Nothing
R/InputChecks.R
In MACPET: Model based analysis for paired-end data
Defines functions
Break_output_fun
Input_check_S4_fun
Input_check_S3_fun
Input_check_S2_fun
Input_check_S1_fun
Input_check_S0_fun
Input_check_SA_fun
InputCheckMACPETUlt
#' @importFrom stats p.adjust.methods
#' @importFrom methods is
#' @importFrom ShortRead countLines
#' @importFrom futile.logger flog.appender flog.layout layout.format appender.tee flog.info flog.warn
#------------------------------------
# input check for MACPETUlt.R
#------------------------------------
# main function for checking the inputs:
InputCheckMACPETUlt = function(InArg) {
LogFile = list() #for the log file.
LogFile[1] = "|%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%|"
LogFile[2] = "|-------------MACPET analysis input checking------------|"
LogFile[3] = "|%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%|"
#------------------------------------
# all stages input:
#------------------------------------
Input_check_SA_fun(InArg = InArg)
LogFile[4] = "Common stage inputs...OK"
LogFile[5] = paste("Stages to run: ", paste((InArg$SA_stages), collapse = "-"),
sep = "")
# write in log and print:
for (lf in seq_len(5)) futile.logger::flog.info(LogFile[[lf]], name = "SA_LogFile",
capture = FALSE)
#------------------------------------
# 0 stage input:
#------------------------------------
if (c(0) %in% InArg$SA_stages) {
InArg = Input_check_S0_fun(InArg)
}
#------------------------------------
# 1 stage input:
#------------------------------------
if (c(1) %in% InArg$SA_stages) {
InArg = Input_check_S1_fun(InArg)
}
#------------------------------------
# 2 stage input:
#------------------------------------
if (c(2) %in% InArg$SA_stages) {
InArg = Input_check_S2_fun(InArg)
}
#------------------------------------
# 3 stage input:
#------------------------------------
if (c(3) %in% InArg$SA_stages) {
InArg = Input_check_S3_fun(InArg)
}
#------------------------------------
# 4 stage input:
#------------------------------------
if (c(4) %in% InArg$SA_stages) {
InArg = Input_check_S4_fun(InArg)
}
#--------------------------
# Break output:
#--------------------------
InArg = Break_output_fun(InArg = InArg)
#--------------------------
# Finallize
#--------------------------
futile.logger::flog.info("All inputs correct! Starting MACPET analysis...", name = "SA_LogFile",
capture = FALSE)
return(InArg)
}
# Done
#---------------------
#---------------------
# function for checking inputs for stage SA
Input_check_SA_fun = function(InArg) {
#------------
# check directory:
#------------
if (!methods::is(InArg$SA_AnalysisDir, "character")) {
stop("SA_AnalysisDir:", InArg$SA_AnalysisDir, " is not a directory!", call. = FALSE)
} else if (!dir.exists(InArg$SA_AnalysisDir)) {
stop("SA_AnalysisDir:", InArg$SA_AnalysisDir, " directory does not exist!",
call. = FALSE)
}
#------------
# check stages:
#------------
if (!methods::is(InArg$SA_stages, "numeric")) {
stop("SA_stages: ", InArg$SA_stages, " variable has to be a numeric or numeric vector!",
call. = FALSE)
} else if (any(!InArg$SA_stages %in% c(0, 1, 2, 3, 4))) {
stop("SA_stages: ", InArg$SA_stages, " variable has to be a numeric or numeric vector with values c(0,1,2,3,4)!",
call. = FALSE)
} else {
stageseq = seq(from = min(InArg$SA_stages), to = max(InArg$SA_stages))
if (any(!stageseq %in% InArg$SA_stages)) {
stop("SA_stages: ", InArg$SA_stages, " cannot have skipped intermediate stages!",
call. = FALSE)
}
}
#------------
# check prefix:
#------------
if (!methods::is(InArg$SA_prefix, "character")) {
stop("SA_prefix: ", InArg$SA_prefix, " variable has to be a string!", call. = FALSE)
} else if (nchar(InArg$SA_prefix) == 0) {
stop("SA_prefix: ", InArg$SA_prefix, " variable has to be a non-empty string!",
call. = FALSE)
}
#------------
# create log file
#------------
SA_LogFile.dir = file.path(InArg$SA_AnalysisDir, paste(InArg$SA_prefix, "_analysis.log",
sep = ""))
if (file.exists(SA_LogFile.dir))
