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intervals.R
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intervals.R
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.gintervals <- function(chroms, starts, ends, strands) {
if (is.null(strands)) {
intervals <- data.frame(chrom = .gchroms(chroms), start = starts, end = ends)
} else {
intervals <- data.frame(chrom = .gchroms(chroms), start = starts, end = ends, strand = strands)
}
numintervals <- nrow(intervals)
maxends <- get("ALLGENOME", envir = .misha)[[1]]$end[match(as.character(intervals$chrom), get("ALLGENOME", envir = .misha)[[1]]$chrom)]
maxidx <- intervals$end == -1
intervals$end[maxidx] <- maxends[maxidx]
err.intervs <- intervals[intervals$start < 0, ]
if (nrow(err.intervs) > 0) {
stop(sprintf("Invalid interval (%s, %g, %g): start coordinate is out of range", err.intervs$chrom[1], err.intervs$start[1], err.intervs$end[1]), call. = FALSE)
}
err.intervs <- intervals[intervals$end > maxends, ]
if (nrow(err.intervs) > 0) {
stop(sprintf("Invalid interval (%s, %g, %g): end coordinate exceeds chromosome boundaries", err.intervs$chrom[1], err.intervs$start[1], err.intervs$end[1]), call. = FALSE)
}
err.intervs <- intervals[intervals$start >= intervals$end, ]
if (nrow(err.intervs) > 0) {
stop(sprintf("Invalid interval (%s, %g, %g): start coordinate exceeds or equals to end coordinate", err.intervs$chrom[1], err.intervs$start[1], err.intervs$end[1]), call. = FALSE)
}
if (!is.null(strands)) {
if (!is.numeric(intervals$strand)) {
stop("Invalid strand values", call. = FALSE)
}
err.intervs <- intervals[intervals$strand != as.integer(intervals$strand) | intervals$strand < -1 | intervals$strand > 1, ]
if (nrow(err.intervs) > 0) {
stop(sprintf("Invalid strand value %g of interval (%s, %g, %g)", err.intervs$strand[1], err.intervs$chrom[1], err.intervs$start[1], err.intervs$end[1]))
}
}
intervals
}
.gintervals.apply <- function(chroms, intervals, intervals.set.out, FUN, ...) {
if (!is.null(intervals.set.out)) {
fullpath <- .gintervals.check_new_set(intervals.set.out)
}
if (is.data.frame(intervals)) {
intervals <- list(intervals)
}
# sort chroms
chroms$size <- NULL
if ("chrom" %in% colnames(chroms)) {
chroms <- data.frame(chrom = chroms[with(chroms, order(chrom)), ])
} else {
chroms <- chroms[with(chroms, order(chrom1, chrom2)), ]
}
# let's assume that if any of the input intervals sets is big then intervals.set.out should be big as well
if (any(unlist(lapply(intervals, function(intervals) {
.gintervals.is_bigset(intervals) || .gintervals.needs_bigset(intervals)
})))) {
stats <- NULL
zeroline <- NULL
success <- FALSE
t <- Sys.time()
progress.percentage <- -1
tryCatch(
{
# if any of the source intervals sets is big then create the output intervals set big too
if (!is.null(intervals.set.out)) {
dir.create(fullpath, recursive = TRUE, mode = "0777")
}
if (.gintervals.is1d(intervals[[1]])) {
mapply(function(chrom) {
loaded_intervals <- lapply(intervals, function(intervals) {
.gintervals.load_ext(intervals, chrom = chrom)
})
res <- do.call(FUN, list(loaded_intervals, ...))
if (!is.null(intervals.set.out) && !is.null(res) && nrow(res) > 0) {
zeroline <<- res[0, ]
.gintervals.big.save(fullpath, res, chrom = chrom)
stat <- .gcall("gintervals_stats", res, .misha_env())
stats <<- rbind(stats, data.frame(chrom = chrom, stat))
}
if (as.integer(difftime(Sys.time(), t, units = "secs")) > 3) {
t <<- Sys.time()
percentage <- as.integer(100 * match(chrom, chroms$chrom) / nrow(chroms))
if (percentage < 100 && progress.percentage != percentage) {
message(sprintf("%d%%...", percentage), appendLF = FALSE)
progress.percentage <<- percentage
}
}
}, chroms$chrom)
} else {
mapply(function(chrom1, chrom2) {
loaded_intervals <- lapply(intervals, function(intervals) {
.gintervals.load_ext(intervals, chrom1 = chrom1, chrom2 = chrom2)
})
res <- do.call(FUN, list(loaded_intervals, ...))
