R/analyse TCR.R
In debdagybra/IMIabgd: Analyze Tcells data with mixcr and vdjtools
#' @title analyse_tcr
#' @description execute a list of commmand on all .fastq.gz files in `input_dir`
#' @param java_param a character string containing java parameters
#' @param path_vdjtools the path to vdjtools.jar
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir directory where the files are (also look in sub-directories)
#' @param tcr_chain The type of Tcells to analyse (A, B, G or D).
#' "auto" to let R detect the type of Tcells automatically.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @param ... Parameters to pass to the called functions (e.g. report_name)
#' @return runs command lines in console. Creates .vdjca files
#' in the same directory than the fastq.gz files
#' @author DEBOT Damien <damien.debot@@gmail.com>
#' @importFrom magrittr %>%
#' @export
#'
#'
# TEST :
# test <- analyse_tcells(java_param="java -Xmx4g -Xms3g -jar",
# path_vdjtools="D:/Maria/Maria_Analysis/vdjtools-1.1.7/vdjtools-1.1.7.jar",
# path_mixcr="D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar",
# input_dir="D:/Projets R/IMIabgd/data/Gamma_SR11-20/",
# replace=FALSE,
# string_only=FALSE)
analyse_tcr <- function(java_param="java -Xmx4g -Xms3g -jar",
path_vdjtools,
path_mixcr,
input_dir,
tcr_chain="auto",
replace=FALSE,
string_only=FALSE,
...) {
starttime <- proc.time()
# checks args
# java_param
if (!is.character(java_param)) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
if (length(java_param) > 1) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
# path_vdjtools
path_vdjtools <- check_path_program(path_vdjtools, program = "vdjtools")
# path_mixcr
path_mixcr <- check_path_program(path_mixcr, program = "mixcr")
# input_dir
if (!is.character(input_dir)) stop("`input_dir` must be a character vector of length 1.")
if (length(input_dir) > 1) stop("`input_dir` must be a character vector of length 1.")
input_dir <- correct_paths(input_dir)
if (!dir.exists(input_dir)) {
stop("`input_dir` must be a valid directory.")
}
# tcr_chain
tcr_chain <- match.arg(tcr_chain, c("auto", "A", "B", "G", "D"))
# replace
if (!is.logical(replace)) stop("`replace` must be logical.")
# string_only
if (!is.logical(string_only)) stop("`string_only` must be logical.")
if (string_only == TRUE) message("string_only is ON. Commands will not be executed.")
# lists all files '.fatsq.gz' in directory 'input_dir' and all the sub-directories
files_fastq.gz <- list.files(
path = input_dir, recursive = TRUE,
full.names = TRUE, pattern = ".fastq.gz"
) %>%
.[substr(., nchar(.) - 8, nchar(.)) == ".fastq.gz"] %>%
.[grep("_R1_", .)] %>%
gsub("//", "/", .) %>%
unique()
# execute all commands for each file
command_txt <- character(0)
for (f in 1:length(files_fastq.gz)) {
# erase file extension
input_filename <- basename(files_fastq.gz[f]) %>%
gsub(".fastq.gz", "", .)
# determine the folder of this specific file
input_dir_file <- paste0(dirname(files_fastq.gz[f]), "/")
input_parentdir_file <- paste0(dirname(input_dir_file), "/")
message(paste0(
"Analyse file (", f, "/", length(files_fastq.gz), ") : ",
paste0(input_filename, ".fastq.gz")
))
# guests the Tcell type from filename
short_input_filename <- substr(
input_filename, 1,
gregexpr("-", input_filename)[[1]][2] + 1
)
if (tcr_chain == "auto") {
tcr_chain <- toupper(substr(
short_input_filename,
nchar(short_input_filename),
nchar(short_input_filename)
))
if (!tcr_chain %in% c("A", "B", "G", "D")) {
stop(
"Unable to autodetect Tcell type for file ",
input_filename, "."
)
}
}
# the functions return the name of the output file
# (or the command in string when string_only=TRUE)
# command_txt is used to store all the commands in a vector
# execute the command `align -OvParameters.geneFeatureToAlign=VTranscript`
lastreturned_value <- align_fastq_to_vdjca(
java_param = java_param, path_mixcr = path_mixcr,
input_dir = input_dir_file, input_filename = input_filename,
# report_name="alignmentReport",
replace = replace, string_only = string_only, ...
)
command_txt <- c(command_txt, lastreturned_value)
# execute the command `assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10`
lastreturned_value <- assemble_vdjca_to_clns(
java_param = java_param, path_mixcr = path_mixcr,
input_dir = input_dir_file, input_filename = basename(lastreturned_value),
output_filename = short_input_filename,
replace = replace, string_only = string_only, ...
)
command_txt <- c(command_txt, lastreturned_value)
# execute the command `exportClones TR` & tcr_chain
lastreturned_value <- export_clones(
java_param = java_param, path_mixcr = path_mixcr,
input_dir = input_dir_file, input_filename = basename(lastreturned_value),
# output_dir = input_parentdir_file,
output_filename = paste0(short_input_filename, "_clonesMin10)"),
tcr_chain = tcr_chain,
replace = replace, string_only = string_only, ...
