Nothing
run.read.MDscan <-
function(input,k, len_motif, num_motif, call.MDscan){
require("seqinr")
write.fasta <- get("write.fasta",pos="package:seqinr")
read.fasta <- get("read.fasta",pos="package:seqinr")
write.fasta(input, names="sequenciaEstudi", nbchar = k, file.out="sequenciaEstudi.fa",open="w")
mdscan<-paste(call.MDscan," -i sequenciaEstudi.fa -w")
system(paste(paste(paste(paste(paste(paste(paste(mdscan, len_motif,sep=" "),"-t", sep=" "), num_motif,sep=" "),"-b background.fa", sep=" "),"-r",sep=" "), num_motif,sep=" ") ,"-o res"))
resultat<-readLines("res")
resultats_MDscan<-lapply(seq(1, num_motif, 1), function(x){ })
j<-0
options(warn=-1)
if (call.MDscan=="MDscan/MDscan.linux"){
for (i in c(1:length(resultat))) {
if(substr(resultat[i],start=1,stop=5)=="Motif") {
j<-j+1
Score<-as.numeric(substr(resultat[i],start=15,stop=19))
Sites<-as.numeric(substr(resultat[i],start=27,stop=28))
Consensus<-substr(resultat[i],start=34,stop=(34+(len_motif-1)))
Secuencia<-matrix(,Sites,3)
for (ii in c(1: Sites)){
x<-regexpr(resultat[i+ii],resultat[i+ii])
Secuencia[ii,2]<-as.character(substr(resultat[i+ii],start=1,stop=1))
for (iii in c(0:(attr(x,"match.length")-len_motif))) {
if(is.na(as.numeric(substr(resultat[i+ii],start=3,stop=(4+iii))))) {
}else{
Secuencia[ii,3]<-as.numeric( substr(resultat[i+ii],start=3,stop=(4+iii)))
Secuencia[ii,1]<-as.character(substr(resultat[i+ii],start=(4+iii+1),stop=(4+iii+len_motif)))}
}
}
}
resultats_MDscan[[j]]<-list( Score=Score,Sites=Sites,Secuencia=Secuencia)
}
}
if (call.MDscan=="../MDscan/MDscan.mac"){
if (len_motif<10){
for (i in c(1:length(resultat))) {
if(substr(resultat[i],start=1,stop=5)=="Motif") {
j<-j+1
wid<-as.numeric(substr(resultat[i],start=14,stop=14))
Score<-as.numeric(substr(resultat[i],start=22,stop=27))
Sites<-as.numeric(substr(resultat[i],start=36,stop=37))
if (is.na(Sites)){Sites<-as.numeric(substr(resultat[i],start=36,stop=36))}
Secuencia<-matrix(,Sites,3)
for (ii in c(1: Sites)){
Secuencia[ii,1]<-as.character(substr(resultat[i+(2*ii-1)+wid+3],start=1,stop=len_motif))
if (ii<10){
Secuencia[ii,2]<-as.character(substr(resultat[i+(2*ii-1)+wid+2],start=35,stop=35))
}else{
Secuencia[ii,2]<-as.character(substr(resultat[i+(2*ii-1)+wid+2],start=36,stop=36))}
Secuencia[ii,3]<-as.numeric(substr(resultat[i+(2*ii-1)+wid+2],start=37,stop=50))
}
resultats_MDscan[[j]]<-list( Score=Score,Sites=Sites,Secuencia=Secuencia)
}
}
}else{
for (i in c(1:length(resultat))) {
if(substr(resultat[i],start=1,stop=5)=="Motif") {
j<-j+1
wid<-as.numeric(substr(resultat[i],start=14,stop=15))
Score<-as.numeric(substr(resultat[i],start=24,stop=28))
Sites<-as.numeric(substr(resultat[i],start=37,stop=38))
if (is.na(Sites)){Sites<-as.numeric(substr(resultat[i],start=37,stop=37))}
Secuencia<-matrix(,Sites,3)
for (ii in c(1: Sites)){
Secuencia[ii,1]<-as.character(substr(resultat[i+(2*ii-1)+wid+3],start=1,stop=len_motif))
if (ii<10){
Secuencia[ii,2]<-as.character(substr(resultat[i+(2*ii-1)+wid+2],start=35,stop=35))
}else{
Secuencia[ii,2]<-as.character(substr(resultat[i+(2*ii-1)+wid+2],start=36,stop=36))}
Secuencia[ii,3]<-as.numeric(substr(resultat[i+(2*ii-1)+wid+2],start=37,stop=50))
}
resultats_MDscan[[j]]<-list( Score=Score,Sites=Sites,Secuencia=Secuencia)
}
}
}
}
return(resultats_MDscan)
}
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