if (!is.null(intervals.set.out) && !is.null(res) && nrow(res) > 0) {
zeroline <<- res[0, ]
.gintervals.big.save(fullpath, res, chrom1 = chrom1, chrom2 = chrom2)
stat <- .gcall("gintervals_stats", res, .misha_env())
stats <<- rbind(stats, data.frame(chrom1 = chrom1, chrom2 = chrom2, stat))
}
if (as.integer(difftime(Sys.time(), t, units = "secs")) > 3) {
t <<- Sys.time()
percentage <- as.integer(100 * which(chroms$chrom1 == chrom1 & chroms$chrom2 == chrom2) / nrow(chroms))
if (percentage < 100 && progress.percentage != percentage) {
message(sprintf("%d%%...", percentage), appendLF = FALSE)
progress.percentage <<- percentage
}
}
}, chroms$chrom1, chroms$chrom2)
}
if (!is.null(intervals.set.out)) {
if (is.null(stats)) {
return(retv <- NULL)
}
.gintervals.big.save_meta(fullpath, stats, zeroline)
}
if (progress.percentage >= 0) {
message("100%")
}
success <- TRUE
# check whether the output intervals set needs to remain in big format
if (!is.null(intervals.set.out) && !.gintervals.needs_bigset(intervals.set.out)) {
.gintervals.big2small(intervals.set.out)
}
},
finally = {
if (!success && !is.null(intervals.set.out)) {
unlink(fullpath, recursive = TRUE)
}
}
)
} else {
loaded_intervals <- lapply(intervals, .gintervals.load_ext)
res <- do.call(FUN, list(loaded_intervals, ...))
if (!is.null(intervals.set.out) && !is.null(res) && nrow(res) > 0) {
if (.gintervals.is1d(res)) {
res <- res[order(res$chrom), ]
} else {
res <- res[order(res$chrom1, res$chrom2), ]
}
if (.gintervals.needs_bigset(res)) {
.gintervals.small2big(intervals.set.out, res)
} else {
.gintervals.save_file(fullpath, res)
}
} else {
return(NULL)
}
}
# refresh the list of GINTERVS, etc.
if (!is.null(intervals.set.out)) {
.gdb.add_intervals.set(intervals.set.out)
}
}
.gintervals.check_new_set <- function(intervals.set) {
if (!is.na(match(intervals.set, get("GINTERVS", envir = .misha)))) {
stop(sprintf("Intervals set %s already exists", intervals.set), call. = FALSE)
}
if (!length(grep("^[A-Za-z][\\w.]*$", intervals.set, perl = TRUE))) {
stop("Invalid interval name %s. Only alphanumeric characters and _ are allowed in the name.")
}
path <- gsub(".", "/", intervals.set, fixed = TRUE)
path <- paste(path, ".interv", sep = "")
fullpath <- paste(get("GWD", envir = .misha), path, sep = "/")
dir <- dirname(path)
fulldir <- paste(get("GWD", envir = .misha), dir, sep = "/")
if (!file.exists(fulldir)) {
stop(sprintf("Directory %s does not exist", dir), call. = FALSE)
}
if (file.exists(fullpath)) {
stop(sprintf("File %s already exists", path), call. = FALSE)
}
if (!is.na(match(intervals.set, get("GTRACKS", envir = .misha)))) {
stop(sprintf("Track %s already exists", intervals.set), call. = FALSE)
}
if (!is.na(match(intervals.set, gvtrack.ls()))) {
stop(sprintf("Virtual track %s already exists", intervals.set), call. = FALSE)
}
if (.ggetOption(".gautocompletion", FALSE) && exists(intervals.set, envir = .misha)) {
stop(sprintf("Variable \"%s\" shadows the name of the new intervals set.\nPlease remove this variable from the environment or switch off autocompletion mode.", intervals.set), call. = FALSE)
}
fullpath
}
.gintervals.load_ext <- function(intervals.set = NULL, chrom = NULL, chrom1 = NULL, chrom2 = NULL, progress = FALSE) {
if (is.null(intervals.set)) {
stop("Usage: gintervals.load(intervals.set, chrom = NULL, chrom1 = NULL, chrom2 = NULL)", call. = FALSE)
}
.gcheckroot()
if (is.character(intervals.set) && length(intervals.set) == 1 && is.na(match(intervals.set, get("GINTERVS", envir = .misha))) && is.na(match(intervals.set, get("GTRACKS", envir = .misha)))) {
stop(sprintf("Intervals set %s does not exist", intervals.set), call. = FALSE)
}
.gintervals.load(intervals.set, chrom, chrom1, chrom2, progress)
}
.gintervals.load <- function(intervals.set = NULL, chrom = NULL, chrom1 = NULL, chrom2 = NULL, progress = FALSE) {
if (!is.null(chrom)) {
chrom <- .gchroms(chrom)