)
command_txt <- c(command_txt, lastreturned_value)
command_txt <- c(command_txt, "")
}
# endtime
message(paste0("Done in ", round((proc.time() - starttime)[[3]], 2), " seconds"))
if (string_only == TRUE) return(noquote(command_txt))
invisible()
}
#' @title align_fastq_to_vdjca
#' @description execute the command : 'align -OvParameters.geneFeatureToAlign=VTranscript
# --report alignmentReport.log input_R1.fastq input_R2.fastq alignments.vdjca'
#' @param java_param a character string containing java parameters
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (type R1.fastq.gz), (with or without the extension)
#' @param report_name the name of the file alignmentReport. (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @return run command line in console. Creates .vdjca files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.com>
#' @importFrom magrittr %>%
#' @export
align_fastq_to_vdjca <- function(java_param="java -Xmx4g -Xms3g -jar",
path_mixcr,
input_dir,
input_filename,
output_filename="auto",
report_name="alignmentReport",
replace=FALSE,
string_only=FALSE) {
# TEST : java_param <- "java -Xmx4g -Xms3g -jar" ; path_mixcr <- "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar"
# input_dir <- 'D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/'
# input_filename <- "70-SR13-Gamma_S70_L001_R1_001"
# report_name <- "alignmentReport" ; replace <- FALSE ; string_only <- TRUE
# check args
{
# input_dir
if (!is.character(input_dir)) stop("`input_dir` must be a character vector of length 1.")
if (length(input_dir) > 1) stop("`input_dir` must be a character vector of length 1.")
input_dir <- correct_paths(input_dir)
if (!dir.exists(input_dir)) {
stop("`input_dir` must be a valid directory.")
}
# input_filename
if (!is.character(input_filename)) stop("`input_filename` must be a character vector of length 1.")
if (length(input_filename) > 1) stop("`input_filename` must be a character vector of length 1.")
input_filename <- correct_paths(input_filename)
input_filename <- gsub(".fastq.gz", "", input_filename) # erase file extension
if (!file.exists(paste0(input_dir, input_filename, ".fastq.gz"))) {
stop("`input_filename` must be a valid file in `input_dir` directory.")
}
}
# end check args
input_ext <- ".fastq.gz"
output_ext <- ".vdjca"
# From input_filename
# check if there are 2 files R1,R2
# define the name of the output file
input_1 <- paste0(gsub("_R2_", "_R1_", input_filename), input_ext)
if (!file.exists(paste0(input_dir, input_1))) {
stop(
input_dir, " doesn't contains an R1 file. \n",
"Expected file: ", input_1
)
}
input_2 <- paste0(gsub("_R1_", "_R2_", input_filename), input_ext)
if (!file.exists(paste0(input_dir, input_1))) {
warning(
input_dir, " doesn't contains an R2 file. \n",
"The analyse is done only with the R1 file. \n",
"Expected file: ", input_2
)
input_2 <- ""
if (output_filename == "auto") output_filename <- gsub("_R2_", "_R1_", input_filename)
} else {
if (output_filename == "auto") {
output_filename <- gsub("_R2_", "_R1R2_", input_filename) %>%
gsub("_R1_", "_R1R2_", .)
}
}
# merge the R1 & R2 input files
input_filename <- paste(input_1, input_2, collapse = " ")
run_command_vdj(
java_param = java_param,
path_vdjtools = "",
path_mixcr = path_mixcr,
input_dir = input_dir,
input_filename = input_filename,
input_ext = ".fastq.gz",
check_input_filename = FALSE,
output_filename = output_filename,
output_ext = ".vdjca",
command_vdj = "align -OvParameters.geneFeatureToAlign=VTranscript",
report_name = report_name,
replace = replace,
fullpath = FALSE,
string_only = string_only
)
}
#' @title assemble_vdjca_to_clns
#' @description execute the command : 'assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10
# --report assembleReport.log alignments.vdjca clones.clns'
#' @param java_param a character string containing java parameters
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (type .vdjca), (with or without the extension)
#' @param output_filename the name of the output file (without extension)
#' @param report_name the name of the file assembleReport (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @return run command line in console. Creates .clns files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.be>
#' @export
assemble_vdjca_to_clns <- function(java_param="java -Xmx4g -Xms3g -jar",
path_mixcr,
input_dir,
input_filename,
output_filename,
report_name="assembleReport",
replace=FALSE,
string_only=FALSE) {
# TO DO add Tcells_type ----
# to choose between Min10 or regular
# check if result is different when no need Min10
run_command_vdj(
java_param = java_param,
path_vdjtools = "",
path_mixcr = path_mixcr,
input_dir = input_dir,
input_filename = input_filename,
input_ext = ".vdjca",
output_filename = output_filename,
output_ext = ".clns",
command_vdj = "assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10",
report_name = report_name,
replace = replace,
fullpath = FALSE,
string_only = string_only
)
}
#' @title export_clones
#' @description execute the command : 'assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10
# --report assembleReport.log alignments.vdjca clones.clns'
#' @param java_param a character string containing java parameters
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (type .vdjca), (with or without the extension)
#' @param output_filename the name of the output file (without extension)
#' @param report_name the name of the file assembleReport (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @return run command line in console. Creates .clns files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.be>
#' @export
export_clones <- function(java_param="java -Xmx4g -Xms3g -jar",
path_mixcr,
input_dir,
input_filename,
output_filename,
tcr_chain="auto",
report_name="",
replace=FALSE,
string_only=FALSE) {
# #java -Xmx4g -Xms3g -jar path\mixcr.jar exportClones --chains TRG clones.clns TRGclones.txt
# #print("Cmd exportClones TRD/G")
# if ( !(file.exists(paste0(input_parentdir,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),"_clonesMin10.txt")) & replace_if_existing==FALSE) ) {
# # system(paste(java.param,path_mixcr, paste0("exportClones --chains TR",toupper(substr(input_filename,Length_id,Length_id))),
# # string_f, paste0(input_parentdir,substr(input_filename,1,Length_id),"_clones.clns"),
# # paste0(input_parentdir,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),"_clones.txt")))
# system(paste(java.param,path_mixcr,
# paste0("exportClones --chains TR",toupper(substr(input_filename,Length_id,Length_id))),
# string_f,
# paste0('"',input_dir,substr(input_filename,1,Length_id),'_clonesMin10.clns"'),
#
# paste0('"',input_parentdir,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),'_clonesMin10.txt"')))
# } else message(paste0("File '",paste0(path,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),"_clonesMin10.txt"),"' already exists"))
#
# tcr_chain
tcr_chain <- match.arg(tcr_chain, c("auto", "A", "B", "G", "D"))
run_command_vdj(
java_param = java_param,
path_vdjtools = "",
path_mixcr = path_mixcr,
input_dir = input_dir,
input_filename = input_filename,
input_ext = ".clns",
output_filename = output_filename,
output_ext = ".txt",
command_vdj = paste0("exportClones --chains TR", tcr_chain, " "),
report_name = report_name,
replace = replace,
fullpath = FALSE,
string_only = string_only
)
}
#' @title run_command_vdj
#' @description execute a command in the windows console.
