R/getSeq-methods.R

In Bioconductor/BSgenome: Software infrastructure for efficient representation of full genomes and their SNPs

### =========================================================================
### The "getSeq" method for BSgenome objects.
### -------------------------------------------------------------------------


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Low-level helpers called by "getSeq" method for BSgenome objects.
###

.normargStrand <- function(strand, length)
{
    if (is(strand, "Rle"))
        strand <- as.vector(strand)
    if (is.factor(strand))
        strand <- as.vector(strand)
    if (!is.character(strand))
        stop("invalid 'strand'")
    lvls <- levels(strand())
    if (!all(strand %in% lvls))
        stop("strand values must be in '", paste(lvls, collapse="' '"), "'")
    if (length(strand) > length)
        stop("too many elements in 'strand'")
    if (length(strand) < length) {
        if (length(strand) == 0L)
            stop("cannot recycle zero-length 'strand'")
        strand <- S4Vectors:::recycleVector(strand, length)
    }
    strand
}

### Make 'strand' star-free.
### If applied on the output of .normargStrand(), then returns a character
### vector guaranteed to have only "+" or "-" elements (no "*").
### If applied on the output of strand(GRanges), then returns a 'factor' Rle
### guaranteed to have only "+" or "-" elements (no "*").
.starfreeStrand <- function(strand)
{
    ustrand <- unique(strand)
    if (length(ustrand) == 1L && ustrand == "*") {
        ## Strand is "*" for all the elements. Replace it by "+".
        strand[] <- "+"
        return(strand)
    }
    if ("*" %in% ustrand)
        stop("cannot mix \"*\" with other strand values")
    strand
}

### Assumes 'names' is a character vector.
.normGetSeqArgs <- function(names, start, end, width, strand)
{
    start <- IRanges:::.normargSEW(start, "start")
    end <- IRanges:::.normargSEW(end, "end")
    width <- IRanges:::.normargSEW(width, "width")
    l0 <- length(names)
    l1 <- length(start)
    l2 <- length(end)
    l3 <- length(width)
    max0123 <- max(l0, l1, l2, l3)
    ## Recycling will fail for vectors of length 0.
    names <- S4Vectors:::recycleVector(names, max0123)
    start <- S4Vectors:::recycleVector(start, max0123)
    end <- S4Vectors:::recycleVector(end, max0123)
    width <- S4Vectors:::recycleVector(width, max0123)
    strand <- .starfreeStrand(.normargStrand(strand, max0123))
    list(names=names, start=start, end=end, width=width, strand=strand)
}

### Assumes 'x' is an IntegerRangesList object with names.
.newGRangesFromNamedRangesList <- function(x, strand)
{
    seqnames <- rep.int(names(x), elementNROWS(x))
    ranges <- unlist(x, use.names=FALSE)
    strand <- .normargStrand(strand, length(ranges))
    GRanges(seqnames=seqnames, ranges=ranges, strand=strand)
}

### Assumes 'x' is an IntegerRanges object with names.
.newGRangesFromNamedRanges <- function(x, strand)
{
    strand <- .normargStrand(strand, length(x))
    GRanges(seqnames=names(x), ranges=unname(x), strand=strand)
}

### Error messages refer to 'x' as "names" because of the context in which
### .toGRanges() is called.
.toGRanges <- function(x, strand)
{
    if (is(x, "IntegerRangesList") || is(x, "IntegerRanges")) {
        if (is.null(names(x)))
            stop("when 'names' is an IntegerRangesList or IntegerRanges ",
                 "object, it must be named with the sequence names")
        if (is(x, "IntegerRangesList"))
            ans <- .newGRangesFromNamedRangesList(x, strand)
        else
            ans <- .newGRangesFromNamedRanges(x, strand)
        return(ans)
    } 
    stop("invalid 'names'")
}

.drop_unused_seqlevels <- function(x)
{
    seqlevels(x) <- seqlevelsInUse(x)
    x
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### .extractFromBSgenomeSingleSequences()
###

### 'names' must be a character vector or a GRanges object.
### If 'names' is character vector, then 'start', 'end', 'width', and 'strand'
### are assumed to be already normalized (and star-free for 'strand').
### Otherwise, they are ignored and 'strand(names)' is assumed to be star-free.
.extractFromBSgenomeSingleSequences <- function(x, names,
                                                start, end, width, strand)
{
    if (is.character(names)) {
        #idx <- which(is.na(start) & is.na(width))
        #if (length(idx) != 0L)
        #    start[idx] <- 1L
        #idx <- which(is.na(end) & is.na(width))
        #if (length(idx) != 0L)
        #    end[idx] <- unname(seqlengths(x)[names])
        #ranges <- IRanges(start=start, end=end, width=width)
        refwidths <- seqlengths(x)[names]
        ranges <- solveUserSEW(refwidths, start=start, end=end, width=width)
        names <- GRanges(seqnames=names, ranges=ranges, strand=strand)
    }