if (length(chrom) > 1) {
stop("chrom parameter should mark only one chromosome")
}
}
if (!is.null(chrom1)) {
chrom1 <- .gchroms(chrom1)
if (length(chrom1) > 1) {
stop("chrom1 parameter should mark only one chromosome")
}
}
if (!is.null(chrom2)) {
chrom2 <- .gchroms(chrom2)
if (length(chrom2) > 1) {
stop("chrom2 parameter should mark only one chromosome")
}
}
if (!is.null(chrom) && !is.null(chrom1)) {
stop("Cannot use chrom and chrom1 parameters in the same call", call. = FALSE)
}
if (!is.null(chrom) && !is.null(chrom2)) {
stop("Cannot use chrom and chrom2 parameters in the same call", call. = FALSE)
}
if (is.character(intervals.set) && length(intervals.set) != 1 || !is.character(intervals.set) && !.gintervals.is1d(intervals.set) && !.gintervals.is2d(intervals.set)) {
stop("Invalid format of intervals", call. = FALSE)
}
res <- NULL
if (.gintervals.is_bigset(intervals.set)) {
meta <- .gintervals.big.meta(intervals.set)
zeroline <- meta$zeroline
t <- Sys.time()
progress.percentage <- -1
if (.gintervals.big.is1d(intervals.set)) {
if (!is.null(chrom1) || !is.null(chrom2)) {
stop(sprintf("%s is a 1D big intervals set.\nchrom1 or chrom2 parameters can be applied only to 2D intervals.", intervals.set), call. = FALSE)
}
if (!is.null(chrom)) {
meta$stats <- meta$stats[meta$stats$chrom == chrom, ]
}
if (!.gintervals.loadable(intervals.set, chrom = chrom)) {
if (is.null(chrom)) {
stop(sprintf(
"Cannot load a big intervals set %s: its size (%d) exceeds the limit (%d) controlled by gmax.data.size option.\nFor big intervals sets only one chromosome pair can be loaded at a time.",
intervals.set, sum(meta$stats$size), .ggetOption("gmax.data.size", 10000000)
), call. = FALSE)
} else {
stop(sprintf(
"Cannot load chromosome %s of an intervals set %s: its size (%d) exceeds the limit (%d) controlled by gmax.data.size option.",
chrom, intervals.set, sum(meta$stats$size), .ggetOption("gmax.data.size", 10000000)
), call. = FALSE)
}
}
if (nrow(meta$stats) > 1) {
res <- list(zeroline)
lapply(
meta$stats$chrom,
function(chrom) {
loaded_intervs <- .gintervals.load_file(intervals.set, chrom = chrom)
if (!identical(sapply(loaded_intervs, "class"), sapply(zeroline, "class"))) {
stop(sprintf("Intervals set %s, chrom %s: invalid columns definition", intervals.set, chrom), call. = FALSE)
}
res <<- c(res, list(loaded_intervs))
if (as.integer(difftime(Sys.time(), t, units = "secs")) > 3) {
t <<- Sys.time()
percentage <- as.integer(100 * match(chrom, meta$stats$chrom) / length(meta$stats$chrom))
if (progress && percentage < 100 && progress.percentage != percentage) {
message(sprintf("%d%%...", percentage), appendLF = FALSE)
progress.percentage <<- percentage
}
}
}
)
res <- do.call(.grbind, res) # much faster than calling rbind incrementally in mapply
} else if (nrow(meta$stats) == 1) {
res <- .gintervals.load_file(intervals.set, chrom = meta$stat$chrom[1])
if (!identical(sapply(res, "class"), sapply(zeroline, "class"))) {
stop(sprintf("Intervals set %s, chrom %s: invalid columns definition", intervals.set, meta$stat$chrom[1]), call. = FALSE)
}
} else {
res <- meta$zeroline
}
} else {
if (!is.null(chrom)) {
stop(sprintf("%s is a 2D big intervals set.\nchrom parameter can be applied only to 1D intervals.", intervals.set), call. = FALSE)
}
if (!is.null(chrom1)) {
meta$stats <- meta$stats[meta$stats$chrom1 == chrom1, ]
}
if (!is.null(chrom2)) {
meta$stats <- meta$stats[meta$stats$chrom2 == chrom2, ]
}
if (!.gintervals.loadable(intervals.set, chrom1 = chrom1, chrom2 = chrom2)) {
if (!is.null(chrom1) && !is.null(chrom2)) {
stop(sprintf(
"Cannot load chromosome pair (%s, %s) of an intervals set %s: its size (%d) exceeds the limit (%d) controlled by gmax.data.size option.",
chrom1, chrom2, intervals.set, sum(meta$stats$size), .ggetOption("gmax.data.size", 10000000)
), call. = FALSE)
} else if (!is.null(chrom1)) {
stop(sprintf(