#' @param java_param a character string containing java parameters
#' @param path_vdjtools the path to vdjtools.jar
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (without the extension). If empty, loads all files in `input_dir`
#' @param input_ext the extension of the `input_filename` (e.g. `.vdjca`)
#' @param output_dir where the output files will be. If empty, the default value is the same as `input_dir`.
#' Warning: It's not always possible to choose the `output_dir` in mixcr/vdjtools.
#' Warning: You 'll need probably to set fullpath=TRUE.
#' @param output_filename the name of the output file (without extension)
#' @param output_ext the extension of the `output_filename` (e.g. `.txt`)
#' @param command_vdj the command to run
#' @param report_name the name of the file assembleReport (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param fullpath if TRUE, the fullpath of `input_filename` and `output_filename` will be written in command.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @details execute a command in the windows console.
#' The scruture follows the order:
#' java_param + path_vdjtools + path_mixcr + report_name +
#' command_vdj + input_filename + output_filename
#' if an argument is NULL, it will be ignored
#' @return run command line in console. Creates .clns files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.be>
#' @importFrom magrittr %>%
#' @export
run_command_vdj <- function(java_param="java -Xmx4g -Xms3g -jar",
path_vdjtools="",
path_mixcr="",
input_dir,
input_filename="auto",
input_ext,
check_input_filename=TRUE,
output_dir,
output_filename="auto",
output_ext,
command_vdj,
report_name="",
replace=FALSE,
fullpath = TRUE,
string_only=FALSE,
...) {
# TEST : java_param <- "java -Xmx4g -Xms3g -jar" ; path_mixcr <- "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar"
# input_dir <- 'D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/'
# input_filename <- "70-SR13-Gamma_S70_L001_R1R2_001"
# report_name <- "assembleReport" ; replace <- FALSE ; string_only <- FALSE
# checks args ----
# java_param
if (!is.character(java_param)) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
if (length(java_param) > 1) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
# path_vdjtools
if (path_vdjtools != "") path_vdjtools <- check_path_program(path_vdjtools, program = "vdjtools")
# path_mixcr
if (path_mixcr != "") path_mixcr <- check_path_program(path_mixcr, program = "mixcr")
# input_dir
if (!is.character(input_dir)) stop("`input_dir` must be a character vector of length 1.")
if (length(input_filename) > 1 & length(input_dir) != length(input_filename)) {
stop(
"`input_dir` must be a character vector of length 1 or equal to length of input_filename.", "\n",
"Length of `input_dir`: ", length(input_dir), "\n",
"Length of `input_filename`: ", length(input_filename)
)
}
input_dir <- correct_paths(input_dir)
if (any(!dir.exists(input_dir))) {
stop(
"`input_dir` must be a valid directory.", "\n",
"Invalid: ", "\n",
paste(input_dir[!dir.exists(input_dir)], collapse = "\n")
)
}
# check_input_filename
if (!is.logical(check_input_filename)) stop("`check_input_filename` must be TRUE or FALSE")
# input_ext
if (missing(input_ext)) {
stop("`input_ext` is missing.")
}
if (!is.character(input_ext)) {
stop("`input_ext` must be a character vector of length 1, starting with a dot.")
}
if (nchar(input_ext) == 0) {
stop("`input_ext` must be a non-empty character vector of length 1, starting with a dot.")
}
if (substr(input_ext, 1, 1) != ".") {
stop(
"`input_ext` must be a character vector of length 1, starting with a dot.", "\n",
"Did you mean: `.", input_ext, "` ?"
)
}
# input_filename
if (!is.character(input_filename)) stop("`input_filename` must be a character vector.")
# if (length(input_filename) > 1) stop("`input_filename` must be a character vector.")
if (all(input_filename %in% c("", "auto"))) {
input_filename <- list.files(
path = input_dir, recursive = TRUE,
full.names = TRUE, pattern = input_ext
) %>%
.[substr(., nchar(.) - nchar(input_ext) + 1, nchar(.)) == input_ext] %>%
gsub("//", "/", .) %>%
unique()
# input_dir for each file
input_dir <- paste0(dirname(input_filename), "/")
input_filename <- basename(input_filename)
}
input_filename <- correct_paths(input_filename)
if (check_input_filename == TRUE) input_filename <- gsub(input_ext, "", input_filename) # erase file extension
if (any(!file.exists(paste0(input_dir, input_filename, input_ext)) & check_input_filename == TRUE)) {
stop(
"`input_filename`+`input_ext` must be a valid file in `input_dir` directory.", "\n",
"Your file: ", input_filename, input_ext, " doesn't exist in ", input_dir, "."
)
}
# outputfilename
if (all(output_filename == "auto")) {
if (any(is.na(gregexpr("-", input_filename)[[1]][2]))) {
stop(
"`output_filename` can't be determined automatically because ",
"at least one of the files doensn't contain `-` in his title.", "\n",
"Your file(s): ", "\n", paste(paste0(input_filename, input_ext), collapse = "\n")
)
} else {
output_filename <- substr(input_filename, 1, gregexpr("-", input_filename)[[1]][2] + 1)
}
}
if (length(output_filename) == 1 & length(input_filename) > 1) {
output_filename <- rep(output_filename, length(input_filename))
}
if (length(output_filename) != length(input_filename)) {
stop("`output_ext` must be a character vector with the same length than `input_filename`.")
}
# output_ext
if (!is.character(output_ext)) {
stop("`output_ext` must be a character vector of length 1, starting with a dot.")