    ## Check that 'seqlengths(names)' is compatible with 'x'.
    #if (!all(names(seqlengths(names)) %in% names(seqlengths(x))))
    #    stop("sequence names in GRanges are incompatible with BSgenome object")
    #if (!all(is.na(seqlengths(names)))
    # && !identical(seqlengths(names),
    #               seqlengths(x)[names(seqlengths(names))]))
    #    stop("sequence lengths in GRanges are incompatible ",
    #         "with BSgenome object")

    ## Split 'names' by sequence names.
    grl <- split(names, seqnames(names))
    grl_seqlevels <- names(grl)

    ## Loop over the sequence names and extract the ranges.
    dnaset_list <- lapply(seq_len(length(grl)),
        function(i)
        {
            gr <- grl[[i]]
            if (length(gr) == 0L)
                return(DNAStringSet())
            seqlevel <- grl_seqlevels[i]
            is_circular <- isCircular(x)[[seqlevel]]
            idx <- match(seqlevel, x@user_seqnames)
            if (is.na(idx))
                stop("invalid sequence name: ", seqlevel)
            seqname <- names(x@user_seqnames)[[idx]]
            if (is.null(snplocs(x, seqname))) {
                ## Try to grab the subject sequence from the cache.
                subject <- try(get(seqname, envir=x@.seqs_cache,
                                   inherits=FALSE), silent=TRUE)
                if (is(subject, "try-error")) {
                    ## The subject sequence was not in the cache.
                    ans <- loadSubseqsFromStrandedSequence(
                                   x@single_sequences,
                                   seqname, ranges(gr), strand(gr),
                                   is_circular)
                    return(ans)
                }
                ## The subject sequence was in the cache.
                .linkToCachedObject(subject) <- .newLinkToCachedObject(
                                                    seqname,
                                                    x@.seqs_cache,
                                                    x@.link_counts)
            } else {
                subject <- x[[seqlevel]]
            }
            masks(subject) <- NULL
            loadSubseqsFromStrandedSequence(
                                   subject,
                                   seqlevel, ranges(gr), strand(gr),
                                   is_circular)
        }
    )
    ## "unsplit" 'dnaset_list'.
    unsplit_list_of_XVectorList("DNAStringSet", dnaset_list,
                                as.factor(seqnames(names)))
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### .extractFromBSgenomeMultipleSequences()
###

### Assumes that 'strand' is star-free.
.getOneSeqFromBSgenomeMultipleSequences <- function(x, name,
                                                    start, end, width, strand,
                                                    exact.match)
{
    nhits <- 0L
    for (mseqname in mseqnames(x)) {
        mseq <- x[[mseqname]]
        if (exact.match) {
            ii <- which(names(mseq) == name)
        } else {
            ii <- grep(name, names(mseq))
        }
        if (nhits == 0L && length(ii) == 1L)
            subject <- mseq[[ii]]
        nhits <- nhits + length(ii)
    }
    if (nhits == 0L)
        stop("sequence ", name, " not found")
    if (nhits > 1L)
        stop("sequence ", name, " found more than once, ",
             "please use a non-ambiguous name")
    ans <- subseq(subject, start=start, end=end, width=width)
    if (strand == "+")
        return(xvcopy(ans))
    else
        return(reverseComplement(ans))
}

### Assumes 'x' is a list of DNAString objects and turns it into a
### DNAStringSet object.
### TODO: Find a better way to do this (current implementation is not very
### efficient). Also maybe make this a "DNAStringSet" method for list objects.
.listOfDNAStringToDNAStringSet <- function(x)
{
    if (length(x) == 0L)
        return(DNAStringSet())
    subject <- do.call(xscat, x)
    DNAStringSet(successiveViews(subject, elementNROWS(x)))
}

### 'names' must be a character vector or a GRanges object.
### If 'names' is character vector, then 'start', 'end', 'width', and 'strand'
### are assumed to be already normalized (and star-free for 'strand').
### Otherwise, they are ignored and 'strand(names)' is assumed to be star-free.
.extractFromBSgenomeMultipleSequences <- function(x, names,
                                                  start, end, width, strand)
{
    if (is.character(names)) {
        ans <- lapply(seq_len(length(names)),
            function(i)
                .getOneSeqFromBSgenomeMultipleSequences(x, names[i],
                                start[i], end[i], width[i], strand[i],
                                exact.match=FALSE)
        )
    } else {
        ans <- lapply(seq_len(length(names)),
            function(i)
            {
                name <- as.character(seqnames(names))[i]
                start <- start(names)[i]
                width <- width(names)[i]
                strand <- as.character(strand(names))[i]
                .getOneSeqFromBSgenomeMultipleSequences(x, name,
                                start, NA, width, strand,
                                exact.match=TRUE)
            }
        )
    }
    .listOfDNAStringToDNAStringSet(ans)
}


### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### The "getSeq" generic and methods for BSgenome and XStringSet objects.
###

setMethod("getSeq", "BSgenome",
    function(x, names, start=NA, end=NA, width=NA, strand="+",
             as.character=FALSE)
    {
        if (!isTRUEorFALSE(as.character))
            stop("'as.character' must be TRUE or FALSE")
        if (missing(names)) {
            names <- seqnames(x)
        } else {
            if (is(names, "Rle"))
                names <- as.vector(names)
            if (is.factor(names))
                names <- as.vector(names)
        }
        if (is.character(names)) {
            args <- .normGetSeqArgs(names, start, end, width, strand)
            sseq_idx <- args$names %in% seqnames(x)
            sseq_args <- list(names=args$names[sseq_idx],
                              start=args$start[sseq_idx],
                              end=args$end[sseq_idx],
                              width=args$width[sseq_idx],
                              strand=args$strand[sseq_idx])
            mseq_idx <- !sseq_idx
            mseq_args <- list(names=args$names[mseq_idx],
                              start=args$start[mseq_idx],
                              end=args$end[mseq_idx],
                              width=args$width[mseq_idx],
                              strand=args$strand[mseq_idx])
        } else {
            if (!identical(c(start, end, width), c(NA, NA, NA)))
                stop("'start', 'end' and 'width' can only be specified when ",
                     "'names' is either missing, a character vector/factor, ",
                     "a character-Rle, or a factor-Rle")
            if (is(names, "GRanges") || is(names, "GRangesList")) {
                if (!identical(strand, "+"))
                    stop("'strand' cannot be specified ",
                         "when 'names' is a GRanges or GRangesList object")
                if (is(names, "GRangesList")) {
                    unlisted_names <- unlist(names, use.names=FALSE)
                    unlisted_ans <- getSeq(x, unlisted_names,
                                           as.character=as.character)
                    return(relist(unlisted_ans, names))
                }
            } else {
                names <- .toGRanges(names, strand)
            }
            ## We don't need the result of merge(). By calling merge() here
            ## we're just making sure that 'x' and 'names' are based on
            ## compatible reference genomes (merge() will raise an error if
            ## they are not).
            merge(seqinfo(x), seqinfo(names))
            strand(names) <- .starfreeStrand(strand(names))
            seqnames <- as.character(seqnames(names))
            sseq_idx <- seqnames %in% seqnames(x)
            sseq_args <- list(names=.drop_unused_seqlevels(names[sseq_idx]))
            mseq_idx <- !sseq_idx
            mseq_args <- list(names=names[mseq_idx])
        }
        ans <- rep.int(DNAStringSet(""), length(sseq_idx))
        ans[sseq_idx] <- .extractFromBSgenomeSingleSequences(x,
                                   sseq_args$names,
                                   sseq_args$start,
                                   sseq_args$end,
                                   sseq_args$width,
                                   sseq_args$strand)
        ans[mseq_idx] <- .extractFromBSgenomeMultipleSequences(x,
                                   mseq_args$names,
                                   mseq_args$start,
                                   mseq_args$end,
                                   mseq_args$width,
                                   mseq_args$strand)
        if (is(names, "GRanges"))
            names(ans) <- names(names)
        else if (is.character(names))
            names(ans) <- names
        if (as.character)
            return(as.character(ans))
        if (length(ans) == 1L && is.character(names))
            return(ans[[1L]])  # turn 1st and unique element into DNAString
        ans
    }
)

setMethod("getSeq", "XStringSet", 
    function(x, names) 
    {
        stopifnot(is.character(names) || is(names, "GRanges") ||
                  is(names, "GRangesList"),
                  !is.null(names(x)))
        if (is.character(names)) {
            found <- names %in% names(x)
            regexNames <- unlist(lapply(names[!found], grep, names(x),
                                        value=TRUE))
            names <- c(names[found], regexNames)
            return(x[names])
        } else if (is(names, "GRangesList")) {
            gr <- unlist(names, use.names=FALSE)
        } else {
            gr <- names
        }
        ignoringStrand <- any(strand(gr) != "*") &&
            !hasMethod(reverseComplement, class(x))
        if (ignoringStrand) {
            warning("some strand(x) != '*' but ",
                    "strand has no meaning for ", class(x))
        }
        rl <- as(gr, "IntegerRangesList")
        ans <- unsplit(extractAt(x[names(rl)], unname(rl)), seqnames(gr))
        if (!ignoringStrand) {
            minus <- strand(gr) == "-"
            ans[minus] <- reverseComplement(ans[minus])
        }
        if (is(names, "GRangesList")) {
            ans <- relist(ans, names)
        }
        ans
    }
)

setMethod("[", c("XStringSet", "GenomicRanges"),
          function (x, i, j, ..., drop = TRUE) {
              if (!missing(j)) 
                  stop("invalid subsetting")
              getSeq(x, i, ...)
          })

setMethod("[", c("XStringSet", "GRangesList"),
          function (x, i, j, ..., drop = TRUE) {
              if (!missing(j)) 
                  stop("invalid subsetting")
              unstrsplit(getSeq(x, i, ...))
          })