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v1.2.7
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Updates:
- codes optimization
- notch searches (off-sets in precursor masses)
- bug fixes
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@qzhang503
qzhang503 committed Jun 15, 2023
1 parent af4608e commit eaccf2c
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: mzion
Type: Package
Title: Database Searches of Proteomic Mass-spectrometrirc Data
Version: 1.2.6.3
Version: 1.2.7
Authors@R:
person(given = "Qiang",
family = "Zhang",
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137 changes: 74 additions & 63 deletions R/bin_masses.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,11 @@
#' @inheritParams load_mgfs
#' @inheritParams calc_pepmasses2
bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,
ppm_ms1 = 20L, use_ms1_cache = TRUE,
.path_cache = NULL, .path_ms1masses = NULL,
is_ms1_three_frame = TRUE,
out_path = NULL, sys_ram = 24L)
min_len = 7L, max_len = 40L, ppm_ms1 = 20L,
use_ms1_cache = TRUE, .path_cache = NULL,
.path_ms1masses = NULL, is_ms1_three_frame = TRUE,
out_path = NULL, enzyme = "trypsin_p",
sys_ram = 24L)
{
old_opts <- options()
options(warn = 1L)
Expand All @@ -38,11 +39,10 @@ bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,

# checks pre-existed precursor masses
.time_stamp <- get(".time_stamp", envir = .GlobalEnv, inherits = FALSE)
.path_mass <- file.path(.path_ms1masses, .time_stamp)
.path_mass <- file.path(.path_ms1masses, .time_stamp)
masses <- list.files(path = .path_mass, pattern = paste0("^pepmasses_", "\\d+\\.rds$"))
len_m <- length(masses)

if (!len_m)
if (!(len_m <- length(masses)))
stop("File not found: ",
file.path(.path_mass, paste0("pepmasses_", "[...].rds")))

Expand All @@ -51,72 +51,68 @@ bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,
"calc_pepmasses2",
.time_stamp),
fun = fun,
nms = c("min_mass", "max_mass", "ppm_ms1"))
nms = c("min_mass", "max_mass", "min_len",
"max_len", "ppm_ms1"))

# already binned
len_bts <- length(.time_bin)

if (len_bts > 1L)
if ((len_bts <- length(.time_bin)) > 1L)
stop("More than one cached results found: \n\n",
paste(file.path(.path_ms1masses, .time_stamp, fun), collapse = "\n"),
"\n\nDelete the caches and start over.",
call. = FALSE)
"\n\nDelete the caches and start over.")

if (len_bts && use_ms1_cache) {
.path_bin <- file.path(.path_ms1masses, .time_stamp, fun, .time_bin)

bins <- list.files(path = .path_bin, pattern = "binned_theopeps_\\d+\\.rds$")
len_b <- length(bins)

if (len_b == len_m) {
if (length(bins) == len_m) {
message("Loading bins of MS1 masses from cache.")

.savecall <- FALSE

# no need of global `.time_bin`
assign(".path_bin", .path_bin, envir = .GlobalEnv)

return(NULL)
return(.path_bin)
}
}


# to be binned
message("Binning MS1 masses...")

.time_bin <- format(Sys.time(), ".%Y-%m-%d_%H%M%S")
.path_bin <- create_dir(file.path(.path_ms1masses, .time_stamp, fun, .time_bin))

if (!is.null(res)) {
# (a) process directly
binTheoSeqs(idxes = NULL,
res = res,
min_mass = min_mass,
max_mass = max_mass,
ppm_ms1 = ppm_ms1_bin,
out_path = file.path(.path_bin, "binned_theopeps.rds"))
}
else {

if (is.null(res)) {
# (b) reload
idxes <- local({
idxes <- gsub("^pepmasses_(\\d+)\\.rds$", "\\1", masses)
idxes <- as.integer(idxes)
idxes <- idxes[order(idxes)]
})

if (FALSE) {
n_cores <- local({
fct <- 20
free_mem <- find_free_mem(sys_ram)
max_sz <- max(file.size(file.path(.path_mass, masses)))/1024^2

n_cores <- min(floor(free_mem/max_sz/fct), detect_cores(8L))

if (n_cores < 1L) {
warning("May be out of RAM with large peptide tables.")
n_cores <- 1L
}

n_cores
})
}

n_cores <- local({
fct <- 20
free_mem <- find_free_mem(sys_ram)
max_sz <- max(file.size(file.path(.path_mass, masses)))/1024^2
n_cores <- detect_cores(15L)

n_cores <- min(floor(free_mem/max_sz/fct), detect_cores(8L))

if (n_cores < 1L) {
warning("May be out of RAM with large peptide tables.")
n_cores <- 1L
}
if (len_m > n_cores)
n_cores <- min(floor(n_cores/2L), len_m)
else
n_cores <- min(n_cores, len_m)

n_cores
if (enzyme == "noenzyme")
n_cores <- floor(n_cores/2L)

n_cores <- max(1L, n_cores)
})

if (n_cores > 1L) {
Expand All @@ -129,6 +125,7 @@ bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,
c("binTheoSeqs_i",
"binTheoSeqs2",
"bin_theoseqs",
"s_readRDS",
"find_ms1_cutpoints"),
envir = environment(mzion::matchMS))