"Cannot load chromosome %s of an intervals set %s: its size (%d) exceeds the limit (%d) controlled by gmax.data.size option.",
chrom1, intervals.set, sum(meta$stats$size), .ggetOption("gmax.data.size", 10000000)
), call. = FALSE)
} else if (!is.null(chrom2)) {
stop(sprintf(
"Cannot load chromosome %s of an intervals set %s: its size (%d) exceeds the limit (%d) controlled by gmax.data.size option.",
chrom2, intervals.set, sum(meta$stats$size), .ggetOption("gmax.data.size", 10000000)
), call. = FALSE)
} else {
stop(sprintf(
"Cannot load a big intervals set %s: its size (%d) exceeds the limit (%d) controlled by gmax.data.size option.\nFor big intervals sets only one chromosome pair can be loaded at a time.",
intervals.set, sum(meta$stats$size), .ggetOption("gmax.data.size", 10000000)
), call. = FALSE)
}
}
if (nrow(meta$stats) > 1) {
res <- list(zeroline)
mapply(
function(chrom1, chrom2) {
loaded_intervs <- .gintervals.load_file(intervals.set, chrom1 = chrom1, chrom2 = chrom2)
if (!identical(sapply(loaded_intervs, "class"), sapply(zeroline, "class"))) {
stop(sprintf("Interval set %s, chrom1 %s, chrom2 %s: invalid columns definition", intervals.set, chrom1, chrom2), call. = FALSE)
}
res <<- c(res, list(loaded_intervs))
if (as.integer(difftime(Sys.time(), t, units = "secs")) > 3) {
t <<- Sys.time()
percentage <- as.integer(100 * which(meta$stats$chrom1 == chrom1 & meta$stats$chrom2 == chrom2) / nrow(meta$stats))
if (progress && percentage < 100 && progress.percentage != percentage) {
message(sprintf("%d%%...", percentage), appendLF = FALSE)
progress.percentage <<- percentage
}
}
},
meta$stats$chrom1, meta$stats$chrom2
)
res <- do.call(.grbind, res) # much faster than calling rbind incrementally in mapply
} else if (nrow(meta$stats) == 1) {
res <- .gintervals.load_file(intervals.set, chrom1 = meta$stat$chrom1[1], chrom2 = meta$stat$chrom2[1])
if (!identical(sapply(res, "class"), sapply(zeroline, "class"))) {
stop(sprintf("Interval set %s, chrom1 %s, chrom2 %s: invalid columns definition", intervals.set, meta$stat$chrom1[1], meta$stat$chrom2[1]), call. = FALSE)
}
} else {
res <- meta$zeroline
}
}
if (progress.percentage >= 0) {
message("100%")
}
} else {
if (is.character(intervals.set) && length(intervals.set) == 1) {
res <- .gintervals.load_file(intervals.set)
} else {
res <- intervals.set
}
if (!is.null(res)) {
if (!.gintervals.is1d(res) && !is.null(chrom)) {
stop("chrom parameter can be applied only to 1D intervals", call. = FALSE)
}
if (!.gintervals.is2d(res) && (!is.null(chrom1) || !is.null(chrom2))) {
stop("chrom1 or chrom2 parameters can be applied only to 2D intervals", call. = FALSE)
}
if (nrow(res) > 0) {
if (!is.null(chrom)) {
res <- res[res$chrom == chrom, ]
if (nrow(res)) {
rownames(res) <- 1:nrow(res)
}
}
if (!is.null(chrom1)) {
res <- res[res$chrom1 == chrom1, ]
if (nrow(res)) {
rownames(res) <- 1:nrow(res)
}
}
if (!is.null(chrom2)) {
res <- res[res$chrom2 == chrom2, ]
if (nrow(res)) {
rownames(res) <- 1:nrow(res)
}
}
}
}
}
res
}
.gintervals.load_file <- function(intervals.set, chrom = NULL, chrom1 = NULL, chrom2 = NULL) {
intervfname <- sprintf("%s.interv", paste(get("GWD", envir = .misha), gsub("\\.", "/", intervals.set), sep = "/"))
if (!is.null(chrom)) {
chrom <- .gchroms(chrom)
intervfname <- sprintf("%s/%s", intervfname, chrom)
} else if (!is.null(chrom1) && !is.null(chrom2)) {
chrom1 <- .gchroms(chrom1)
chrom2 <- .gchroms(chrom2)
intervfname <- sprintf("%s/%s-%s", intervfname, chrom1, chrom2)
}
if (intervals.set %in% get("GTRACKS", envir = .misha)) {
.gcall("gtrack_intervals_load", intervals.set, chrom, chrom1, chrom2, .misha_env())
} else {
if (file.exists(intervfname) || (is.null(chrom) && is.null(chrom1) && is.null(chrom2))) {
f <- file(intervfname, "rb")
intervals.set <- unserialize(f)
close(f)
intervals.set
} else {
if (.gintervals.is_bigset(intervals.set)) {
.gintervals.big.meta(intervals.set)$zeroline
} else {
stop(sprintf("File %s does not exist", intervfname), call. = FALSE)
