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v1.3.4
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@qzhang503
qzhang503 committed Nov 14, 2023
1 parent c3612f6 commit 597bde1
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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: Proteomics Database Searches of Mass-spectrometrirc Data.
Version: 1.3.3.3
Version: 1.3.4
Authors@R:
person(given = "Qiang",
family = "Zhang",
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2 changes: 2 additions & 0 deletions R/bin_masses.R
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,8 @@ bin_ms1masses <- function (res = NULL, min_mass = 200L, max_mass = 4500L,

if (len_bts && use_ms1_cache) {
.path_bin <- file.path(.path_ms1masses, .time_stamp, fun, .time_bin)
# in the next version...
# .path_bin <- fs::fs_path(.path_bin)
bins <- list.files(path = .path_bin, pattern = "binned_theopeps_\\d+\\.rds$")

if (length(bins) == len_m) {
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115 changes: 63 additions & 52 deletions R/mapMS2ions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -76,29 +76,33 @@ mapMS2ions <- function (out_path = NULL, in_name = "psmQ.txt",
type_ms2ions = "by", width = 12.5, height = 6)
{
if (is.null(out_path) || is.na(out_path) || out_path == "") {
warning("\"out_path\" cannot be empty.", call. = FALSE)
warning("\"out_path\" cannot be empty.")
return(NULL)
}

if (is.null(raw_file) || is.na(raw_file) || raw_file == "" ) {
warning("\"raw_file\" cannot be empty.", call. = FALSE)
warning("\"raw_file\" cannot be empty.")
return(NULL)
}

if (is.null(in_name) || is.na(in_name) || in_name == "" ) {
warning("\"in_name\" is empty; assume `psmQ.txt`.", call. = FALSE)
warning("\"in_name\" is empty; assume `psmQ.txt`.")
in_name <- "psmQ.txt"
}

if (is.null(out_name) || out_name == "") {
warning("\"out_name\" is empty; use `bar.png`.", call. = FALSE)
warning("\"out_name\" is empty; use `bar.png`.")
out_name <- "bar.png"
}

out_name <- check_ggname(out_name)

# MGF
fi_psm <- file.path(out_path, in_name)
if (!file.exists(fi_psm <- file.path(out_path, in_name))) {
warning("PSM file not found: ", fi_psm)
return(NULL)
}

mgf_path <- match_mgf_path(out_path)
raw_id <- match_raw_id(raw_file, mgf_path)
scan <- as.character(scan)
Expand All @@ -110,50 +114,59 @@ mapMS2ions <- function (out_path = NULL, in_name = "psmQ.txt",
return(NULL)
}

mgf <- data.frame(ms2_moverz = mgf_ok$ms2_moverz[[1]],
ms2_int = mgf_ok$ms2_int[[1]])
req_cols <- c("ms2_moverzs", "ms2_ints")

if (!all(oks <- req_cols %in% names(mgf_ok))) {
warning("Developer: missing PSM columns ",
paste(req_cols[!oks], collapse = ", "))
return(NULL)
}

mgf <- data.frame(ms2_moverz = mgf_ok$ms2_moverzs[[1]],
ms2_int = mgf_ok$ms2_ints[[1]])
mgf$iex <- seq_len(nrow(mgf))

## PSMs
cols_excl <- c("pep_ms2_moverzs", "pep_ms2_ints", "pep_ms2_theos",
"pep_ms2_theos2", "pep_ms2_exptints", "pep_ms2_exptints2",
"pep_n_matches", "pep_n_matches2")

if (file.exists(fi_psm)) {
gl_vals <- ls(all.names = TRUE, envir = .GlobalEnv)
ok_psms <- any(gl_vals == ".psms")

ok_file <- if (any(gl_vals == ".psm_file"))
identical(get(".psm_file", envir = .GlobalEnv), fi_psm)
else
FALSE

if (ok_psms && ok_file) {
.psms <- get(".psms", envir = .GlobalEnv)
}
else {
# some columns in psmQ.txt not in psmC.txt
.psms <- suppressWarnings(
readr::read_tsv(fi_psm, show_col_types = FALSE,
col_types = get_mzion_coltypes()))
.psms <- .psms[, -which(names(.psms) %in% cols_excl), drop = FALSE]
assign(".psms", .psms, envir = .GlobalEnv)
assign(".psm_file", file.path(out_path, in_name), envir = .GlobalEnv)
}

psm <- .psms |>
dplyr::filter(pep_scan_num == scan,
.data$raw_file == .env$raw_file,
pep_rank == rank,
pep_isdecoy == is_decoy)
psm <- psm[, -grep("^prot_", names(psm)), drop = FALSE]
# can be duplicated by prot_accs
psm <- unique(psm)
gl_vals <- ls(all.names = TRUE, envir = .GlobalEnv)
ok_psms <- any(gl_vals == ".psms")

ok_file <- if (any(gl_vals == ".psm_file"))
identical(get(".psm_file", envir = .GlobalEnv), fi_psm)
else
FALSE