Expand All @@ -147,23 +144,35 @@ bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,

parallel::stopCluster(cl)
}
else {
else
lapply(idxes, binTheoSeqs_i, min_mass, max_mass, ppm_ms1_bin,
.path_mass, .path_bin)
}
}
else {
# (a) process directly
binTheoSeqs(idxes = NULL,
res = res,
min_mass = min_mass,
max_mass = max_mass,
ppm_ms1 = ppm_ms1_bin,
enzyme = enzyme,
out_path = file.path(.path_bin, "binned_theopeps.rds"))
}

pat_b <- "^binned_theopeps_[0-9]+\\.rds"
len_b <- length(list.files(.path_bin, pattern = pat_b))

if (len_b != len_m)
stop("May need more RAM: expect ", len_m, " \"", pat_b, "\" files, ",
"but found ", len_b, " files under \n\"", .path_bin, "\"\n")

.savecall <- TRUE

assign(".time_bin", .time_bin, envir = .GlobalEnv)
assign(".path_bin", .path_bin, envir = .GlobalEnv)

local({
file <- file.path(out_path, "Calls", ".cache_info.rds")

if (file.exists(file)) {
if (file.exists(file))
.cache_info <- qs::qread(file)
}

.cache_info$.time_bin <- .time_bin
.cache_info$.path_bin <- .path_bin
Expand All @@ -173,24 +182,23 @@ bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,

message("Completed precusor bins at: ", Sys.time())

invisible(NULL)
invisible(.path_bin)
}


#' Helper of \link{binTheoSeqs2}.
#'
#' @param in_path An input path of \code{pepmasses_}.
#' @inheritParams binTheoSeqs2
binTheoSeqs_i <- function (idx = 1L, min_mass = 200L,max_mass = 4500L,
binTheoSeqs_i <- function (idx = 1L, min_mass = 200L, max_mass = 4500L,
ppm_ms1 = 10L, in_path = NULL, out_path = NULL)
{
if (is.null(in_path))
stop("`in_path` cannot be NULL.")

message("\tSet: ", idx)

in_nm <- paste0("pepmasses_", idx, ".rds")
res <- s_readRDS(in_nm, in_path)
res <- s_readRDS(paste0("pepmasses_", idx, ".rds"), in_path)

binTheoSeqs2(idx = idx,
res = res,
Expand Down Expand Up @@ -241,7 +249,6 @@ bin_theoseqs <- function (peps = NULL, out_nm = NULL, min_mass = 200L,
if (!length(peps)) {
out <- NULL
qs::qsave(out, out_nm, preset = "fast")

return(NULL)
}

Expand All @@ -255,7 +262,7 @@ bin_theoseqs <- function (peps = NULL, out_nm = NULL, min_mass = 200L,

out <- dplyr::arrange(out, frame, pep_seq)
out <- split(out, out$frame, drop = FALSE)

out <- lapply(out, function (x) { x[["frame"]] <- NULL; x })
qs::qsave(out, out_nm, preset = "fast")

invisible(NULL)
Expand All @@ -272,6 +279,7 @@ bin_theoseqs <- function (peps = NULL, out_nm = NULL, min_mass = 200L,
#' @param max_mass Numeric; the maximum MS1 mass.
#' @param ppm_ms1 Numeric; (half of) the error tolerance of MS1 mass in ppm.
#' @param out_path The output path.
#' @param enzyme The assume enzyme activity.
#' @examples
#' \donttest{
#' library(mzion)
Expand All @@ -281,9 +289,9 @@ bin_theoseqs <- function (peps = NULL, out_nm = NULL, min_mass = 200L,
#' }
#' @return Lists of theoretical peptides binned by MS1 masses. The lists
#' correspond to the lists of \code{res}.
#' @import parallel
binTheoSeqs <- function (idxes = NULL, res = NULL, min_mass = 200L,
max_mass = 4500L, ppm_ms1 = 10L, out_path = NULL)
max_mass = 4500L, ppm_ms1 = 10L, enzyme = "trypsin_p",
out_path = NULL)
{
if (is.null(res))
stop("`res` cannot be NULL.")
Expand All @@ -305,20 +313,23 @@ binTheoSeqs <- function (idxes = NULL, res = NULL, min_mass = 200L,

n_cores <- local({
len <- length(res)
n_cores <- detect_cores(16L)
n_cores <- detect_cores(15L)

if (len > n_cores)
n_cores <- min(floor(n_cores/2L), len)
else
n_cores <- min(n_cores, len)

if (enzyme == "noenzyme")
n_cores <- floor(n_cores/2L)

n_cores <- max(1L, n_cores)
})

cl <- parallel::makeCluster(getOption("cl.cores", n_cores))

parallel::clusterExport(cl, list("qread", "qsave"), envir = environment(qs::qsave))

parallel::clusterExport(cl, list("qread", "qsave"),
envir = environment(qs::qsave))
parallel::clusterExport(cl, c("bin_theoseqs", "find_ms1_cutpoints"),
envir = environment(mzion::matchMS))

Expand Down
6 changes: 2 additions & 4 deletions R/funs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -16,10 +16,8 @@
#
# $ion_ladder.R
# [1] "ms2ions_by_type" "byions" "czions" "axions" "bions_base" "yions_base"
# [7] "b2ions_base" "bstarions" "bstar2ions" "b0ions" "b02ions" "y2ions"
# [13] "ystarions" "ystar2ions" "y0ions" "y02ions" "cions_base" "c2ions"
# [19] "zions_base" "z2ions" "aions_base" "a2ions" "astarions" "astar2ions"
# [25] "a0ions" "a02ions" "xions_base" "x2ions"
# [7] "cions_base" "zions_base" "c2ions" "z2ions" "aions_base" "xions_base"
# [13] "a2ions" "astarions" "astar2ions" "a0ions" "a02ions" "x2ions"
#
# $mapMS2ions.R
# [1] "mapMS2ions" "match_mgf_path" "match_raw_id" "add_raw_ids"
Expand Down
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