}
if (any(nchar(output_ext) == 0 & nchar(output_filename) > 0)) {
stop("`output_ext` can't be empty if `output_filename` isn't also empty.")
}
if (nchar(output_ext) > 0 && substr(output_ext, 1, 1) != ".") {
stop(
"`output_ext` must be a character vector of length 1, starting with a dot.", "\n",
"Did you mean: `.", output_ext, "` ?"
)
}
# output_dir
if (base::missing(output_dir)) output_dir <- input_dir
if (!is.character(output_dir)) {
stop("`output_dir` must be a character vector of length 1 or same length than `output_filename`")
}
if (length(output_filename) > 1 & length(output_dir) != length(output_filename)) {
stop(
"`output_dir` must be a character vector of length 1 or equal to length of output_filename", "\n",
"Length of `output_dir`: ", length(output_dir), "\n",
"Length of `output_filename`: ", length(output_filename)
)
}
output_dir <- correct_paths(output_dir)
if (any(!dir.exists(output_dir))) {
stop(
"`output_dir` must be a valid directory.", "\n",
"Invalid: ", "\n",
paste(output_dir[!dir.exists(output_dir)], collapse = "\n")
)
}
# command_vdj
if (!is.character(command_vdj)) {
stop("`command_vdj` must be a character vector of length 1.")
}
# report_name
if (!is.character(report_name)) {
stop("`report_name` must be a character vector of length 1 or NULL.")
}
report_name <- gsub(".log", "", report_name) # erase file extension
# replace
if (!is.logical(replace)) stop("`replace` must be logical.")
# string_only
if (!is.logical(string_only)) stop("`string_only` must be logical.")
# ...
if (any(names(list(...)) %in% "tcr_chain")) {
# tcr_chain
tcr_chain <- match.arg(list(...)$tcr_chain, c("auto", "A", "B", "G", "D"))
if (tcr_chain == "auto") {
tcr_chain <- toupper(substr(
input_filename,
nchar(input_filename),
nchar(input_filename)
))
if (!tcr_chain %in% c("A", "B", "G", "D")) {
stop(
"Unable to autodetect Tcell type for file ",
input_filename, "."
)
}
command_vdj <- gsub("auto", tcr_chain, command_vdj)
}
}
# end checks args
# create command ----
command_request <- character(0)
for (i in 1:length(input_filename)) {
# write the command(s)
command_request <- c(command_request, paste(
java_param, # e.g. 'java -Xmx4g -Xms3g -jar'
if (path_vdjtools!="") {
paste0("\"", path_vdjtools,"\"")
} else path_vdjtools,
if (path_mixcr!="") {
paste0("\"", path_mixcr,"\"")
} else path_mixcr,
command_vdj,
if (report_name == "") {
report_name
} else {
paste0("--report ", report_name, ".log") # e.g. '--report alignmentReport.log'
},
if (replace == TRUE) "-f" else "", # e.g. '-f'
# TO DO ----
# if fullpath, must be between double quotes
# ok to keep space
paste0( # e.g. 'input_filename.vdjca'
if (fullpath == TRUE & check_input_filename == TRUE) paste0("\"", input_dir[i]) else "",
input_filename[i],
if (check_input_filename == TRUE) input_ext else "",
if (fullpath == TRUE & check_input_filename == TRUE) "\"" else ""
),
paste0(
"\"", if (fullpath == TRUE) output_dir[i] else "",
output_filename[i], output_ext
), # e.g. 'output_file.clns
"\"",
sep = " "
))
}
if (string_only == TRUE) return(noquote(command_request))
# execute the command in the console ----
# but only if replace = TRUE or the output file doesn't exist yet
for (i in 1:length(input_filename)) {
if (length(input_filename) > 1) {
message(paste0(
"Processing file (", i, "/", length(input_filename), ") : ",
paste0(input_filename[i], input_ext)
))
}
if (!(file.exists(paste0(output_dir[i], output_filename[i], output_ext)) & replace == FALSE)) {
inital_wd <- getwd()
setwd(input_dir[i]) # R active directory -> set cd in console
# execute command
# status: 0 = success / 1 = error => replaced by the error message
status <- suppressMessages(suppressWarnings(tryCatch(system(command_request[i], intern = TRUE),
warning = function(w) list(
rvalue = system(command_request[i], intern = TRUE),
warn = conditionMessage(w)
),
error = function(e) list(
rvalue = system(command_request[i], intern = TRUE),
err = conditionMessage(e)
)
)))
setwd(inital_wd)
if (is.list(status) && attributes(status[[1]])$status != 0) {
stop(
"Your command line ended with an error.", "\n",
"The reason might be that:", "\n",
" - the command does not exist or contains an error ", "\n",
" - a required argument is missing or incorrect ", "\n",
" - the `fullpath` argument should be different (now: ", !fullpath, ").", "\n", "\n",
status[[2]], "\n",
status[[1]]
)
} else {
cat(paste0(paste(status, collapse = "\n"), "\n"))
}
# check that the file is created
if (!file.exists(paste0(output_dir[i], output_filename[i], output_ext))) {
warning("Output file: `", paste0(output_dir[i], output_filename[i], output_ext), "` not found.")
}
} else {
message(paste0("File '", paste0(output_dir[i], output_filename[i], output_ext),
"' already exists and is not replaced."))
}
}
# return names of created files
paste0(input_dir, output_filename, output_ext)
}
debdagybra/IMIabgd documentation built on May 21, 2019, 12:19 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
#' @title analyse_tcr
#' @description execute a list of commmand on all .fastq.gz files in `input_dir`
#' @param java_param a character string containing java parameters
#' @param path_vdjtools the path to vdjtools.jar
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir directory where the files are (also look in sub-directories)
#' @param tcr_chain The type of Tcells to analyse (A, B, G or D).
