/
MoVRs_Motif2meme.R
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MoVRs_Motif2meme.R
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#!/usr/bin/Rscript
#... converts a Homer trainingset??motifs.homer PWM/PFM file into MEME format
motif2meme <- function(inFile,outFile) {
library(tools)
#establishing the number of distinct motifs in the file and parsing it accordingly
stopifnot(is.character(inFile))
thisFile <- file(outFile)
fileName <- file_path_sans_ext(inFile)
#reading the input file
motif.file <- scan(file=inFile,character(0), sep="\n",quote=NULL)
motif.index <- grep(pattern="^>",motif.file)
n.motifs <- length(motif.index)
total.len <- length(motif.file)
#print(n.motifs)
sink(thisFile,append=TRUE)
cat("MEME version 4\n\n",file=thisFile,append=TRUE)
cat("ALPHABET= ACGT\n\n",file=thisFile,append=TRUE)
cat("strands: + -\n\n")
nameSplit <- strsplit(fileName,"_")
nameNum <- nameSplit[[1]][1]
motifNum <- sub("^trainingSet(..)motifs.*", "\\1", nameNum) # fifth
for (i in 1:(n.motifs-1)) {
# print(i)
# print(" ")
(motif.index[i]+1) -> index.start
((motif.index[i+1])-1) -> index.end
motif.file[index.start:index.end] -> this_motif
strsplit(this_motif,split="\t") -> motif_split
#print(head(motif_split))
length(this_motif) -> motif_row
array(NA,c(motif_row,4)) -> motif_array
for (n in 1:motif_row) {
as.numeric(motif_split[[n]]) -> motif_array[n,]
}
motif_array <- as.data.frame(motif_array)
motif.file[motif.index[i]] -> header.string
strsplit(header.string,split="[\t]") -> prob.string
prob.string[[1]][6] -> prob.string2
strsplit(prob.string2,"[:]") -> prob.string3
prob.string3[[1]][4] -> this.p.val
prob.string[[1]][2] -> name.string
strsplit(name.string,split=",") -> name.string2
name.string2[[1]][1] -> name.string3
motif_name <- paste("motif",motifNum,i,sep="_")
cat("MOTIF",motif_name,name.string3,"\n",file=thisFile, append=TRUE)
cat("letter-probability matrix: ",file=thisFile, append=TRUE)
cat("alength= 4 w=", motif_row, file=thisFile, append=TRUE)
cat(" nsites= 20 ",file=thisFile, append=TRUE)
cat("E= ",file=thisFile, append=TRUE)
cat(this.p.val,"\n",file=thisFile, append=TRUE)
write.table(motif_array,file=thisFile,append=TRUE,col.names=FALSE,row.names=FALSE,sep="\t")
cat("\n",file=thisFile, append=TRUE)
}
i <- i+1
(motif.index[n.motifs]+1) -> index.start
total.len -> index.end
motif.file[index.start:index.end] -> this_motif
strsplit(this_motif,split="\t") -> motif_split
#print(head(motif_split))
length(this_motif) -> motif_row
array(NA,c(motif_row,4)) -> motif_array
for (n in 1:motif_row) {
as.numeric(motif_split[[n]]) -> motif_array[n,]
}
motif_array <- as.data.frame(motif_array)
motif.file[motif.index[i]] -> header.string
strsplit(header.string,split="[\t]") -> prob.string
prob.string[[1]][6] -> prob.string2
strsplit(prob.string2,"[:]") -> prob.string3
prob.string3[[1]][4] -> this.p.val
prob.string[[1]][2] -> name.string
strsplit(name.string,split=",") -> name.string2
name.string2[[1]][1] -> name.string3
motif_name <- paste("motif",motifNum,i,sep="_")
cat("MOTIF",motif_name,name.string3,"\n",file=thisFile, append=TRUE)
cat("letter-probability matrix: ",file=thisFile, append=TRUE)
cat("alength= 4 w=", motif_row, file=thisFile, append=TRUE)
cat(" nsites= 20 ",file=thisFile, append=TRUE)
cat("E= ",file=thisFile, append=TRUE)
cat(this.p.val,"\n",file=thisFile, append=TRUE)
write.table(motif_array,file=thisFile,append=TRUE,col.names=FALSE,row.names=FALSE,sep="\t")
cat("\n",file=thisFile, append=TRUE)
sink()
close(thisFile)
cat("... done converting from HOMER to MEME motif format")
}
#parse command line argument and run this function
args = commandArgs(trailingOnly = TRUE)
if (length(args)!=2) {
stop("Need input and output file name, homer ===> meme\n",call. = TRUE)
} else {
inFile=args[1]
outFile=args[2]
}
motif2meme(inFile,outFile)