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safety_func.R
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safety_func.R
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ra.merge = function (..., pad = 0, ind = FALSE, ignore.strand = FALSE) {
ra = list(...)
ra = ra[which(!sapply(ra, is.null))]
nm = names(ra)
if (is.null(nm)) {
nm = paste("ra", 1:length(ra), sep = "")
}
nm = paste("seen.by", nm, sep = ".")
if (length(nm) == 0) {
return(NULL)
}
out = ra[[1]]
values(out) = cbind(as.data.frame(matrix(FALSE, nrow = length(out),
ncol = length(nm), dimnames = list(NULL, nm))), values(out))
if (!ind) {
values(out)[, nm[1]] = TRUE
}
else {
values(out)[, nm[1]] = 1:length(out)
}
if (length(ra) > 1) {
for (i in 2:length(ra)) {
this.ra = ra[[i]]
if (length(this.ra) > 0) {
values(this.ra) = cbind(as.data.frame(matrix(FALSE,
nrow = length(this.ra), ncol = length(nm),
dimnames = list(NULL, nm))), values(this.ra))
ovix = ra.overlaps(out, this.ra, pad = pad, ignore.strand = ignore.strand)
if (!ind) {
values(this.ra)[[nm[i]]] = TRUE
}
else {
values(this.ra)[[nm[i]]] = 1:length(this.ra)
}
if (!ind) {
if (!all(is.na(ovix))) {
values(out)[, nm[i]][ovix[, 1]] = TRUE
}
}
else {
values(out)[, nm[i]] = NA
if (!all(is.na(ovix))) {
values(out)[, nm[i]][ovix[, 1]] = ovix[,
1]
}
}
if (!all(is.na(ovix))) {
nix = setdiff(1:length(this.ra), ovix[, 2])
}
else {
nix = 1:length(this.ra)
}
if (length(nix) > 0) {
val1 = values(out)
val2 = values(this.ra)
if (ind) {
val2[, nm[1:(i - 1)]] = NA
}
else {
val2[, nm[1:(i - 1)]] = FALSE
}
values(out) = NULL
values(this.ra) = NULL
out = grl.bind(out, this.ra[nix])
values(out) = rrbind(val1, val2[nix, ])
} else if (length(setxor(1:length(this.ra), ovix[, 2])) == 0) { ## fix if there is perfect overlap... this case was previously not dealt with
merge_cols = setdiff(colnames(values(this.ra)), nm)
merge_cols = setdiff(merge_cols, colnames(mcols(out)))
if (length(merge_cols) > 0) {
tmp_field = "out_ix_50169346127375946273"
val1 = values(out)
val2 = values(this.ra)
val1[[tmp_field]] = seq_along(out)
val2[ovix[,2],tmp_field] = ovix[,1]
new_val = merge(val1, val2[,c(tmp_field, merge_cols)], by = tmp_field, all.x = TRUE)
new_val = new_val[order(new_val[[tmp_field]]),]
new_val[[tmp_field]] = NULL
values(out) = new_val
}
}
}
}
}
return(out)
}
ra_breaks = function (rafile, keep.features = T, seqlengths = hg_seqlengths(),
chr.convert = T, geno = NULL, flipstrand = FALSE, swap.header = NULL,
breakpointer = FALSE, seqlevels = NULL, force.bnd = FALSE,
skip = NA, get.loose = FALSE, dedup = TRUE, pad = 500)
{
if (is.character(rafile)) {
if (grepl(".rds$", rafile)) {
ra = readRDS(rafile)
return(junctions(ra))
}
else if (grepl("(.bedpe$)", rafile)) {
ra.path = rafile
cols = c("chr1", "start1", "end1", "chr2", "start2",
"end2", "name", "score", "str1", "str2")
ln = readLines(ra.path)
if (is.na(skip)) {
nh = min(c(Inf, which(!grepl("^((#)|(chrom))",
ln)))) - 1
if (is.infinite(nh)) {
nh = 1
}
}
else {
nh = skip
}
if ((length(ln) - nh) == 0) {
return(GRangesList(GRanges(seqlengths = seqlengths))[c()])
}
if (nh == 0) {
rafile = fread(rafile, header = FALSE)
}
else {
rafile = tryCatch(fread(ra.path, header = FALSE,
skip = nh), error = function(e) NULL)
if (is.null(rafile)) {
rafile = tryCatch(fread(ra.path, header = FALSE,
skip = nh, sep = "\\t"), error = function(e) NULL)
}
if (is.null(rafile)) {
rafile = tryCatch(fread(ra.path, header = FALSE,
skip = nh, sep = ","), error = function(e) NULL)
}
if (is.null(rafile)) {
stop("Error reading bedpe")
}
}
setnames(rafile, 1:length(cols), cols)
rafile[, `:=`(str1, ifelse(str1 %in% c("+", "-"),
str1, "*"))]
rafile[, `:=`(str2, ifelse(str2 %in% c("+", "-"),
str2, "*"))]
}
else if (grepl("(vcf$)|(vcf.gz$)", rafile)) {
require(VariantAnnotation)
vcf = readVcf(rafile, Seqinfo(seqnames = names(seqlengths),
seqlengths = seqlengths))
vgr = read_vcf(rafile, swap.header = swap.header,
geno = geno)
## browser()
mc = data.table(as.data.frame(mcols(vgr)))
if (!("SVTYPE" %in% colnames(mc))) {
warning("Vcf not in proper format. Is this a rearrangement vcf?")
