R/seqname-utils.R

In jotsetung/ensembldb: Utilities to create and use Ensembl-based annotation databases

####============================================================
##  Methods and functions to allow usage of EnsDb objects also
##  with genomic resources that do not use Ensembl based
##  seqnames
##  We're storing the seqname style into the .properties slot
##  of the EnsDb object.
####------------------------------------------------------------
.ENSOPT.SEQNOTFOUND="ensembldb.seqnameNotFound"
####============================================================
##  formatSeqnamesForQuery
##
##  Formating/renamaing the seqname(s) according to the specified
##  style.
##  x is an EnsDb,
##  sn the seqnames to convert...
##  If a seqname can not be mapped NA will be returned.
####------------------------------------------------------------
setMethod("formatSeqnamesForQuery", "EnsDb", function(x, sn, ifNotFound){
    .formatSeqnameByStyleForQuery(x, sn, ifNotFound)
})
## Little helper function that returns eventually the argument.
## Returns MISSING if the argument was not set.
.getSeqnameNotFoundOption <- function() {
    notFound <- "MISSING"
    if(any(names(options()) == .ENSOPT.SEQNOTFOUND)){
        notFound <- getOption(.ENSOPT.SEQNOTFOUND)
        ## Do some sanity checks?
    }
    notFound
}
.formatSeqnameByStyleForQuery <- function(x, sn, ifNotFound){
    ## Fixing ifNotFound, allowing that this can be set using options.
    if(missing(ifNotFound)){
        ifNotFound <- .getSeqnameNotFoundOption()
    }
    ## Map whatever to Ensembl seqnames, such that we can perform queries.
    ## Use mapSeqlevels, or rather genomeStyles and do it hand-crafted!
    sst <- seqlevelsStyle(x)
    dbSst <- dbSeqlevelsStyle(x)
    if(sst == dbSst)
        return(sn)
    map <- getProperty(x, "genomeStyle")
    if(!is(map, "data.frame"))
        map <- genomeStyles(organism(x))
    ## sn are supposed to be in sst style, map them to dbSst
    idx <- match(sn, map[, sst])
    mapped <- map[idx, dbSst]
    if(any(is.na(mapped))){
        noMap <- which(is.na(mapped))
        seqNoMap <- unique(sn[noMap])
        if(length(seqNoMap) > 5){
            theMess <- paste0("More than 5 seqnames could not be mapped to ",
                              "the seqlevels style of the database (", dbSst, ")!")
        }else{
            theMess <- paste0("Seqnames: ", paste(seqNoMap, collapse=", "),
                              " could not be mapped to ",
                              " the seqlevels style of the database (", dbSst, ")!")
        }
        if(is.na(ifNotFound) | is.null(ifNotFound)){
            ## Replacing the missing seqname mappings with ifNotFound.
            mapped[noMap] <- ifNotFound
            warnMess <- paste0(" Returning ", ifNotFound, " for these.")
        }else{
            ## If MISSING -> STOP
            if(ifNotFound == "MISSING"){
                stop(theMess)
            }else{
                ## Next special case: use the original names, i.e. don't map at all.
                if(ifNotFound == "ORIGINAL"){
                    mapped[noMap] <- sn[noMap]
                    warnMess <- "Returning the orginal seqnames for these."
                }else{
                    mapped[noMap] <- ifNotFound
                    warnMess <- paste0(" Returning ", ifNotFound, " for these.")
                }
            }
        }
        warning(theMess, warnMess)
    }
    mapped
}
setMethod("formatSeqnamesFromQuery", "EnsDb", function(x, sn, ifNotFound){
    return(.formatSeqnameByStyleFromQuery(x, sn, ifNotFound))
})
.formatSeqnameByStyleFromQuery <- function(x, sn, ifNotFound){
    ## Fixing ifNotFound, allowing that this can be set using options.
    if(missing(ifNotFound)){
        ifNotFound <- .getSeqnameNotFoundOption()
    }
    ## Map Ensembl seqnames resulting form queries to the seqlevel style by
    ## seqlevelsStyle.
    sst <- seqlevelsStyle(x)
    dbSst <- dbSeqlevelsStyle(x)
    if(sst == dbSst)
        return(sn)
    ## Otherwise...
    map <- getProperty(x, "genomeStyle")
    if(!is(map, "data.frame"))
        map <- genomeStyles(organism(x))
    ## sn are supposed to be in sst style, map them to dbSst
    idx <- match(sn, map[, dbSst])
    mapped <- map[idx, sst]
    if(any(is.na(mapped))){
        noMap <- which(is.na(mapped))
        seqNoMap <- unique(sn[noMap])
        if(length(seqNoMap) > 5){
            theMess <- paste0("More than 5 seqnames with seqlevels style of the database (",
                              dbSst, ") could not be mapped to the seqlevels style: ",
                              sst, "!)")
        }else{
            theMess <- paste0("Seqnames: ", paste(seqNoMap, collapse=", "),
                              " with seqlevels style of the database (", dbSst,
                              ") could not be mapped to seqlevels style: ", sst,
                              "!")
        }

        if(is.na(ifNotFound) | is.null(ifNotFound)){
            ## Replacing the missing seqname mappings with ifNotFound.
            mapped[noMap] <- ifNotFound
            warnMess <- paste0(" Returning ", ifNotFound, " for these.")
        }else{
            ## If MISSING -> STOP
            if(ifNotFound == "MISSING"){
                stop(theMess)
            }else{
                ## Next special case: use the original names, i.e. don't map at all.
                if(ifNotFound == "ORIGINAL"){
                    mapped[noMap] <- sn[noMap]
                    warnMess <- " Returning the orginal seqnames for these."
                }else{
                    mapped[noMap] <- ifNotFound
                    warnMess <- paste0(" Returning ", ifNotFound, " for these.")
                }
            }
        }
        warning(theMess, warnMess)
    }
    return(mapped)
}