unlink(SA_LogFile.dir, recursive = TRUE, force = TRUE)
# create the log file:
futile.logger::flog.appender(futile.logger::appender.tee(SA_LogFile.dir), "SA_LogFile")
futile.logger::flog.layout(futile.logger::layout.format("~m"), name = "SA_LogFile")
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S0- fastq split
Input_check_S0_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 0 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check fastq files:
#------------
# 1:
if (!methods::is(InArg$S0_fastq1, "character")) {
stop("S0_fastq1: ", InArg$S0_fastq1, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S0_fastq1)) {
stop("S0_fastq1: ", InArg$S0_fastq1, " file does not exist!", call. = FALSE)
} else {
fastq1 = basename(InArg$S0_fastq1)
if (!grepl(".fastq.gz", fastq1) & !grepl(".fastq", fastq1)) {
stop("S0_fastq1: ", InArg$S0_fastq1, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
# 2:
if (!methods::is(InArg$S0_fastq2, "character")) {
stop("S0_fastq2: ", InArg$S0_fastq2, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S0_fastq2)) {
stop("S0_fastq2: ", InArg$S0_fastq2, " file does not exist!", call. = FALSE)
} else {
fastq2 = basename(InArg$S0_fastq2)
if (!grepl(".fastq.gz", fastq2) & !grepl(".fastq", fastq2)) {
stop("S0_fastq2: ", InArg$S0_fastq2, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
#----------------
# preliminary fastq check:
#----------------
cat("Preliminary fastq checking...")
# count fast1 lines:
Lines_fastq = ShortRead::countLines(dirPath = c(InArg$S0_fastq1, InArg$S0_fastq2))
if (Lines_fastq[[1]] != Lines_fastq[[2]]) {
stop("S0_fastq1: ", InArg$S0_fastq1, " and S0_fastq2: ", InArg$S0_fastq2,
" files are not of same length.", call. = FALSE)
}
cat("OK\n")
S0_Totfastqreads = Lines_fastq[[1]]/4 #four lines per entry
# new variable to use in stage 0:
InArg$S0_Totfastqreads = S0_Totfastqreads
#----------------
# check linkers
#----------------
if (!methods::is(InArg$S0_LinkerA, "character")) {
stop("S0_LinkerA: ", InArg$S0_LinkerA, " has to be a string!", call. = FALSE)
} else if (nchar(InArg$S0_LinkerA) == 0) {
stop("S0_LinkerA: ", InArg$S0_LinkerA, " has to be a non-empty string!",
call. = FALSE)
}
futile.logger::flog.info(paste("Linker A sequence chosen:", InArg$S0_LinkerA),
name = "SA_LogFile", capture = FALSE)
if (!methods::is(InArg$S0_LinkerB, "character")) {
stop("S0_LinkerB: ", InArg$S0_LinkerB, " has to be a string!", call. = FALSE)
} else if (nchar(InArg$S0_LinkerB) == 0) {
stop("S0_LinkerB: ", InArg$S0_LinkerB, " has to be a non-empty string!",
call. = FALSE)
}
futile.logger::flog.info(paste("Linker B sequence chosen:", InArg$S0_LinkerB),
name = "SA_LogFile", capture = FALSE)
# linker match:
if (nchar(InArg$S0_LinkerA) != nchar(InArg$S0_LinkerB)) {
LogFile = paste("WARNING: S0_LinkerA:", InArg$S0_LinkerA, "and S0_LinkerB:",
InArg$S0_LinkerB, " lengths do not match.")
futile.logger::flog.warn(LogFile, name = "SA_LogFile", capture = FALSE)
}
#----------------
# check S0_LinkerOccurence:
#----------------
if (!methods::is(InArg$S0_LinkerOccurence, "numeric")) {
stop("S0_LinkerOccurence: ", InArg$S0_LinkerOccurence, " has to be an integer!",
call. = FALSE)
} else if (!InArg$S0_LinkerOccurence %in% c(0, 1, 2, 3, 4)) {
stop("S0_LinkerOccurence: ", InArg$S0_LinkerOccurence, " has to be one of 0, 1, 2, 3, 4!",
call. = FALSE)
}
if (InArg$S0_LinkerOccurence == 0) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with any read with no linker will be moved to ambiguous class.")
} else if (InArg$S0_LinkerOccurence == 1) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with left read with no linker, but right read with linker, will be moved to usable class.")
} else if (InArg$S0_LinkerOccurence == 2) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with right read with no linker, but left read with linker, will be moved to usable class.")
} else if (InArg$S0_LinkerOccurence == 3) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with any or both reads without linkers, will be moved to usable class.")
