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### -----------------------------------------------------------------
### make FlatFileDir from JASPAR database: including *.pfm and matrix_list.txt
### The matrix_list.txt has columns: ID, InformationContent, Name, Class, Tags
### Exported!
makeFlatFileDir <- function(JASPAR){
outputDir <- "FlatFileDir"
dir.create(outputDir)
# Make the matrix_list.txt
pfms <- getMatrixSet(JASPAR, opts=list(all=TRUE))
pfmIDs <- ID(pfms)
pfmICs <- sapply(pfms, function(x){sum(totalIC(toICM(x)))})
pfmNames <- name(pfms)
## There are cases that have more than two classes
pfmClasses <- sapply(matrixClass(pfms), paste, collapse="/")
pfmTags <- lapply(pfms, function(x){sapply(x@tags, paste,
collapse="/")})
pfmTags <- sapply(pfmTags, function(x){x[order(names(x))]})
pfmTags <- sapply(pfmTags, function(x){paste(";", paste0(names(x), " \"", x,
"\" ", collapse="; "))})
ans <- cbind(data.frame(IDs=pfmIDs,
ICs=pfmICs,
Names=pfmNames,
Classes=pfmClasses,
Tags=pfmTags
))
write.table(ans, file=file.path(outputDir, "matrix_list.txt"),
quote=FALSE, sep="\t",
col.names = FALSE, row.names = FALSE)
# Make the *.pfm
lapply(pfms, function(x){write.table(x@profileMatrix,
file=file.path(outputDir,
paste0(x@ID, ".pfm")),
quote=FALSE, sep="\t",
col.names = FALSE, row.names = FALSE)})
return("success")
}
### -----------------------------------------------------------------
### readJASPARMatrix: read the jaspar format PFM in txt file
### "individual" format:
### >MA0001.1 AGL3
### A [ 0 3 79 40 66 48 65 11 65 0 ]
### C [94 75 4 3 1 2 5 2 3 3 ]
### G [ 1 0 3 4 1 0 5 3 28 88 ]
### T [ 2 19 11 50 29 47 22 81 1 6 ]
### "all" format: multiple "individual" matrices and seperated with a blank line
### Exported
.processJASPARText <- function(text){
ID <- sub("^>", "", strsplit(text[1], "\t")[[1]][1])
name <- strsplit(text[1], "\t")[[1]][2]
if(!identical(substr(text[2:5], 1, 1), DNA_BASES)){
stop("The second to fifth lines of the file must start with",
"`A`, `C`, `G`, `T`, respectively.")
}
profileMatrix <- do.call(rbind, strsplit(sub(" *]$", "",
sub("^(A|C|G|T) \\[ *", "",
text[2:5])), " +"))
mode(profileMatrix) <- "integer"
rownames(profileMatrix) <- DNA_BASES
ans <- PFMatrix(ID=ID, name=name, profileMatrix=profileMatrix)
}
readJASPARMatrix <- function(fn, type=c("individual", "all")){
type <- match.arg(type)
text <- readLines(fn)
if(type == "individual"){
if(length(text) != 5L){
stop("The `individual` format is supposed to have 5 lines!")
}
ans <- .processJASPARText(text)
}else{
if(length(text) %% 6 != 0L){
stop("The `all` format is supposed to have a number of lines",
"mutipled by 6!")
}
text2 <- split(text, rep(1:(length(text)/6), rep(6, length(text)/6)))
ans <- lapply(text2, .processJASPARText)
names(ans) <- lapply(ans, name)
ans <- do.call(PFMatrixList, ans)
}
return(ans)
}
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