####============================================================
##  dbSeqlevelsStyle
##
##  Returns the seqname style used by the database. Defaults to
##  Ensembl and reads the property: dbSeqlevelsStyle.
####------------------------------------------------------------
setMethod("dbSeqlevelsStyle", "EnsDb", function(x){
    stl <- getProperty(x, "dbSeqlevelsStyle")
    if(is.na(stl))
        stl <- "Ensembl"
    return(stl)
})
####============================================================
##  seqlevelStyle
##
##  Get or set the seqlevel style. If we can't find the stype in
##  GenomeInfoDb throw and error.
####------------------------------------------------------------
setMethod("seqlevelsStyle", "EnsDb", function(x){
    st <- getProperty(x, "seqlevelsStyle")
    if(is.na(st))
        st <- "Ensembl"
    return(st)
})

#' set seq level style for an EnsDb.
#'
#' @param x `EnsDb` object
#'
#' @param value either `character(1)` defining the style (needs to be one of
#'     the supported ones from `GenomeInfoDb`) or a `data.frame` defining the
#'     mapping between the seq levels of `x` and the new *custom* style.
#'
#' @noRd
setReplaceMethod("seqlevelsStyle", "EnsDb", function(x, value) {
    if (is.data.frame(value)) {
        cn <- colnames(value)
        if (!any(cn == "Ensembl"))
            stop("If a 'data.frame' is submitted with 'seqlevelsStyle' one",
                 " column needs to be named \"Ensembl\".", .call = FALSE)
        if (ncol(value) < 2)
            stop("'value' needs to have at least two columns.",
                 .call = FALSE)
        ## Use first non-Ensembl colname as "seqlevel style"
        sls <- cn[cn != "Ensembl"][1L]
        x <- setProperty(x, seqlevelsStyle = sls)
        x <- setProperty(x, genomeStyle = list(value))
    } else {
        if (value == dbSeqlevelsStyle(x)) {
            x <- setProperty(x, seqlevelsStyle=value)
        } else {
            dbStyle <- dbSeqlevelsStyle(x)
            genSt <- try(genomeStyles(organism(x)), silent=TRUE)
            if(is(genSt, "try-error"))
                stop("No mapping of seqlevel styles available in GenomeInfoDb ",
                     "for species ", organism(x), "! Please refer to the ",
                     "Vignette of the GenomeInfoDb package if you would like ",
                     "to provide this mapping.")
            if (!any(colnames(genSt) == value)) {
                stop("The provided seqlevels style is not known to ",
                     "GenomeInfoDb!")
            }
            if (!any(colnames(genSt) == dbStyle)) {
                stop("The seqlevels style of the database (", dbStyle,
                     ") is not known to GenomeInfoDb!")
            }
            ## If we got that far it should be OK
            x <- setProperty(x, seqlevelsStyle=value)
            x <- setProperty(x, genomeStyle=list(genSt))
        }
    }
    x
})

####============================================================
##  supportedSeqlevelsStyles
##
##  Get all supported seqlevels styles for the species of the EnsDb
####------------------------------------------------------------
setMethod("supportedSeqlevelsStyles", "EnsDb", function(x){
    map <- genomeStyles(organism(x))
    cn <- colnames(map)
    cn <- cn[!(cn %in% c("circular", "auto", "sex"))]
    return(colnames(cn))
})


####==================== OLD STUFF BELOW ====================

###==============================================================
##  Prefix chromosome names with "chr" if ucscChromosomeNames option
##  is set, otherwise, use chromosome names "as is".
##  This function should be used in functions that return results from
##  EnsDbs.
###--------------------------------------------------------------
prefixChromName <- function(x, prefix="chr"){
    ucsc <- getOption("ucscChromosomeNames", default=FALSE)
    if(ucsc){
        ## TODO fix also the mitochondrial chromosome name.
        mapping <- ucscToEnsMapping()
        for(i in 1:length(mapping)){
            x <- sub(x, pattern=names(mapping)[i], replacement=mapping[i],
                     fixed=TRUE)
        }
        ## Replace chr if it's already there
        x <- gsub(x, pattern="^chr", replacement="", ignore.case=TRUE)
        x <- paste0(prefix, x)
    }
    return(x)
}

###==============================================================
##  Remove leading "chr" to fit Ensembl based chromosome names.
##  This function should be called in functions that fetch data from
##  EnsDbs.
###--------------------------------------------------------------
ucscToEns <- function(x){
    ## TODO rename all additional chromosome names.
    mapping <- ucscToEnsMapping()
    for(i in 1:length(mapping)){
        x <- sub(x, pattern=mapping[i], replacement=names(mapping)[i],
                 fixed=TRUE)
    }
    x <- gsub(x, pattern="^chr", replacement="", ignore.case=TRUE)
    return(x)
}
###============================================================
##  Returns a character vector, elements representing UCSC chromosome
##  names with their names corresponding to the respective Ensembl
##  chromosome names.
###------------------------------------------------------------
ucscToEnsMapping <- function(){
    theMap <- c(MT="chrM")
    return(theMap)
}