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Chages to parse.grl #33

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10 changes: 7 additions & 3 deletions R/gUtils.R
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Original file line number Diff line number Diff line change
Expand Up @@ -4128,18 +4128,22 @@ parse.gr = function(...)
#'
#' @param x character vector representing a GRangesList with UCSC style coordinates (chr:start-end[+-]) representing a [signed] Granges and ";" separators within each item of x separating individaul each GRAnges
#' @param seqlengths named integer vector representing genome (default = hg_seqlengths())
#' @param separator/s charachters used to separate between distinct ranges in each gr (default = c(';')). A single character could be provided or a vector that includes various optional separators
#' @author Marcin Imielinski
#' @return GRangesList parsed from IGV-/UCSC-style strings
#' @export
parse.grl = function(x, seqlengths = hg_seqlengths(), meta = NULL)
parse.grl = function(x, seqlengths = hg_seqlengths(), meta = NULL, separators = c(';'))
{
nm = names(x)
tmp = strsplit(x, '\\s*[;\\,\\|]\\s*')
split_chr = paste0('\\s*[\\', paste(separators, collapse = '\\'), ']\\s*')
tmp = strsplit(x,split_chr)
tmp.u = unlist(tmp)
tmp.u = gsub('\\,', '', tmp.u)
tmp.id = rep(1:length(tmp), sapply(tmp, length))
str = gsub('.*([\\+\\-])$','\\1', tmp.u)
spl = strsplit(tmp.u, "[\\-\\+\\:]", perl = T)
tmp.l = strsplit(tmp.u, ':', perl = T) # treat seqnames and ranges separately in order to work well with seqnames that contain "-"
l1 = lapply(tmp.l, function(s){strsplit(s[2], "[\\-\\+]", perl = T)[[1]]}) # split according to "-" and also get rid of the trailing "-" and "+"
spl = lapply(seq_along(tmp.l), function(ix){c(tmp.l[[ix]][1], l1[[ix]])})

if (any(ix <- sapply(spl, length)==2)){
spl[ix] = lapply(which(ix), function(x) spl[[x]][c(1:2,2)])
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6 changes: 6 additions & 0 deletions tests/testthat/test_rangeops.R
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Expand Up @@ -1429,6 +1429,12 @@ test_that("parse.grl", {
expect_equal(width(grl_example[[2]][1]), 3000001)
expect_equal(width(grl_example[[2]][2]), 79)

grl_example_alt_sep = parse.grl(c('chr1:1e6-5e6+,5:10-2000', 'chr2:2e6-5e6-|chr10:100231321-100231399'),
separators = c('|', ','))
expect_equal(width(grl_example_alt_sep[[1]][1]), 4000001)
expect_equal(width(grl_example_alt_sep[[1]][2]), 1991)
expect_equal(width(grl_example_alt_sep[[2]][1]), 3000001)
expect_equal(width(grl_example_alt_sep[[2]][2]), 79)
})


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