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readMEME<-function(resultat, num_motif){
j<-0
mi<-0
iii<-0
Sequencies<-vector(mode="list", length=num_motif)
MEME.aligned<-vector(mode="list", length=(num_motif+1))
Sites<-vector(mode="logical", length=num_motif)
width<-vector(mode="logical", length=num_motif)
consensus<-vector(mode="logical", length=num_motif)
for(i in 1:length(resultat)){
if(substr(resultat[i], start=1, stop=5)=="MOTIF"){
#print(i)
mi<-mi+1
width[mi]<-as.numeric(substr(resultat[i], start=20, stop=21))
Sites[mi]<-as.numeric(substr(resultat[i], start=34, stop=35))
#print("Sites=")
#print(substr(resultat[i], start=34, stop=35))
#print("mi=")
#print(mi)
}
else if(substr(resultat[i], start=1, stop=13)=="Sequence name" && substr(resultat[i], start=27, stop=31)== "Start"){
j<-j+1
#print("j=")
#print(j)
#print("Sites=")
#print(Sites[j])
m<-i+2
Sequencies[[j]]<-resultat[m:(m+Sites[j]-1)]
print(Sequencies[[j]])
} else if(substr(resultat[i], start=1, stop=10)=="Multilevel"){
iii<-iii+1
#print("iii=")
#print(iii)
consensus[iii]=substr(resultat[i], start=22, stop=(22+width[iii]))
#print("consensus=")
#print(consensus[iii])
}
}
for(i in 1:length(Sequencies)){
#print("alineacio")
#print(i)
alineacio<-Sequencies[[i]]
if(is.null(alineacio)){
print("null")
}else{
alineacio<-strsplit(alineacio, NULL)
alineacio<-sapply(alineacio,function(X){X<-X[42:length(X)]} )
alineacio<-t(alineacio)
suma<-apply(alineacio,2,function(X){sum(X==" ")})
alineacio<-alineacio[,suma<dim(alineacio)[1]]
suma<-apply(alineacio,2,function(X){sum(X==".")})
alineacio<-alineacio[,suma<dim(alineacio)[1]]
alineacio[alineacio==" "]<-"-"
alineacio[alineacio=="."]<-"-"
}
MEME.aligned[[i]]<-alineacio
}
print(consensus)
MEME.aligned[[(num_motif+1)]]<-consensus
return(MEME.aligned)
}
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