#' "auto" to let R detect the type of Tcells automatically.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @param ... Parameters to pass to the called functions (e.g. report_name)
#' @return runs command lines in console. Creates .vdjca files
#' in the same directory than the fastq.gz files
#' @author DEBOT Damien <damien.debot@@gmail.com>
#' @importFrom magrittr %>%
#' @export
#'
#'
# TEST :
# test <- analyse_tcells(java_param="java -Xmx4g -Xms3g -jar",
# path_vdjtools="D:/Maria/Maria_Analysis/vdjtools-1.1.7/vdjtools-1.1.7.jar",
# path_mixcr="D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar",
# input_dir="D:/Projets R/IMIabgd/data/Gamma_SR11-20/",
# replace=FALSE,
# string_only=FALSE)
analyse_tcr <- function(java_param="java -Xmx4g -Xms3g -jar",
path_vdjtools,
path_mixcr,
input_dir,
tcr_chain="auto",
replace=FALSE,
string_only=FALSE,
...) {
starttime <- proc.time()
# checks args
# java_param
if (!is.character(java_param)) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
if (length(java_param) > 1) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
# path_vdjtools
path_vdjtools <- check_path_program(path_vdjtools, program = "vdjtools")
# path_mixcr
path_mixcr <- check_path_program(path_mixcr, program = "mixcr")
# input_dir
if (!is.character(input_dir)) stop("`input_dir` must be a character vector of length 1.")
if (length(input_dir) > 1) stop("`input_dir` must be a character vector of length 1.")
input_dir <- correct_paths(input_dir)
if (!dir.exists(input_dir)) {
stop("`input_dir` must be a valid directory.")
}
# tcr_chain
tcr_chain <- match.arg(tcr_chain, c("auto", "A", "B", "G", "D"))
# replace
if (!is.logical(replace)) stop("`replace` must be logical.")
# string_only
if (!is.logical(string_only)) stop("`string_only` must be logical.")
if (string_only == TRUE) message("string_only is ON. Commands will not be executed.")
# lists all files '.fatsq.gz' in directory 'input_dir' and all the sub-directories
files_fastq.gz <- list.files(
path = input_dir, recursive = TRUE,
full.names = TRUE, pattern = ".fastq.gz"
) %>%
.[substr(., nchar(.) - 8, nchar(.)) == ".fastq.gz"] %>%
.[grep("_R1_", .)] %>%
gsub("//", "/", .) %>%
unique()
# execute all commands for each file
command_txt <- character(0)
for (f in 1:length(files_fastq.gz)) {
# erase file extension
input_filename <- basename(files_fastq.gz[f]) %>%
gsub(".fastq.gz", "", .)
# determine the folder of this specific file
input_dir_file <- paste0(dirname(files_fastq.gz[f]), "/")
input_parentdir_file <- paste0(dirname(input_dir_file), "/")
message(paste0(
"Analyse file (", f, "/", length(files_fastq.gz), ") : ",
paste0(input_filename, ".fastq.gz")
))
# guests the Tcell type from filename
short_input_filename <- substr(
input_filename, 1,
gregexpr("-", input_filename)[[1]][2] + 1
)
if (tcr_chain == "auto") {
tcr_chain <- toupper(substr(
short_input_filename,
nchar(short_input_filename),
nchar(short_input_filename)
))
if (!tcr_chain %in% c("A", "B", "G", "D")) {
stop(
"Unable to autodetect Tcell type for file ",
input_filename, "."
)
}
}
# the functions return the name of the output file
# (or the command in string when string_only=TRUE)
# command_txt is used to store all the commands in a vector
# execute the command `align -OvParameters.geneFeatureToAlign=VTranscript`
lastreturned_value <- align_fastq_to_vdjca(
java_param = java_param, path_mixcr = path_mixcr,
input_dir = input_dir_file, input_filename = input_filename,
# report_name="alignmentReport",
replace = replace, string_only = string_only, ...
)
command_txt <- c(command_txt, lastreturned_value)
# execute the command `assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10`
lastreturned_value <- assemble_vdjca_to_clns(
java_param = java_param, path_mixcr = path_mixcr,
input_dir = input_dir_file, input_filename = basename(lastreturned_value),
output_filename = short_input_filename,
replace = replace, string_only = string_only, ...
)
command_txt <- c(command_txt, lastreturned_value)
# execute the command `exportClones TR` & tcr_chain
lastreturned_value <- export_clones(
java_param = java_param, path_mixcr = path_mixcr,
input_dir = input_dir_file, input_filename = basename(lastreturned_value),
# output_dir = input_parentdir_file,
output_filename = paste0(short_input_filename, "_clonesMin10)"),
tcr_chain = tcr_chain,
replace = replace, string_only = string_only, ...
)
command_txt <- c(command_txt, lastreturned_value)
command_txt <- c(command_txt, "")
}
# endtime
message(paste0("Done in ", round((proc.time() - starttime)[[3]], 2), " seconds"))
if (string_only == TRUE) return(noquote(command_txt))
invisible()
}
#' @title align_fastq_to_vdjca
#' @description execute the command : 'align -OvParameters.geneFeatureToAlign=VTranscript
# --report alignmentReport.log input_R1.fastq input_R2.fastq alignments.vdjca'
#' @param java_param a character string containing java parameters
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (type R1.fastq.gz), (with or without the extension)
#' @param report_name the name of the file alignmentReport. (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @return run command line in console. Creates .vdjca files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.com>
#' @importFrom magrittr %>%
#' @export
align_fastq_to_vdjca <- function(java_param="java -Xmx4g -Xms3g -jar",
path_mixcr,
input_dir,
input_filename,
output_filename="auto",
report_name="alignmentReport",
replace=FALSE,
string_only=FALSE) {
# TEST : java_param <- "java -Xmx4g -Xms3g -jar" ; path_mixcr <- "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar"
# input_dir <- 'D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/'
# input_filename <- "70-SR13-Gamma_S70_L001_R1_001"
# report_name <- "alignmentReport" ; replace <- FALSE ; string_only <- TRUE
# check args
{
# input_dir
if (!is.character(input_dir)) stop("`input_dir` must be a character vector of length 1.")
if (length(input_dir) > 1) stop("`input_dir` must be a character vector of length 1.")
input_dir <- correct_paths(input_dir)
if (!dir.exists(input_dir)) {
stop("`input_dir` must be a valid directory.")