return(GRangesList())
}
if (any(w.0 <- (width(vgr) < 1))) {
warning("Some breakpoint width==0.")
vgr[which(w.0)] = gr.start(vgr[which(w.0)]) %-%
1
}
if (any(duplicated(names(vgr))))
names(vgr) = NULL
if (length(vgr) == 0)
return(GRangesList())
.vcf2bnd = function(vgr) {
if (!"END" %in% colnames(values(vgr)))
stop("Non BND SV should have the second breakpoint coor in END columns!")
if (!"CHR2" %in% colnames(values(vgr)) | any(is.na(vgr$CHR2)))
vgr$CHR2 = as.character(seqnames(vgr))
bp2 = data.table(as.data.frame(mcols(vgr)))
bp2[, `:=`(seqnames = CHR2, start = as.numeric(END),
end = as.numeric(END))]
bp2.gr = dt2gr(bp2)
mcols(bp2.gr) = mcols(vgr)
if (!is.null(names(vgr)) & !anyDuplicated(names(vgr))) {
jid = names(vgr)
}
else {
jid = seq_along(vgr)
}
names(vgr) = paste(paste0("exp", jid), "1", sep = ":")
names(bp2.gr) = paste(paste0("exp", jid), "2",
sep = ":")
vgr = resize(c(vgr, bp2.gr), 1)
if (all(grepl("[_:][12]$", names(vgr)))) {
nm <- vgr$MATEID <- names(vgr)
ix <- grepl("1$", nm)
vgr$MATEID[ix] = gsub("(.*?)(1)$", "\\12",
nm[ix])
vgr$MATEID[!ix] = gsub("(.*?)(2)$", "\\11",
nm[!ix])
vgr$SVTYPE = "BND"
}
return(vgr)
}
if (!"MATEID" %in% colnames(mcols(vgr))) {
if (length(fake.bix <- which(values(vgr)$SVTYPE ==
"BND")) != 0) {
values(vgr[fake.bix])$SVTYPE = "TRA"
}
if (all(names(vgr) == "N" | is.null(names(vgr)) |
all(grepl("^DEL|DUP|INV|BND", names(vgr))))) {
vgr = .vcf2bnd(vgr)
}
}
else if (any(is.na(mid <- as.character(vgr$MATEID)))) {
if (is.null(vgr$CHR2)) {
vgr$CHR2 = as.character(NA)
}
names(vgr) = gsub("_", ":", names(vgr))
vgr$MATEID = sapply(vgr$MATEID, function(x) gsub("_",
":", x))
values(vgr) = data.table(as.data.frame(values(vgr)))
if ("STRANDS" %in% colnames(mc) & any(ns <- sapply(vgr$STRANDS,
length) > 1)) {
if (any(fuix <- sapply(vgr[which(!ns)]$STRANDS,
str_count, ":") > 1)) {
tofix <- which(!ns)[fuix]
vgr$STRANDS[tofix] = lapply(vgr$STRANDS[tofix],
function(x) {
strsplit(gsub("(\\d)([\\+\\-])", "\\1,\\2",
x), ",")[[1]]
})
ns[tofix] = TRUE
}
vgr.double = vgr[which(ns)]
j1 = j2 = vgr.double
st1 = lapply(vgr.double$STRANDS, function(x) x[1])
st2 = lapply(vgr.double$STRANDS, function(x) x[2])
j1$STRANDS = st1
j2$STRANDS = st2
vgr.double = c(j1, j2)
names(vgr.double) = dedup(names(vgr.double))
vgr = c(vgr[which(!ns)], vgr.double)
}
mid <- as.logical(sapply(vgr$MATEID, length))
vgr.bnd = vgr[which(mid)]
vgr.nonbnd = vgr[which(!mid)]
vgr.nonbnd = .vcf2bnd(vgr.nonbnd)
mc.bnd = data.table(as.data.frame(values(vgr.bnd)))
mc.nonbnd = data.table(as.data.frame(values(vgr.nonbnd)))
mc.bnd$MATEID = as.character(mc.bnd$MATEID)
vgr = c(vgr.bnd[, c()], vgr.nonbnd[, c()])
values(vgr) = rbind(mc.bnd, mc.nonbnd)
