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Move collapsing earlier in readFragPipeInfo
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@csoneson
csoneson committed Apr 23, 2024
1 parent b9faaa2 commit e8dd451
Showing 1 changed file with 32 additions and 24 deletions.
56 changes: 32 additions & 24 deletions R/readFragPipeInfo.R
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Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,9 @@ readFragPipeInfo <- function(fragpipeDir) {
if (!is.null(configDf)) {
fpVersion <- gsub(".+\\((.+)\\).+", "\\1", configDf$parameter[1])
} else if (!is.null(logDf)) {
fpVersion <- gsub("# (.+)ui state cache", "\\1",
logDf$info[grep("# FragPipe v", logDf$info)])
fpVersion <- paste(gsub("# (.+)ui state cache", "\\1",
logDf$info[grep("# FragPipe v", logDf$info)]),
collapse = ", ")
} else {
fpVersion <- NULL
}
Expand Down Expand Up @@ -178,26 +179,30 @@ readFragPipeInfo <- function(fragpipeDir) {
## Search parameters
## -------------------------------------------------------------------------
if (!is.null(configDf)) {
fpSearchEngine <- gsub(
fpSearchEngine <- paste(gsub(
".+(MSFragger-.+).jar", "\\1",
configDf$value[configDf$parameter ==
"fragpipe-config.bin-msfragger"])
fpFastaFiles <- gsub("\\\\", "/",
configDf$value[configDf$parameter ==
"database.db-path"])
"fragpipe-config.bin-msfragger"]),
collapse = ", ")
fpFastaFiles <- paste(gsub("\\\\", "/",
configDf$value[configDf$parameter ==
"database.db-path"]),
collapse = ", ")
# fpContaminants <- "cRAP" ## cRAP in FASTA format can be obtained from
# the GPM FTP site, using the URL ftp://ftp.thegpm.org/fasta/cRAP.
} else if (!is.null(logDfConf)) {
fpSearchEngine <- gsub(
fpSearchEngine <- paste(gsub(
".+(MSFragger-.+).jar", "\\1",
logDfConf$value[logDfConf$parameter ==
"fragpipe-config.bin-msfragger"])
fpFastaFiles <- gsub(
"fragpipe-config.bin-msfragger"]),
collapse = ", ")
fpFastaFiles <- paste(gsub(
"/:/", ":/",
gsub("//", "/",
gsub("\\\\", "/",
logDfConf$value[logDfConf$parameter ==
"database.db-path"])))
"database.db-path"]))),
collapse = ", ")
# fpContaminants <- "cRAP"
} else {
fpSearchEngine <- fpFastaFiles <- NULL
Expand All @@ -220,8 +225,9 @@ readFragPipeInfo <- function(fragpipeDir) {
fpPepMassHi <-
logDfConf$value[logDfConf$parameter ==
"msfragger.misc.fragger.digest-mass-hi"]
fpPepSel <- paste0("length: ", fpPepLengthL, "-", fpPepLengthU,
" AA; mass: ", fpPepMassLo, "-", fpPepMassHi, " Da")
fpPepSel <- paste(paste0("length: ", fpPepLengthL, "-", fpPepLengthU,
" AA; mass: ", fpPepMassLo, "-", fpPepMassHi, " Da"),
collapse = ", ")

fpPmassTolUnits <- ifelse(
logDfConf$value[logDfConf$parameter ==
Expand Down Expand Up @@ -272,7 +278,7 @@ readFragPipeInfo <- function(fragpipeDir) {
paste("Top N ions:",
dataDf$value[dataDf$parameter == "ionquant.tp"]),
sep = ", ")
fpEnzymes <- paste0(
fpEnzymes <- paste(paste0(
dataDf$value[dataDf$parameter == "msfragger.search_enzyme_name_1"],
paste0("[", paste(
dataDf$value[dataDf$parameter ==
Expand All @@ -282,7 +288,8 @@ readFragPipeInfo <- function(fragpipeDir) {
"-terminal"),
paste0(dataDf$value[dataDf$parameter ==
"msfragger.allowed_missed_cleavage_2"],
" missed cleavages", "]"), sep = ", ")))
" missed cleavages", "]"), sep = ", "))),
collapse = ", ")

if ("msfragger.search_enzyme_name_2" %in% dataDf$parameter &&
dataDf$value[dataDf$parameter ==
Expand Down Expand Up @@ -318,27 +325,28 @@ readFragPipeInfo <- function(fragpipeDir) {
## Database decoy tag
## -------------------------------------------------------------------------
if (!is.null(dataDf)) {
fpDecoyTag <- dataDf$value[dataDf$parameter ==
"database.decoy-tag"]
fpDecoyTag <- paste(dataDf$value[dataDf$parameter ==
"database.decoy-tag"],
collapse = ";")
} else {
fpDecoyTag <- "rev_"
}

l <- list("FragPipe version" = paste(fpVersion, collapse = ", "),
l <- list("FragPipe version" = fpVersion,
"FragPipe parameter file" = fpConfigFile,
"FragPipe log file" = fpLogFile,
"Search engine" = paste(fpSearchEngine, collapse = ", "),
"Search engine" = fpSearchEngine,
"Raw file location" = fpRawDirs,
"Raw files" = fpRawFiles,
"Sample names" = fpExperiments,
"Databases" = paste(fpFastaFiles, collapse = ", "),
"Databases" = fpFastaFiles,
# "Contaminants" = fpContaminants,
"Peptides (ranges)" = paste(fpPepSel, collapse = ", "),
"Peptides (ranges)" = fpPepSel,
"Mass error tolerances" = fpMassTol,
"Quantification settings (LFQ)" = paste(fpQuantMethods, collapse = ", "),
"Enzymes" = paste(fpEnzymes, collapse = ", "),
"Quantification settings (LFQ)" = fpQuantMethods,
"Enzymes" = fpEnzymes,
"Variable modifications" = fpVariableModifications,
"Fixed modifications" = fpFixedModifications,
"Database decoy tag" = paste(fpDecoyTag, collapse = ", "))
"Database decoy tag" = fpDecoyTag)
l[vapply(l, length, 0) > 0]
}

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