}
# input_filename
if (!is.character(input_filename)) stop("`input_filename` must be a character vector of length 1.")
if (length(input_filename) > 1) stop("`input_filename` must be a character vector of length 1.")
input_filename <- correct_paths(input_filename)
input_filename <- gsub(".fastq.gz", "", input_filename) # erase file extension
if (!file.exists(paste0(input_dir, input_filename, ".fastq.gz"))) {
stop("`input_filename` must be a valid file in `input_dir` directory.")
}
}
# end check args
input_ext <- ".fastq.gz"
output_ext <- ".vdjca"
# From input_filename
# check if there are 2 files R1,R2
# define the name of the output file
input_1 <- paste0(gsub("_R2_", "_R1_", input_filename), input_ext)
if (!file.exists(paste0(input_dir, input_1))) {
stop(
input_dir, " doesn't contains an R1 file. \n",
"Expected file: ", input_1
)
}
input_2 <- paste0(gsub("_R1_", "_R2_", input_filename), input_ext)
if (!file.exists(paste0(input_dir, input_1))) {
warning(
input_dir, " doesn't contains an R2 file. \n",
"The analyse is done only with the R1 file. \n",
"Expected file: ", input_2
)
input_2 <- ""
if (output_filename == "auto") output_filename <- gsub("_R2_", "_R1_", input_filename)
} else {
if (output_filename == "auto") {
output_filename <- gsub("_R2_", "_R1R2_", input_filename) %>%
gsub("_R1_", "_R1R2_", .)
}
}
# merge the R1 & R2 input files
input_filename <- paste(input_1, input_2, collapse = " ")
run_command_vdj(
java_param = java_param,
path_vdjtools = "",
path_mixcr = path_mixcr,
input_dir = input_dir,
input_filename = input_filename,
input_ext = ".fastq.gz",
check_input_filename = FALSE,
output_filename = output_filename,
output_ext = ".vdjca",
command_vdj = "align -OvParameters.geneFeatureToAlign=VTranscript",
report_name = report_name,
replace = replace,
fullpath = FALSE,
string_only = string_only
)
}
#' @title assemble_vdjca_to_clns
#' @description execute the command : 'assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10
# --report assembleReport.log alignments.vdjca clones.clns'
#' @param java_param a character string containing java parameters
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (type .vdjca), (with or without the extension)
#' @param output_filename the name of the output file (without extension)
#' @param report_name the name of the file assembleReport (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @return run command line in console. Creates .clns files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.be>
#' @export
assemble_vdjca_to_clns <- function(java_param="java -Xmx4g -Xms3g -jar",
path_mixcr,
input_dir,
input_filename,
output_filename,
report_name="assembleReport",
replace=FALSE,
string_only=FALSE) {
# TO DO add Tcells_type ----
# to choose between Min10 or regular
# check if result is different when no need Min10
run_command_vdj(
java_param = java_param,
path_vdjtools = "",
path_mixcr = path_mixcr,
input_dir = input_dir,
input_filename = input_filename,
input_ext = ".vdjca",
output_filename = output_filename,
output_ext = ".clns",
command_vdj = "assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10",
report_name = report_name,
replace = replace,
fullpath = FALSE,
string_only = string_only
)
}
#' @title export_clones
#' @description execute the command : 'assemble -OcloneFactoryParameters.dParameters.absoluteMinScore=10
# --report assembleReport.log alignments.vdjca clones.clns'
#' @param java_param a character string containing java parameters
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (type .vdjca), (with or without the extension)
#' @param output_filename the name of the output file (without extension)
#' @param report_name the name of the file assembleReport (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @return run command line in console. Creates .clns files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.be>
#' @export
export_clones <- function(java_param="java -Xmx4g -Xms3g -jar",
path_mixcr,
input_dir,
input_filename,
output_filename,
tcr_chain="auto",
report_name="",
replace=FALSE,
string_only=FALSE) {
# #java -Xmx4g -Xms3g -jar path\mixcr.jar exportClones --chains TRG clones.clns TRGclones.txt
# #print("Cmd exportClones TRD/G")
# if ( !(file.exists(paste0(input_parentdir,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),"_clonesMin10.txt")) & replace_if_existing==FALSE) ) {
# # system(paste(java.param,path_mixcr, paste0("exportClones --chains TR",toupper(substr(input_filename,Length_id,Length_id))),
# # string_f, paste0(input_parentdir,substr(input_filename,1,Length_id),"_clones.clns"),
# # paste0(input_parentdir,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),"_clones.txt")))
# system(paste(java.param,path_mixcr,
# paste0("exportClones --chains TR",toupper(substr(input_filename,Length_id,Length_id))),
# string_f,
# paste0('"',input_dir,substr(input_filename,1,Length_id),'_clonesMin10.clns"'),
#
# paste0('"',input_parentdir,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),'_clonesMin10.txt"')))
# } else message(paste0("File '",paste0(path,substr(input_filename,1,Length_id),"_TR",toupper(substr(input_filename,Length_id,Length_id)),"_clonesMin10.txt"),"' already exists"))
#
# tcr_chain
tcr_chain <- match.arg(tcr_chain, c("auto", "A", "B", "G", "D"))
run_command_vdj(
java_param = java_param,
path_vdjtools = "",
path_mixcr = path_mixcr,
input_dir = input_dir,
input_filename = input_filename,
input_ext = ".clns",
output_filename = output_filename,
output_ext = ".txt",
command_vdj = paste0("exportClones --chains TR", tcr_chain, " "),
report_name = report_name,
replace = replace,
fullpath = FALSE,
string_only = string_only
)
}
#' @title run_command_vdj
#' @description execute a command in the windows console.