}
if (!any(c("MATEID", "SVTYPE") %in% colnames(mcols(vgr))))
stop("MATEID or SVTYPE not included. Required")
vgr$mateid = vgr$MATEID
vgr$svtype = vgr$SVTYPE
if (!is.null(info(vcf)$SCTG))
vgr$SCTG = info(vcf)$SCTG
if (force.bnd)
vgr$svtype = "BND"
if (sum(vgr$svtype == "BND") == 0)
warning("Vcf not in proper format. Will treat rearrangements as if in BND format")
if (!all(vgr$svtype == "BND")) {
warning(sprintf("%s rows of vcf do not have svtype BND, treat them as non-BND!",
sum(vgr$svtype != "BND")))
}
bix = which(vgr$svtype == "BND")
vgr = vgr[bix]
alt <- sapply(vgr$ALT, function(x) x[1])
## browser()
if ("CT" %in% colnames(mcols(vgr))) {
message("CT INFO field found.")
if ("SVLEN" %in% colnames(values(vgr))) {
del.ix = which(vgr$SVTYPE == "DEL")
dup.ix = which(vgr$SVTYPE == "DUP")
vgr$CT[del.ix] = "3to5"
vgr$CT[dup.ix] = "5to3"
}
ori = strsplit(vgr$CT, "to")
iid = sapply(strsplit(names(vgr), ":"), function(x) as.numeric(x[2]))
orimap = setNames(c("+", "-"), c("5", "3"))
strd = orimap[sapply(seq_along(ori), function(i) ori[[i]][iid[i]])]
strand(vgr) = strd
vgr.pair1 = vgr[which(iid == 1)]
vgr.pair2 = vgr[which(iid == 2)]
}
else if ("STRANDS" %in% colnames(mcols(vgr))) {
message("STRANDS INFO field found.")
## browser()
iid = sapply(strsplit(names(vgr), ":"), function(x) as.numeric(x[2]))
vgr$iid = iid
vgr = vgr[order(names(vgr))]
iid = vgr$iid
ori = strsplit(substr(unlist(vgr$STRANDS), 1,
2), character(0))
orimap = setNames(c("+", "-"), c("-", "+"))
strd = orimap[sapply(seq_along(ori), function(i) ori[[i]][iid[i]])]
strand(vgr) = setNames(strd, NULL)
vgr.pair1 = vgr[which(iid == 1)]
vgr.pair2 = vgr[which(iid == 2)]
}
else if (any(grepl("\\[", alt))) {
message("ALT field format like BND")
vgr$first = !grepl("^(\\]|\\[)", alt)
vgr$right = grepl("\\[", alt)
vgr$coord = as.character(paste(seqnames(vgr),
":", start(vgr), sep = ""))
vgr$mcoord = as.character(gsub(".*(\\[|\\])(.*\\:.*)(\\[|\\]).*",
"\\2", alt))
vgr$mcoord = gsub("chr", "", vgr$mcoord)
geno(vcf)
values(vgr)
if (all(is.na(vgr$mateid)))
if (!is.null(names(vgr)) & !any(duplicated(names(vgr)))) {
warning("MATEID tag missing, guessing BND partner by parsing names of vgr")
vgr$mateid = paste(gsub("::\\d$", "", names(vgr)),
(sapply(strsplit(names(vgr), "\\:\\:"),
function(x) as.numeric(x[length(x)])))%%2 +
1, sep = "::")
}
else if (!is.null(vgr$SCTG)) {
warning("MATEID tag missing, guessing BND partner from coordinates and SCTG")
require(igraph)
ucoord = unique(c(vgr$coord, vgr$mcoord))
vgr$mateid = paste(vgr$SCTG, vgr$mcoord,
sep = "_")
if (any(duplicated(vgr$mateid))) {
warning("DOUBLE WARNING! inferred mateids not unique, check VCF")