if (ok_psms && ok_file) {
.psms <- get(".psms", envir = .GlobalEnv)
}
else {
warning("PSM file not found: ", fi_psm)
# some columns in psmQ.txt not in psmC.txt
.psms <- suppressWarnings(
readr::read_tsv(fi_psm, show_col_types = FALSE,
col_types = get_mzion_coltypes()))
.psms <- .psms[, -which(names(.psms) %in% cols_excl), drop = FALSE]
assign(".psms", .psms, envir = .GlobalEnv)
assign(".psm_file", file.path(out_path, in_name), envir = .GlobalEnv)
}

req_psmcols <- c("pep_scan_num", "raw_file", "pep_rank", "pep_isdecoy")

if (!all(oks <- req_psmcols %in% names(.psms))) {
warning("Developer: missing PSM columns ",
paste(req_psmcols[!oks], collapse = ", "))
return(NULL)
}

psm <- .psms |>
dplyr::filter(pep_scan_num == scan,
.data$raw_file == .env$raw_file,
pep_rank == rank,
pep_isdecoy == is_decoy)
psm <- psm[, -grep("^prot_", names(psm)), drop = FALSE]
psm <- unique(psm) # can be duplicated by prot_accs

if (!(nrow <- nrow(psm))) {
warning("PSM entry not found. Check the correctness of scan number etc.")
Expand All @@ -174,14 +187,13 @@ mapMS2ions <- function (out_path = NULL, in_name = "psmQ.txt",
ion_types <- unlist(strsplit(type_ms2ions, ""))

if (length(ion_types) != 2L)
stop("Not a two-character `type_ms2ions = ", type_ms2ions, "`.",
call. = FALSE)
stop("Not a two-character `type_ms2ions = ", type_ms2ions, "`.")

cols_pri <- c("pep_ms2_deltas", "pep_ms2_ideltas", "pep_ms2_iexs")

if (!all(oks <- cols_pri %in% names(psm))) {
warning("PSM columns not found: ", paste(cols_pri[!oks], collapse = ", "),
"\nPlease use the latest version of mzion.")
warning("Developer: missing PSM columns ",
paste(cols_pri[!oks], collapse = ", "))
return(NULL)
}

Expand Down Expand Up @@ -211,8 +223,8 @@ mapMS2ions <- function (out_path = NULL, in_name = "psmQ.txt",
cols_sec <- c("pep_ms2_deltas2", "pep_ms2_ideltas2", "pep_ms2_iexs2")

if (!all(oks <- cols_sec %in% names(psm))) {
warning("PSM columns not found: ", paste(cols_sec[!oks], collapse = ", "),
"\nPlease use the latest version of mzion.")
warning("Developer: missing PSM columns ",
paste(cols_sec[!oks], collapse = ", "))
return(NULL)
}

Expand Down Expand Up @@ -327,7 +339,7 @@ match_mgf_path <- function (out_path)
rda <- file.path(out_path, "Calls", "matchMS.rda")

if (!file.exists(rda))
stop("Parameter file not found: ", rda, call. = FALSE)
stop("Parameter file not found: ", rda)

load(rda)

Expand All @@ -346,14 +358,13 @@ match_raw_id <- function (raw_file, mgf_path)
if (!file.exists(file))
stop("File not found ", file)

raw_lookup <- qs::qread(file)
raw_id <- unname(raw_lookup[raw_file])
raw_map <- qs::qread(file)
raw_id <- unname(raw_map[raw_file])

if (is.na(raw_id)) {
stop(raw_file, " not found in ", file, ".\n",
"Aside from the possibility of incorrect `raw_file`, ",
"have the folder name been changed?",
call. = FALSE)
"have the folder name been changed?")
}

raw_id
Expand Down Expand Up @@ -416,10 +427,10 @@ find_mgf_query <- function (mgf_path, raw_id, scan, to_global = TRUE)
}
else {
files <- list.files(path = file.path(mgf_path),
pattern = "mgf_queries[_]*[0-9]*\\.rds$")
pattern = "mgf_queries_.*\\.rds$")

if (!length(files)) {
warning("No parsed `mgf_queries.rds` under ", mgf_path, call. = FALSE)
warning("No parsed `mgf_queries.rds` under ", mgf_path)
return(NULL)
}

Expand Down Expand Up @@ -521,7 +532,7 @@ make_speclib <- function (out_path = NULL, in_name = "psmQ.txt", score_co = 15,

if (all(is.na(df$pep_ms2_moverzs)) || all(is.na(df$pep_ms2_ints))) {
mgf_path <- match_mgf_path(out_path)
mgf_files <- list.files(file.path(mgf_path), "mgf_queries[_]*[0-9]*\\.rds$")
mgf_files <- list.files(file.path(mgf_path), "mgf_queries_.*\\.rds$")

if (!length(mgf_files)) {
warning("Processed `mgf_queries.rds` not found under ", mgf_path)
Expand Down
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