#' @param java_param a character string containing java parameters
#' @param path_vdjtools the path to vdjtools.jar
#' @param path_mixcr the path to mixcr.jar
#' @param input_dir where the files are
#' @param input_filename file name (without the extension). If empty, loads all files in `input_dir`
#' @param input_ext the extension of the `input_filename` (e.g. `.vdjca`)
#' @param output_dir where the output files will be. If empty, the default value is the same as `input_dir`.
#' Warning: It's not always possible to choose the `output_dir` in mixcr/vdjtools.
#' Warning: You 'll need probably to set fullpath=TRUE.
#' @param output_filename the name of the output file (without extension)
#' @param output_ext the extension of the `output_filename` (e.g. `.txt`)
#' @param command_vdj the command to run
#' @param report_name the name of the file assembleReport (without the extension)
#' Set to NULL to not create the file.
#' @param replace if TRUE, if the output file already exists, it will be replaced.
#' @param fullpath if TRUE, the fullpath of `input_filename` and `output_filename` will be written in command.
#' @param string_only if TRUE, don't execute the command but returns it in a string
#' @details execute a command in the windows console.
#' The scruture follows the order:
#' java_param + path_vdjtools + path_mixcr + report_name +
#' command_vdj + input_filename + output_filename
#' if an argument is NULL, it will be ignored
#' @return run command line in console. Creates .clns files
#' in the same directory than the fastq.gz files
#' Returns the name of the outputfile if string_only=FALSE
#' Returns command if string_only=TRUE
#' @author DEBOT Damien <damien.debot@@gmail.be>
#' @importFrom magrittr %>%
#' @export
run_command_vdj <- function(java_param="java -Xmx4g -Xms3g -jar",
path_vdjtools="",
path_mixcr="",
input_dir,
input_filename="auto",
input_ext,
check_input_filename=TRUE,
output_dir,
output_filename="auto",
output_ext,
command_vdj,
report_name="",
replace=FALSE,
fullpath = TRUE,
string_only=FALSE,
...) {
# TEST : java_param <- "java -Xmx4g -Xms3g -jar" ; path_mixcr <- "D:/Maria/Maria_Analysis/mixcr-2.1.7/mixcr.jar"
# input_dir <- 'D:/Projets R/IMIabgd/data/Gamma_SR11-20/70-SR13-Gamma_S70-6542654654221/'
# input_filename <- "70-SR13-Gamma_S70_L001_R1R2_001"
# report_name <- "assembleReport" ; replace <- FALSE ; string_only <- FALSE
# checks args ----
# java_param
if (!is.character(java_param)) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
if (length(java_param) > 1) {
stop(
"`java_param` must be a character vector of length 1.",
"e.g. `java -Xmx4g -Xms3g -jar`"
)
}
# path_vdjtools
if (path_vdjtools != "") path_vdjtools <- check_path_program(path_vdjtools, program = "vdjtools")
# path_mixcr
if (path_mixcr != "") path_mixcr <- check_path_program(path_mixcr, program = "mixcr")
# input_dir
if (!is.character(input_dir)) stop("`input_dir` must be a character vector of length 1.")
if (length(input_filename) > 1 & length(input_dir) != length(input_filename)) {
stop(
"`input_dir` must be a character vector of length 1 or equal to length of input_filename.", "\n",
"Length of `input_dir`: ", length(input_dir), "\n",
"Length of `input_filename`: ", length(input_filename)
)
}
input_dir <- correct_paths(input_dir)
if (any(!dir.exists(input_dir))) {
stop(
"`input_dir` must be a valid directory.", "\n",
"Invalid: ", "\n",
paste(input_dir[!dir.exists(input_dir)], collapse = "\n")
)
}
# check_input_filename
if (!is.logical(check_input_filename)) stop("`check_input_filename` must be TRUE or FALSE")
# input_ext
if (missing(input_ext)) {
stop("`input_ext` is missing.")
}
if (!is.character(input_ext)) {
stop("`input_ext` must be a character vector of length 1, starting with a dot.")
}
if (nchar(input_ext) == 0) {
stop("`input_ext` must be a non-empty character vector of length 1, starting with a dot.")
}
if (substr(input_ext, 1, 1) != ".") {
stop(
"`input_ext` must be a character vector of length 1, starting with a dot.", "\n",
"Did you mean: `.", input_ext, "` ?"
)
}
# input_filename
if (!is.character(input_filename)) stop("`input_filename` must be a character vector.")
# if (length(input_filename) > 1) stop("`input_filename` must be a character vector.")
if (all(input_filename %in% c("", "auto"))) {
input_filename <- list.files(
path = input_dir, recursive = TRUE,
full.names = TRUE, pattern = input_ext
) %>%
.[substr(., nchar(.) - nchar(input_ext) + 1, nchar(.)) == input_ext] %>%
gsub("//", "/", .) %>%
unique()
# input_dir for each file
input_dir <- paste0(dirname(input_filename), "/")
input_filename <- basename(input_filename)
}
input_filename <- correct_paths(input_filename)
if (check_input_filename == TRUE) input_filename <- gsub(input_ext, "", input_filename) # erase file extension
if (any(!file.exists(paste0(input_dir, input_filename, input_ext)) & check_input_filename == TRUE)) {
stop(
"`input_filename`+`input_ext` must be a valid file in `input_dir` directory.", "\n",
"Your file: ", input_filename, input_ext, " doesn't exist in ", input_dir, "."