bix = bix[!duplicated(vgr$mateid)]
vgr = vgr[!duplicated(vgr$mateid)]
}
}
else {
stop("Error: MATEID tag missing")
}
vgr$mix = as.numeric(match(vgr$mateid, names(vgr)))
pix = which(!is.na(vgr$mix))
vgr.pair = vgr[pix]
if (length(vgr.pair) == 0) {
stop("Error: No mates found despite nonzero number of BND rows in VCF")
}
vgr.pair$mix = match(vgr.pair$mix, pix)
vix = which(1:length(vgr.pair) < vgr.pair$mix)
vgr.pair1 = vgr.pair[vix]
vgr.pair2 = vgr.pair[vgr.pair1$mix]
tmpix = vgr.pair1$first & vgr.pair1$right
if (any(tmpix)) {
strand(vgr.pair1)[tmpix] = "-"
strand(vgr.pair2)[tmpix] = "+"
}
tmpix = vgr.pair1$first & !vgr.pair1$right
if (any(tmpix)) {
strand(vgr.pair1)[tmpix] = "-"
strand(vgr.pair2)[tmpix] = "-"
}
tmpix = !vgr.pair1$first & !vgr.pair1$right
if (any(tmpix)) {
strand(vgr.pair1)[tmpix] = "+"
strand(vgr.pair2)[tmpix] = "-"
}
tmpix = !vgr.pair1$first & vgr.pair1$right
if (any(tmpix)) {
strand(vgr.pair1)[tmpix] = "+"
strand(vgr.pair2)[tmpix] = "+"
}
pos1 = as.logical(strand(vgr.pair1) == "+")
if (any(pos1)) {
start(vgr.pair1)[pos1] = start(vgr.pair1)[pos1] -
1
end(vgr.pair1)[pos1] = end(vgr.pair1)[pos1] -
1
}
pos2 = as.logical(strand(vgr.pair2) == "+")
if (any(pos2)) {
start(vgr.pair2)[pos2] = start(vgr.pair2)[pos2] -
1
end(vgr.pair2)[pos2] = end(vgr.pair2)[pos2] -
1
}
}
ra = grl.pivot(GRangesList(vgr.pair1[, c()], vgr.pair2[,
c()]))
if (exists("pix") & exists("vix"))
this.inf = values(vgr)[pix[vix], ]
if (exists("iid"))
this.inf = values(vgr[which(iid == 1)])
if (is.null(this.inf$POS)) {
this.inf = cbind(data.frame(POS = ""), this.inf)
}
if (is.null(this.inf$CHROM)) {
this.inf = cbind(data.frame(CHROM = ""), this.inf)
}
if (is.null(this.inf$MATL)) {
this.inf = cbind(data.frame(MALT = ""), this.inf)
}
this.inf$CHROM = seqnames(vgr.pair1)
this.inf$POS = start(vgr.pair1)
this.inf$MATECHROM = seqnames(vgr.pair2)
this.inf$MATEPOS = start(vgr.pair2)
this.inf$MALT = vgr.pair2$AL
values(ra) = this.inf
if (is.null(values(ra)$TIER)) {
values(ra)$tier = ifelse(values(ra)$FILTER %in%
c(".", "PASS"), 2, 3)
}
else {
values(ra)$tier = values(ra)$TIER
}
if (dedup) {
ra = ra.dedup(ra, pad = pad)
}
if (!get.loose | is.null(vgr$mix)) {
return(ra)
}
else {
npix = is.na(vgr$mix)
vgr.loose = vgr[npix, c()]
tmp = tryCatch(values(vgr)[bix[npix], ], error = function(e) NULL)
if (!is.null(tmp)) {
values(vgr.loose) = tmp
}
else {
values(vgr.loose) = cbind(vcf@fixed[bix[npix],
], info(vcf)[bix[npix], ])
}
return(list(junctions = ra, loose.ends = vgr.loose))
}
}
else {
rafile = read.delim(rafile)
}
}
if (is.data.table(rafile)) {
require(data.table)
rafile = as.data.frame(rafile)
}
if (nrow(rafile) == 0) {
out = GRangesList()
values(out) = rafile