}
}
}
}
.gintervals.save_file <- function(filename, intervs) {
if (nrow(intervs)) {
if (.gintervals.is1d(intervs)) {
intervs$chrom <- as.factor(intervs$chrom)
point.intervs <- intervs$start == intervs$end
intervs[point.intervs, ]$end <- intervs[point.intervs, ]$end + 1
} else {
intervs$chrom1 <- as.factor(intervs$chrom1)
intervs$chrom2 <- as.factor(intervs$chrom2)
point.intervs <- intervs$start1 == intervs$end1
intervs[point.intervs, ]$end1 <- intervs[point.intervs, ]$end1 + 1
point.intervs <- intervs$start2 == intervs$end2
intervs[point.intervs, ]$end2 <- intervs[point.intervs, ]$end2 + 1
}
}
f <- file(filename, "wb")
serialize(intervs, f)
close(f)
nrow(intervs)
}
.gintervals.is_bigset <- function(intervals.set, err_if_non_exist = TRUE) {
if (is.character(intervals.set) & length(intervals.set) == 1) {
if (intervals.set %in% get("GTRACKS", envir = .misha)) {
intervfname <- sprintf("%s.track", paste(get("GWD", envir = .misha), gsub("\\.", "/", intervals.set), sep = "/"))
} else {
intervfname <- sprintf("%s.interv", paste(get("GWD", envir = .misha), gsub("\\.", "/", intervals.set), sep = "/"))
}
if (file.exists(intervfname)) {
if (file.info(intervfname)$isdir) {
return(TRUE)
}
} else if (err_if_non_exist) {
stop(sprintf("Intervals set %s does not exist", intervals.set), call. = FALSE)
}
}
FALSE
}
.gintervals.needs_bigset <- function(intervals = NULL, size = NULL) {
if (!is.null(intervals)) {
chromsizes <- gintervals.chrom_sizes(intervals)
nrow(chromsizes) && sum(chromsizes$size) > min(.ggetOption("gmax.data.size", 10000000), .ggetOption("gbig.intervals.size", 1000000))
} else {
size > min(.ggetOption("gmax.data.size", 10000000), .ggetOption("gbig.intervals.size", 1000000))
}
}
.gintervals.loadable <- function(intervals = NULL, size = NULL, chrom = NULL, chrom1 = NULL, chrom2 = NULL) {
if (!is.null(intervals)) {
chromsizes <- gintervals.chrom_sizes(intervals)
if (nrow(chromsizes)) {
if (!is.null(chrom)) {
chromsizes <- chromsizes[chromsizes$chrom == chrom, ]
}
if (!is.null(chrom1)) {
chromsizes <- chromsizes[chromsizes$chrom1 == chrom1, ]
}
if (!is.null(chrom2)) {
chromsizes <- chromsizes[chromsizes$chrom2 == chrom2, ]
}
}
!nrow(chromsizes) || sum(chromsizes$size) <= .ggetOption("gmax.data.size", 10000000)
} else {
size <= .ggetOption("gmax.data.size", 10000000)
}
}
.gintervals.big.is1d <- function(intervals.set) {
"chrom" %in% colnames(.gintervals.big.meta(intervals.set)$stats)
}
.gintervals.big.is2d <- function(intervals.set) {
"chrom1" %in% colnames(.gintervals.big.meta(intervals.set)$stats)
}
.gintervals.big2small <- function(intervals.set) {
# We assume that writing the intervals might be a lengthy process.
# During this time the process might get interrupted leaving the intervals set in incomplete state.
# Even though it's not fully transaction-safe, we prefer to create a temporary file and then move it hoping it's fast enough.
path <- gsub(".", "/", intervals.set, fixed = TRUE)
path <- paste(get("GWD", envir = .misha), path, sep = "/")
path <- paste(path, ".interv", sep = "")
intervals <- .gintervals.load(intervals.set)
tmpfilename <- tempfile(".", dirname(path)) # tmpdir = the parent directory of intervals set, otherwise rename might not work
# (tmpdir might be at another file system)
file.rename(path, tmpfilename)
success <- FALSE
tryCatch(
{
.gintervals.save_file(path, intervals)
success <- TRUE
},
finally = {
if (!success) {
unlink(path, recursive = TRUE)
file.rename(tmpfilename, path)
}
unlink(tmpfilename, recursive = TRUE)
}
)
}
.gintervals.small2big <- function(intervals.set, intervals = NULL) {
# We assume that writing the intervals might be a lengthy process.
# During this time the process might get interrupted leaving the intervals set in incomplete state.
# Even though it's not fully transaction-safe, we prefer to create a temporary file and then move it hoping it's fast enough.