)
}
# outputfilename
if (all(output_filename == "auto")) {
if (any(is.na(gregexpr("-", input_filename)[[1]][2]))) {
stop(
"`output_filename` can't be determined automatically because ",
"at least one of the files doensn't contain `-` in his title.", "\n",
"Your file(s): ", "\n", paste(paste0(input_filename, input_ext), collapse = "\n")
)
} else {
output_filename <- substr(input_filename, 1, gregexpr("-", input_filename)[[1]][2] + 1)
}
}
if (length(output_filename) == 1 & length(input_filename) > 1) {
output_filename <- rep(output_filename, length(input_filename))
}
if (length(output_filename) != length(input_filename)) {
stop("`output_ext` must be a character vector with the same length than `input_filename`.")
}
# output_ext
if (!is.character(output_ext)) {
stop("`output_ext` must be a character vector of length 1, starting with a dot.")
}
if (any(nchar(output_ext) == 0 & nchar(output_filename) > 0)) {
stop("`output_ext` can't be empty if `output_filename` isn't also empty.")
}
if (nchar(output_ext) > 0 && substr(output_ext, 1, 1) != ".") {
stop(
"`output_ext` must be a character vector of length 1, starting with a dot.", "\n",
"Did you mean: `.", output_ext, "` ?"
)
}
# output_dir
if (base::missing(output_dir)) output_dir <- input_dir
if (!is.character(output_dir)) {
stop("`output_dir` must be a character vector of length 1 or same length than `output_filename`")
}
if (length(output_filename) > 1 & length(output_dir) != length(output_filename)) {
stop(
"`output_dir` must be a character vector of length 1 or equal to length of output_filename", "\n",
"Length of `output_dir`: ", length(output_dir), "\n",
"Length of `output_filename`: ", length(output_filename)
)
}
output_dir <- correct_paths(output_dir)
if (any(!dir.exists(output_dir))) {
stop(
"`output_dir` must be a valid directory.", "\n",
"Invalid: ", "\n",
paste(output_dir[!dir.exists(output_dir)], collapse = "\n")
)
}
# command_vdj
if (!is.character(command_vdj)) {
stop("`command_vdj` must be a character vector of length 1.")
}
# report_name
if (!is.character(report_name)) {
stop("`report_name` must be a character vector of length 1 or NULL.")
}
report_name <- gsub(".log", "", report_name) # erase file extension
# replace
if (!is.logical(replace)) stop("`replace` must be logical.")
# string_only
if (!is.logical(string_only)) stop("`string_only` must be logical.")
# ...
if (any(names(list(...)) %in% "tcr_chain")) {
# tcr_chain
tcr_chain <- match.arg(list(...)$tcr_chain, c("auto", "A", "B", "G", "D"))
if (tcr_chain == "auto") {
tcr_chain <- toupper(substr(
input_filename,
nchar(input_filename),
nchar(input_filename)
))
if (!tcr_chain %in% c("A", "B", "G", "D")) {
stop(
"Unable to autodetect Tcell type for file ",
input_filename, "."
)
}
command_vdj <- gsub("auto", tcr_chain, command_vdj)
}
}
# end checks args
# create command ----
command_request <- character(0)
for (i in 1:length(input_filename)) {
# write the command(s)
command_request <- c(command_request, paste(
java_param, # e.g. 'java -Xmx4g -Xms3g -jar'
if (path_vdjtools!="") {
paste0("\"", path_vdjtools,"\"")
} else path_vdjtools,
if (path_mixcr!="") {
paste0("\"", path_mixcr,"\"")
} else path_mixcr,
command_vdj,
if (report_name == "") {
report_name
} else {
paste0("--report ", report_name, ".log") # e.g. '--report alignmentReport.log'
},
if (replace == TRUE) "-f" else "", # e.g. '-f'
# TO DO ----
# if fullpath, must be between double quotes
# ok to keep space
paste0( # e.g. 'input_filename.vdjca'
if (fullpath == TRUE & check_input_filename == TRUE) paste0("\"", input_dir[i]) else "",
input_filename[i],
if (check_input_filename == TRUE) input_ext else "",
if (fullpath == TRUE & check_input_filename == TRUE) "\"" else ""
),
paste0(
"\"", if (fullpath == TRUE) output_dir[i] else "",
output_filename[i], output_ext
), # e.g. 'output_file.clns
"\"",
sep = " "
))
}
if (string_only == TRUE) return(noquote(command_request))
# execute the command in the console ----
# but only if replace = TRUE or the output file doesn't exist yet
for (i in 1:length(input_filename)) {
if (length(input_filename) > 1) {
message(paste0(
"Processing file (", i, "/", length(input_filename), ") : ",
paste0(input_filename[i], input_ext)
))
}
if (!(file.exists(paste0(output_dir[i], output_filename[i], output_ext)) & replace == FALSE)) {
inital_wd <- getwd()
setwd(input_dir[i]) # R active directory -> set cd in console
# execute command
# status: 0 = success / 1 = error => replaced by the error message
status <- suppressMessages(suppressWarnings(tryCatch(system(command_request[i], intern = TRUE),
warning = function(w) list(
rvalue = system(command_request[i], intern = TRUE),
warn = conditionMessage(w)
),
error = function(e) list(
rvalue = system(command_request[i], intern = TRUE),
err = conditionMessage(e)
)
)))
setwd(inital_wd)
if (is.list(status) && attributes(status[[1]])$status != 0) {
stop(
"Your command line ended with an error.", "\n",
"The reason might be that:", "\n",
" - the command does not exist or contains an error ", "\n",
" - a required argument is missing or incorrect ", "\n",
" - the `fullpath` argument should be different (now: ", !fullpath, ").", "\n", "\n",
status[[2]], "\n",
status[[1]]
)
} else {
cat(paste0(paste(status, collapse = "\n"), "\n"))
}
# check that the file is created
if (!file.exists(paste0(output_dir[i], output_filename[i], output_ext))) {
warning("Output file: `", paste0(output_dir[i], output_filename[i], output_ext), "` not found.")
}
} else {
message(paste0("File '", paste0(output_dir[i], output_filename[i], output_ext),
"' already exists and is not replaced."))
}
}
# return names of created files
paste0(input_dir, output_filename, output_ext)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.