} else if (InArg$S0_LinkerOccurence == 4) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with both reads without linkers, will be moved to usable class.")
}
futile.logger::flog.info(LogFile, name = "SA_LogFile", capture = FALSE)
#----------------
# check lengths
#----------------
if (!methods::is(InArg$S0_MinReadLength, "numeric")) {
stop("S0_MinReadLength: ", InArg$S0_MinReadLength, " has to be an integer!",
call. = FALSE)
} else if (InArg$S0_MinReadLength < 0) {
stop("S0_MinReadLength: ", InArg$S0_MinReadLength, " has to be >=0!", call. = FALSE)
} else {
InArg$S0_MinReadLength = ceiling(InArg$S0_MinReadLength)
}
if (!methods::is(InArg$S0_MaxReadLength, "numeric")) {
stop("S0_MaxReadLength: ", InArg$S0_MaxReadLength, " has to be an integer!",
call. = FALSE)
} else if (InArg$S0_MaxReadLength < 0) {
stop("S0_MaxReadLength: ", InArg$S0_MaxReadLength, " has to be >=0!", call. = FALSE)
} else {
InArg$S0_MaxReadLength = ceiling(InArg$S0_MaxReadLength)
}
if (InArg$S0_MinReadLength >= InArg$S0_MaxReadLength) {
stop("S0_MinReadLength: ", InArg$S0_MinReadLength, " has to be < S0_MaxReadLength: ",
InArg$S0_MaxReadLength, " !", call. = FALSE)
}
futile.logger::flog.info(paste("Maximum read length after linker trimming:",
InArg$S0_MaxReadLength), name = "SA_LogFile", capture = FALSE)
futile.logger::flog.info(paste("Minimum read length after linker trimming:",
InArg$S0_MinReadLength), name = "SA_LogFile", capture = FALSE)
#----------------
# checkimage and fastqStream:
#----------------
if (!methods::is(InArg$S0_image, "logical")) {
stop("S0_image ", InArg$S0_image, " has to be logical!", call. = FALSE)
} else if (InArg$S0_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S0_image==TRUE. Please install it.", call. = FALSE)
}
}
if (!methods::is(InArg$S0_fastqStream, "numeric")) {
stop("S0_fastqStream: ", InArg$S0_fastqStream, " has to be a numeric!", call. = FALSE)
} else if (InArg$S0_fastqStream <= 0) {
stop("S0_fastqStream: ", InArg$S0_fastqStream, " has to be a positive numeric!",
call. = FALSE)
} else {
InArg$S0_fastqStream = ceiling(InArg$S0_fastqStream)
}
futile.logger::flog.info("Correct Stage 0 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 0:
#------------
# new variable for stage 0:
InArg$S0_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S0_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S1- mapping and paired-end bam creation
Input_check_S1_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 1 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the logical:
#------------
if (!methods::is(InArg$S1_image, "logical")) {
stop("S1_image: ", InArg$S1_image, " has to be logical!", call. = FALSE)
} else if (InArg$S1_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S1_image==TRUE. Please install it.", call. = FALSE)
}
}
if (!methods::is(InArg$S1_RbowtieIndexBuild, "logical")) {
stop("S1_RbowtieIndexBuild: ", InArg$S1_RbowtieIndexBuild, " has to be logical!",
call. = FALSE)
}
futile.logger::flog.info(paste("Building bowtie index?", InArg$S1_RbowtieIndexBuild),
name = "SA_LogFile", capture = FALSE)
if (!methods::is(InArg$S1_makeSam, "logical")) {
stop("S1_makeSam: ", InArg$S1_makeSam, " has to be logical!", call. = FALSE)
}
#------------
# check S1_BAMStream:
#------------
if (!methods::is(InArg$S1_BAMStream, "numeric")) {
stop("S1_BAMStream: ", InArg$S1_BAMStream, " has to be a numeric!", call. = FALSE)
} else if (InArg$S1_BAMStream <= 0) {
stop("S1_BAMStream: ", InArg$S1_BAMStream, " has to be a positive numeric!",
call. = FALSE)
} else {
InArg$S1_BAMStream = ceiling(InArg$S1_BAMStream)
}
#------------
# check S1_genome:
#------------
if (!methods::is(InArg$S1_genome, "character")) {