if (is.null(intervals)) {
intervals <- .gintervals.load(intervals.set)
}
path <- gsub(".", "/", intervals.set, fixed = TRUE)
path <- paste(get("GWD", envir = .misha), path, sep = "/")
path <- paste(path, ".interv", sep = "")
tmpfilename <- tempfile(".", dirname(path)) # tmpdir = the parent directory of intervals set, otherwise rename might not work
# (tmpdir might be at another file system)
file.rename(path, tmpfilename)
gintervs <- get("GINTERVS", envir = .misha)
assign("GINTERVS", gintervs[gintervs != intervals.set], envir = .misha)
success <- FALSE
tryCatch(
{
.gcall_noninteractive(gintervals.save, intervals.set, intervals)
success <- TRUE
},
finally = {
if (!success) {
unlink(path, recursive = TRUE)
file.rename(tmpfilename, path)
gintervs <- c(gintervs, intervals.set)
gintervs <- unique(gintervs)
sort(gintervs)
assign("GINTERVS", gintervs, envir = .misha)
}
unlink(tmpfilename, recursive = TRUE)
}
)
}
.gintervals.big.meta <- function(intervals.set) {
metafname <- ""
if (intervals.set %in% get("GTRACKS", envir = .misha)) {
metafname <- sprintf("%s.track/.meta", paste(get("GWD", envir = .misha), gsub("\\.", "/", intervals.set), sep = "/"))
if (!file.exists(metafname)) {
.gcall("gtrack_create_meta", intervals.set, .misha_env())
}
} else {
metafname <- sprintf("%s.interv/.meta", paste(get("GWD", envir = .misha), gsub("\\.", "/", intervals.set), sep = "/"))
}
f <- file(metafname, "rb")
res <- unserialize(f)
close(f)
res
}
.gintervals.big.save_meta <- function(path, stats, zeroline) {
f <- file(sprintf("%s/.meta", path), "wb")
serialize(list(stats = stats, zeroline = zeroline), f)
close(f)
}
.gintervals.big.save <- function(path, intervs, chrom = NULL, chrom1 = NULL, chrom2 = NULL) {
if (!is.null(chrom)) {
filename <- sprintf("%s/%s", path, chrom)
} else {
filename <- sprintf("%s/%s-%s", path, chrom1, chrom2)
}
if (is.null(intervs) || nrow(intervs) == 0) {
unlink(filename, recursive = TRUE)
} else {
if (!is.null(chrom)) {
intervs <- intervs[intervs$chrom == chrom, ]
} else {
intervs <- intervs[intervs$chrom1 == chrom1 & intervs$chrom2 == chrom2, ]
}
.gintervals.save_file(filename, intervs)
}
}
.gintervals.is1d <- function(intervals) {
if (is.character(intervals)) {
if (.gintervals.is_bigset(intervals)) {
return(.gintervals.big.is1d(intervals))
}
intervals <- .gintervals.load(intervals)
}
all(colnames(intervals)[1:3] == c("chrom", "start", "end"))
}
.gintervals.is2d <- function(intervals) {
if (is.character(intervals)) {
if (.gintervals.is_bigset(intervals)) {
return(.gintervals.big.is2d(intervals))
}
intervals <- .gintervals.load(intervals)
}
all(colnames(intervals)[1:6] == c("chrom1", "start1", "end1", "chrom2", "start2", "end2"))
}
#' Creates a set of 1D intervals
#'
#' Creates a set of 1D intervals.
#'
#' This function returns a set of one-dimensional intervals. The returned value
#' can be used in all functions that accept 'intervals' argument.
#'
#' One-dimensional intervals is a data frame whose first three columns are
#' 'chrom', 'start' and 'end'. Each row of the data frame represents a genomic
#' interval of the specified chromosome in the range of [start, end).
#' Additional columns can be presented in 1D intervals object yet these columns
#' must be added after the three obligatory ones.
#'
#' If 'strands' argument is not 'NULL' an additional column "strand" is added
#' to the intervals. The possible values of a strand can be '1' (plus strand),
#' '-1' (minus strand) or '0' (unknown).
#'
#' @param chroms chromosomes - an array of strings with or without "chr"
#' prefixes or an array of integers (like: '1' for "chr1")
#' @param starts an array of start coordinates
#' @param ends an array of end coordinates. If '-1' chromosome size is assumed.
#' @param strands 'NULL' or an array consisting of '-1', '0' or '1' values
#' @return A data frame representing the intervals.
#' @seealso \code{\link{gintervals.2d}}, \code{\link{gintervals.force_range}}
#' @keywords ~intervals
#' @examples
#' \dontshow{
#' options(gmax.processes = 2)
#' }
#'
#' gdb.init_examples()
#'
#' ## the following 3 calls produce identical results
#' gintervals(1)
#' gintervals("1")
#' gintervals("chrX")
#'
#' gintervals(1, 1000)
#' gintervals(c("chr2", "chrX"), 10, c(3000, 5000))
#'
#' @export gintervals
gintervals <- function(chroms = NULL, starts = 0, ends = -1, strands = NULL) {
if (is.null(chroms)) {
stop("Usage: gintervals(chroms, starts = 0, ends = -1, strands = NULL)", call. = FALSE)
}
.gcheckroot()
intervals <- .gintervals(chroms, starts, ends, strands)
.gcall("gintervsort", intervals, .misha_env())
}
#' Creates a set of 2D intervals
#'
#' Creates a set of 2D intervals.
#'
#' This function returns a set of two-dimensional intervals. The returned value
#' can be used in all functions that accept 'intervals' argument.
#'
#' Two-dimensional intervals is a data frame whose first six columns are
#' 'chrom1', 'start1', 'end1', 'chrom2', 'start2' and 'end2'. Each row of the
#' data frame represents two genomic intervals from two chromosomes in the
#' range of [start, end). Additional columns can be presented in 2D intervals
#' object yet these columns must be added after the six obligatory ones.
#'
#' @param chroms1 chromosomes1 - an array of strings with or without "chr"
#' prefixes or an array of integers (like: '1' for "chr1")
#' @param starts1 an array of start1 coordinates
#' @param ends1 an array of end1 coordinates. If '-1' chromosome size is
#' assumed.
#' @param chroms2 chromosomes2 - an array of strings with or without "chr"
#' prefixes or an array of integers (like: '1' for "chr1"). If 'NULL',
#' 'chroms2' is assumed to be equal to 'chroms1'.
#' @param starts2 an array of start2 coordinates
#' @param ends2 an array of end2 coordinates. If '-1' chromosome size is
#' assumed.
