using MODEST - a variant of IGLOSS with filtering - on one or more motifs
# motifs should be in files motif1.txt, motif2.txt, etc.
proteome="AT.fasta" # proteome in fasta format
numotifs=3 # number of motifs
scale=[10,10,10] # list of scales, one for each motif
th=0 # threshold 0=IGLOSS, usually 0.001
import os
allP=[]
allmotif=[]
allstart=[]
allstop=[]
allEvalue=[]
for k in range(1,numotifs+1):
os.system("./MODEST "+ proteome + " motif"+str(k)+".txt " + str(scale[k-1]) + " 10 " + str(th) + " > " + " output.txt")
f=open("output.txt","r")
lines=f.readlines()
f.close()
for i in range(min(6,len(lines))):
print(lines[i].rstrip())
P=[]
motif=[]
start=[]
stop=[]
Evalue=[]
ok=0
for i in range(len(lines)):
if "Evalue" in lines[i]:
tempstart=int(lines[i].split()[1].split("-")[0])
tempstop=int(lines[i].split()[1].split("-")[1])
tempEvalue=float(lines[i].split("=")[1].split(")")[0])
if ">" in lines[i]:
tmp=lines[i].split(">")[1].split()[0]
if tmp not in P:
P.append(tmp)
start.append(tempstart)
stop.append(tempstop)
Evalue.append(tempEvalue)
ok=1
if ok==1 and "Evalue" not in lines[i] and ">" not in lines[i]:
motif.append(lines[i].rstrip())
ok=0
for i in range(len(P)):
P[i]=P[i].split(".")[0]
allP.append(P)
allmotif.append(motif)
allstart.append(start)
allstop.append(stop)
allEvalue.append(Evalue)
ind=[]
for i in range(len(allP[0])):
ok=1
indtemp=[]
for k in range(1,numotifs):
if allP[0][i] not in allP[k]:
ok=0
if ok==1:
indtemp.append(i)
for k in range(1,numotifs):
indtemp.append(allP[k].index(allP[0][i]))
if len(indtemp)>0:
ind.append(indtemp)
os.system("rm output.txt")
f=open("MODESToutput.tsv","w")
f.write("SeqID\t")
for k in range(numotifs):
f.write("motif"+str(k+1)+"\t"+"m"+str(k+1)+"_position_start\t"+"m"+str(k+1)+"_position_end\t"+"m"+str(k+1)+"_Evalue\t")
f.write("\n")
for i in range(len(ind)):
f.write("%s\t" % allP[0][ind[i][0]])
for k in range(numotifs):
f.write("%s\t%d\t%d\t%f\t" % (allmotif[k][ind[i][k]],allstart[k][ind[i][k]],allstop[k][ind[i][k]],allEvalue[k][ind[i][k]]))
f.write("\n")
f.close()