Nothing
MEET <-function(TF,nameTF=NULL,seqin,alg=NULL,method,mode,org,vector=NULL,num_motif=NULL,len_motif=NULL,direction="f",threshold=0.1,order=NULL,model=NULL, position=c(501),mv=50,gapopen=-500,maxiters=16,gapextend=-2, optionsFile='.optionsmeet'){
require("seqinr")
#require("fields")
require("MEET")
require("methods")
checkpaths <- function(executable){
out <- switch(.Platform$OS.type,
unix= system(paste('which',executable), intern = TRUE),
windows=)
}
executables <- c("clustalw","meme","mast","transfac2meme","muscle","MDScan-linux")
names(executables) <- c("call.clustalw","call.meme", "all.mast","call.transfac2meme","call.muscle", "call.MDscan")
# Initialitzation code, this checks whether MEME/MAST, clustalx and muscle is present in the system
if ( is.na(file.info(optionsFile)$size) )
{
cat( "Configuration File (",optionsFile,") not found\n")
cat ("\tChecking external dependencies\n")
found <- sapply( executables, function(x) checkpaths(x))
meetconf <- sapply(names(found), function(x) {
if (length(found[[x]]) == 0 ) {
done <- 0
while(!done){
cat(executables[x], ' not found, please enter new path, or ENTER for not available:\n')
cat('\t ',executables[x],' path: ')
npath <- readline()
if ( length(npath) == 1 ) {done <- 1}
if ( !is.na(file.info(npath)$size) ) {done <- 1}
}
npath
} else {
cat("\tFound",x," in ", found[[x]],"\n")
found[[x]]
}
})
write.table(as.data.frame(meetconf),file=optionsFile,sep='=',col.names=FALSE)
} else {
meetconftmp <- read.table(file=optionsFile,sep='=',header=FALSE)
meetconf <- as.character( meetconftmp$V2)
names(meetconf) <- as.character(meetconftmp$V1)
}
options(warn=-1)
data(organism,package="MEET", envir=environment())
organism<-get("organism")
write.fasta <- get("write.fasta",pos="package:seqinr")
read.fasta <- get("read.fasta",pos="package:seqinr")
iicc<-vector(mode="list", length=28)
names(iicc)<-c("mode", "method","nameTF","organism", "background","alignment","pvalue","parameters","model","Transcriptionfactor",
"nummotif","lenmotif","direction","outsequence","position","missing","vector","gapopen","maxiters","gapextend","clustalw","muscle","meme","mast","transfac2meme","Mdscan","DNA", "parameterIdeal")
iicc$mode=mode
iicc$method=method
iicc$nameTF=nameTF
iicc$organism=org
iicc$background= organism[org,]
iicc$alignment=alg
iicc$threshold<-threshold
iicc$parameters<-order
iicc$model<-model
iicc$nummotif<-num_motif
iicc$lenmotif<-len_motif
iicc$direction<-direction
iicc$outsequence<-sequence
iicc$position<-position
iicc$missing<-mv
iicc$vector<-vector
iicc$gapopen<-gapopen
iicc$maxiters<-maxiters
iicc$gapextend<-gapextend
iicc$clustalw<-as.character(meetconf["call.clustalw"])
iicc$muscle<-as.character(meetconf["call.muscle"])
iicc$meme<-as.character(meetconf["call.meme"])
iicc$mast<-as.character(meetconf["call.mast"])
iicc$transfac2meme<-as.character(meetconf["call.transfac2meme"])
iicc$MDscan<-as.character(meetconf["call.MDscan"])
iicc$parameterIdeal<-NULL
if(iicc$direction!="b"){ iicc$DNA<-vector(mode="list", length=1)
if(iicc$direction=="f"){
iicc$DNA[[1]]<-read.fasta(file=seqin,forceDNAtolower=FALSE, set.attributes=FALSE)[[1]]
iicc$DNA[[1]][iicc$DNA[[1]]=="a"]="A"; iicc$DNA[[1]][iicc$DNA[[1]]=="t"]="T";
iicc$DNA[[1]][iicc$DNA[[1]]=="c"]="C"; iicc$DNA[[1]][iicc$DNA[[1]]=="g"]="G";
}else{
iicc$DNA[[1]]<-read.fasta(file=seqin,forceDNAtolower=FALSE, set.attributes=FALSE)[[1]]
iicc$DNA[[1]]<-rev(iicc$DNA[[1]])
iicc$DNA[[1]][iicc$DNA[[1]]=="a"]="A"; iicc$DNA[[1]][iicc$DNA[[1]]=="t"]="T";
iicc$DNA[[1]][iicc$DNA[[1]]=="c"]="C"; iicc$DNA[[1]][iicc$DNA[[1]]=="g"]="G";
}
}else{
iicc$DNA<-vector(mode="list", length=2)
iicc$DNA[[1]]<-read.fasta(file=seqin,forceDNAtolower=FALSE, set.attributes=FALSE)[[1]]
iicc$DNA[[1]][iicc$DNA[[1]]=="a"]="A"; iicc$DNA[[1]][iicc$DNA[[1]]=="t"]="T";
iicc$DNA[[1]][iicc$DNA[[1]]=="c"]="C"; iicc$DNA[[1]][iicc$DNA[[1]]=="g"]="G";
iicc$DNA[[2]][iicc$DNA[[1]]=="A"]="T";iicc$DNA[[2]][iicc$DNA[[1]]=="T"]="A";
iicc$DNA[[2]][iicc$DNA[[1]]=="C"]="G";iicc$DNA[[2]][iicc$DNA[[1]]=="G"]="C"
iicc$DNA[[2]]<-rev(iicc$DNA[[2]])
}
background<-iicc$background
write.table(background, "bfile", col.names=FALSE, quote=FALSE)
output<-vector(mode="list", length=3)
names(output)<-c("Consensus", "Summary", "Results")
if (is.null(iicc$nameTF)=="TRUE"){
alignedSequences<-Alignment(TF,iicc)
iicc$Transcriptionfactor<-alignedSequences
output$Consensus<-CreateConsensus(alignedSequences,iicc,filein=TF )
iicc$Consensus<-output$Consensus
}else{
iicc$Transcriptionfactor<-NULL
iicc$Consensus<-NULL
}
output$Results<-switch(iicc$mode, "training"=ConstructModel(iicc,TF), "detection"=detection(iicc))
output$Summary<-iicc
return(output)
}
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