return(out)
}
if (flipstrand) {
rafile$str1 = ifelse(rafile$strand1 == "+", "-", "+")
rafile$str2 = ifelse(rafile$strand2 == "+", "-", "+")
}
if (!is.null(seqlevels)) {
rafile$chr1 = seqlevels[rafile$chr1]
rafile$chr2 = seqlevels[rafile$chr2]
}
if (is.null(rafile$str1)) {
rafile$str1 = rafile$strand1
}
if (is.null(rafile$str2)) {
rafile$str2 = rafile$strand2
}
if (!is.null(rafile$pos1) & !is.null(rafile$pos2)) {
if (breakpointer) {
rafile$pos1 = rafile$T_BPpos1
rafile$pos2 = rafile$T_BPpos2
}
if (!is.numeric(rafile$pos1)) {
rafile$pos1 = as.numeric(rafile$pos1)
}
if (!is.numeric(rafile$pos2)) {
rafile$pos2 = as.numeric(rafile$pos2)
}
rafile$str1 <- gsub("[()]", "", rafile$str1)
rafile$str2 <- gsub("[()]", "", rafile$str2)
if (is.character(rafile$str1) | is.factor(rafile$str1)) {
rafile$str1 = gsub("0", "-", gsub("1", "+", gsub("\\-",
"1", gsub("\\+", "0", rafile$str1))))
}
if (is.character(rafile$str2) | is.factor(rafile$str2)) {
rafile$str2 = gsub("0", "-", gsub("1", "+", gsub("\\-",
"1", gsub("\\+", "0", rafile$str2))))
}
if (is.numeric(rafile$str1)) {
rafile$str1 = ifelse(rafile$str1 > 0, "+", "-")
}
if (is.numeric(rafile$str2)) {
rafile$str2 = ifelse(rafile$str2 > 0, "+", "-")
}
rafile$rowid = 1:nrow(rafile)
bad.ix = is.na(rafile$chr1) | is.na(rafile$chr2) | is.na(rafile$pos1) |
is.na(rafile$pos2) | is.na(rafile$str1) | is.na(rafile$str2) |
rafile$str1 == "*" | rafile$str2 == "*" | rafile$pos1 <
0 | rafile$pos2 < 0
rafile = rafile[which(!bad.ix), ]
if (nrow(rafile) == 0) {
return(GRanges())
}
seg = rbind(data.frame(chr = rafile$chr1, pos1 = rafile$pos1,
pos2 = rafile$pos1, strand = rafile$str1, ra.index = rafile$rowid,
ra.which = 1, stringsAsFactors = F), data.frame(chr = rafile$chr2,
pos1 = rafile$pos2, pos2 = rafile$pos2, strand = rafile$str2,
ra.index = rafile$rowid, ra.which = 2, stringsAsFactors = F))
if (chr.convert) {
seg$chr = gsub("chr", "", gsub("25", "M", gsub("24",
"Y", gsub("23", "X", seg$chr))))
}
out = seg2gr(seg, seqlengths = seqlengths)[, c("ra.index",
"ra.which")]
out = split(out, out$ra.index)
}
else if (!is.null(rafile$start1) & !is.null(rafile$start2) &
!is.null(rafile$end1) & !is.null(rafile$end2)) {
ra1 = gr.flipstrand(GRanges(rafile$chr1, IRanges(rafile$start1,
rafile$end1), strand = rafile$str1))
ra2 = gr.flipstrand(GRanges(rafile$chr2, IRanges(rafile$start2,
rafile$end2), strand = rafile$str2))
out = grl.pivot(GRangesList(ra1, ra2))
}
if (keep.features) {
values(out) = rafile[, ]
}
## if (!is.null(pad)) {
## out = ra.dedup(out, pad = pad)
## }
if (!get.loose) {
return(out)
}
else {
return(list(junctions = out, loose.ends = GRanges()))
}
return(new("junctions", out))
}