#' @return A data frame representing the intervals.
#' @seealso \code{\link{gintervals}}, \code{\link{gintervals.force_range}}
#' @keywords ~intervals
#' @examples
#' \dontshow{
#' options(gmax.processes = 2)
#' }
#'
#' gdb.init_examples()
#'
#' ## the following 3 calls produce identical results
#' gintervals.2d(1)
#' gintervals.2d("1")
#' gintervals.2d("chrX")
#'
#' gintervals.2d(1, 1000, 2000, "chrX", 400, 800)
#' gintervals.2d(c("chr2", "chrX"), 10, c(3000, 5000), 1)
#'
#' @export gintervals.2d
gintervals.2d <- function(chroms1 = NULL, starts1 = 0, ends1 = -1, chroms2 = NULL, starts2 = 0, ends2 = -1) {
if (is.null(chroms1)) {
stop("Usage: gintervals.2d(chroms1, starts1 = 0, ends1 = -1, chroms2 = NULL, starts2 = 0, ends2 = -1)", call. = FALSE)
}
.gcheckroot()
if (is.null(chroms2)) {
chroms2 <- chroms1
}
intervals1 <- .gintervals(chroms1, starts1, ends1, NULL)
intervals2 <- .gintervals(chroms2, starts2, ends2, NULL)
intervals <- data.frame(
chrom1 = intervals1$chrom, start1 = intervals1$start, end1 = intervals1$end,
chrom2 = intervals2$chrom, start2 = intervals2$start, end2 = intervals2$end
)
.gcall("gintervsort", intervals, .misha_env())
}
#' Returns 2D intervals that cover the whole genome
#'
#' Returns 2D intervals that cover the whole genome.
#'
#' This function returns a set of two-dimensional intervals that cover the
#' whole genome as it is defined by 'chrom_sizes.txt' file.
#'
#' @return A data frame representing the intervals.
#' @seealso \code{\link{gintervals.2d}}
#' @keywords ~genome ~chromosome ~chromosomes ~ALLGENOME
#' @export gintervals.2d.all
gintervals.2d.all <- function() {
.gcheckroot()
get("ALLGENOME", envir = .misha)[[2]]
}
#' Returns 1D intervals that cover the whole genome
#'
#' Returns 1D intervals that cover the whole genome.
#'
#' This function returns a set of one-dimensional intervals that cover the
#' whole genome as it is defined by 'chrom_sizes.txt' file.
#'
#' @return A data frame representing the intervals.
#' @seealso \code{\link{gintervals}}
#' @keywords ~genome ~chromosome ~chromosomes ~ALLGENOME
#' @export gintervals.all
gintervals.all <- function() {
.gcheckroot()
get("ALLGENOME", envir = .misha)[[1]]
}
#' Intersects two-dimensional intervals with a band
#'
#' Intersects two-dimensional intervals with a band.
#'
#' This function intersects each two-dimensional interval from 'intervals' with
#' 'band'. If the intersection is not empty, the interval is shrunk to the
#' minimal rectangle that contains the band and added to the return value.
#'
#' If 'intervals.set.out' is not 'NULL' the result is saved as an intervals
#' set. Use this parameter if the result size exceeds the limits of the
#' physical memory.
#'
#' @param intervals two-dimensional intervals
#' @param band track expression band. If 'NULL' no band is used.
#' @param intervals.set.out intervals set name where the function result is
#' optionally outputted
#' @return If 'intervals.set.out' is 'NULL' a data frame representing the
#' intervals.
#' @seealso \code{\link{gintervals.2d}}, \code{\link{gintervals.intersect}}
#' @keywords ~band ~intersect
#' @examples
#' \dontshow{
#' options(gmax.processes = 2)
#' }
#'
#' gdb.init_examples()
#' gintervals.2d.band_intersect(gintervals.2d(1), c(10000, 20000))
#'
#' @export gintervals.2d.band_intersect
gintervals.2d.band_intersect <- function(intervals = NULL, band = NULL, intervals.set.out = NULL) {
if (is.null(intervals)) {
stop("Usage: gintervals.2d.band_intersect(intervals, band = NULL, intervals.set.out = NULL)", call. = FALSE)
}
intervals <- rescue_ALLGENOME(intervals, as.character(substitute(intervals)))
intervals.set.out <- do.call(.gexpr2str, list(substitute(intervals.set.out)), envir = parent.frame())
if (!is.null(intervals.set.out)) {
fullpath <- .gintervals.check_new_set(intervals.set.out)
}
# intervals can be NULL if gextract is piped with gscreen and the latter returns NULL
success <- FALSE
res <- NULL
tryCatch(
{
if (!is.null(intervals)) {
res <- .gcall("ginterv_intersectband", intervals, band, intervals.set.out, .misha_env())
if (!is.null(intervals.set.out) && .gintervals.is_bigset(intervals.set.out, FALSE) && !.gintervals.needs_bigset(intervals.set.out)) {
.gintervals.big2small(intervals.set.out)
}
}
success <- TRUE
},
finally = {
if (!success && !is.null(intervals.set.out)) {
unlink(fullpath, recursive = TRUE)
}
}
)
# refresh the list of GINTERVS, etc.
if (!is.null(intervals.set.out)) {
.gdb.add_intervals.set(intervals.set.out)
retv <- 0 # suppress return value
} else {
res
}
}
#' Converts intervals to canonic form
#'
#' Converts intervals to canonic form.
#'
#' This function converts 'intervals' into a "canonic" form: properly sorted
#' with no overlaps. The result can be used later in the functions that require
#' the intervals to be in canonic form. Use 'unify_touching_intervals' to
#' control whether the intervals that touch each other (i.e. the end coordinate
#' of one equals to the start coordinate of the other) are unified.
#' 'unify_touching_intervals' is ignored if two-dimensional intervals are used.
#'
#' Since 'gintervals.canonic' unifies overlapping or touching intervals, the
#' number of the returned intervals might be less than the number of the
#' original intervals. To allow the user to find the origin of the new interval
#' 'mapping' attribute is attached to the result. It maps between the original
#' intervals and the resulted intervals. Use 'attr(retv_of_gintervals.canonic,
#' "mapping")' to retrieve the map.
#'
#' @param intervals intervals to be converted
#' @param unify_touching_intervals if 'TRUE', touching one-dimensional
#' intervals are unified
#' @return A data frame representing the canonic intervals and an attribute
#' 'mapping' that maps the original intervals to the resulted ones.
#' @seealso \code{\link{gintervals}}, \code{\link{gintervals.2d}}
#' @keywords ~intervals ~canonic
#' @examples
#' \dontshow{
#' options(gmax.processes = 2)
#' }
#'
#' gdb.init_examples()
#'
#' ## Create intervals manually by using 'data.frame'.
#' ## Note that we add an additional column 'data'.
#' ## Return value:
#' ## chrom start end data
#' ## 1 chr1 11000 12000 10
#' ## 2 chr1 100 200 20
#' ## 3 chr1 10000 13000 30
#' ## 4 chr1 10500 10600 40
#' intervs <- data.frame(
#' chrom = "chr1",
#' start = c(11000, 100, 10000, 10500),
#' end = c(12000, 200, 13000, 10600),
#' data = c(10, 20, 30, 40)
#' )
#'
#' ## Convert the intervals into the canonic form.
#' ## The function discards any columns besides chrom, start and end.
#' ## Return value:
#' ## chrom start end
#' ## 1 chr1 100 200
#' ## 2 chr1 10000 13000
#' res <- gintervals.canonic(intervs)
#'
#' ## By inspecting mapping attribute we can see how the new
#' ## intervals were created: "2 1 2 2" means that the first
#' ## interval in the result was created from the second interval in
#' ## the original set (we look for the indices in mapping where "1"
#' ## appears). Likewise the second interval in the result was
#' ## created from 3 intervals in the original set. Their indices are
#' ## 1, 3 and 4 (once again we look for the indices in mapping where
#' ## "2" appears).
#' ## Return value:
#' ## 2 1 2 2
#' attr(res, "mapping")
#'
#' ## Finally (and that is the most useful part of 'mapping'
#' ## attribute): we add a new column 'data' to our result which is
#' ## the mean value of the original data column. The trick is done
#' ## using 'tapply' on par with 'mapping' attribute. For example,
#' ## 20.00000 equals is a result of 'mean(intervs[2,]$data' while
#' ## 26.66667 is a result of 'mean(intervs[c(1,3,4),]$data)'.
#' ## 'res' after the following call:
#' ## chrom start end data
#' ## 1 chr1 100 200 20.00000
#' ## 2 chr1 10000 13000 26.66667
#' res$data <- tapply(intervs$data, attr(res, "mapping"), mean)
#'
#' @export gintervals.canonic
gintervals.canonic <- function(intervals = NULL, unify_touching_intervals = TRUE) {
if (is.null(intervals)) {
stop("Usage: gintervals.canonic(intervals, unify_touching_intervals = TRUE)", call. = FALSE)
}
intervals <- rescue_ALLGENOME(intervals, as.character(substitute(intervals)))
res <- .gcall("gintervcanonic", intervals, unify_touching_intervals, .misha_env())
res
}
#' Calculates difference of two intervals sets
#'
#' Returns difference of two sets of intervals.
#'
#' This function returns a genomic space that is covered by 'intervals1' but
#' not covered by 'intervals2'.
#'
#' If 'intervals.set.out' is not 'NULL' the result is saved as an intervals
#' set. Use this parameter if the result size exceeds the limits of the
#' physical memory.
#'
#' @param intervals1,intervals2 set of one-dimensional intervals
#' @param intervals.set.out intervals set name where the function result is
#' optionally outputted
#' @return If 'intervals.set.out' is 'NULL' a data frame representing the
#' intervals.
#' @seealso \code{\link{gintervals}}, \code{\link{gintervals.intersect}},
#' \code{\link{gintervals.union}}
#' @keywords ~diff
#' @examples
#' \dontshow{
#' options(gmax.processes = 2)