stop("S1_genome: ", InArg$S1_genome, " has to be a character!", call. = FALSE)
} else if (!InArg$S1_genome %in% names(sysdata)) {
LogFile = paste("WARNING: S1_genome: ", InArg$S1_genome, ", is not a part of ",
paste(names(sysdata), collapse = "/"), ". If S2_BlackList==TRUE, then no black-listed regions will be removed from the data.",
sep = "")
futile.logger::flog.warn(LogFile, name = "SA_LogFile", capture = FALSE)
}
futile.logger::flog.info(paste("Genome chosen:", InArg$S1_genome), name = "SA_LogFile",
capture = FALSE)
#------------
# check S1_RbowtieIndexPrefix:
#------------
if (!methods::is(InArg$S1_RbowtieIndexPrefix, "character")) {
stop("S1_RbowtieIndexPrefix: ", InArg$S1_RbowtieIndexPrefix, " has to be a string!",
call. = FALSE)
} else if (nchar(InArg$S1_RbowtieIndexPrefix) == 0) {
stop("S1_RbowtieIndexPrefix: ", InArg$S1_RbowtieIndexPrefix, " has to be a non-empty string!",
call. = FALSE)
}
#------------
# check S1_RbowtieIndexDir:
#------------
if (!InArg$S1_RbowtieIndexBuild) {
# if the bowtie index is built already:
if (!methods::is(InArg$S1_RbowtieIndexDir, "character")) {
stop("S1_RbowtieIndexDir: ", InArg$S1_RbowtieIndexDir, " variable has to be a directory!",
call. = FALSE)
} else if (!dir.exists(InArg$S1_RbowtieIndexDir)) {
stop("S1_RbowtieIndexDir: ", InArg$S1_RbowtieIndexDir, " directory does not exist!",
call. = FALSE)
}
# check the directory files:
BowtieIndexes = file.path(InArg$S1_RbowtieIndexDir, InArg$S1_RbowtieIndexPrefix)
BowtieIndexes = paste(BowtieIndexes, c(".1.ebwt", ".1.ebwtl", ".2.ebwt",
".2.ebwtl", ".3.ebwt", ".3.ebwtl", ".4.ebwt", ".4.ebwtl", ".rev.1.ebwt",
".rev.1.ebwtl", ".rev.2.ebwt", ".rev.2.ebwtl"), sep = "")
for (i in seq_len(length(BowtieIndexes)/2)) {
if (!file.exists(BowtieIndexes[i]) && !file.exists(BowtieIndexes[i +
1])) {
stop(basename(BowtieIndexes[i]), " or ", basename(BowtieIndexes[i +
1]), " files are missing from S1_RbowtieIndexDir or the S1_RbowtieIndexPrefix is wrong!",
call. = FALSE)
}
}
} else {
# you will build the index, check the fasta files
#------------
# check S1_RbowtieRefDir:
#------------
if (!methods::is(InArg$S1_RbowtieRefDir, "character")) {
stop("S1_RbowtieRefDir: ", InArg$S1_RbowtieRefDir, " has to be a character vector with the paths of the .fa files for building the bowtie index!",
call. = FALSE)
} else if (any(!file.exists(InArg$S1_RbowtieRefDir))) {
Famissing = which(!file.exists(InArg$S1_RbowtieRefDir))
Famissing = InArg$S1_RbowtieRefDir[Famissing]
Famissing = paste(basename(Famissing), collapse = "/")
stop("S1_RbowtieRefDir contains the following missing .fa files: ", Famissing,
call. = FALSE)
}
# give the S1_RbowtieIndexDir, where to save the index:
InArg$S1_RbowtieIndexDir = file.path(InArg$SA_AnalysisDir, "S1_results",
"BowtieIndex")
}
#------------
# check S1_fastq1_usable_dir and S1_fastq2_usable_dir:
#------------
if (!c(0) %in% InArg$SA_stages) {
# then the fastq files are given as input so they have to be checked: 1:
if (!methods::is(InArg$S1_fastq1_usable_dir, "character")) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S1_fastq1_usable_dir)) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " file does not exist!",
call. = FALSE)
} else {
fastq1 = basename(InArg$S1_fastq1_usable_dir)
if (all(!grepl("fastq.gz", fastq1) || !grepl("fastq", fastq1))) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
# 2:
if (!methods::is(InArg$S1_fastq2_usable_dir, "character")) {
stop("S1_fastq2_usable_dir: ", InArg$S1_fastq2_usable_dir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S1_fastq2_usable_dir)) {
stop("S1_fastq2_usable_dir: ", InArg$S1_fastq2_usable_dir, " file does not exist!",
call. = FALSE)
} else {
fastq2 = basename(InArg$S1_fastq2_usable_dir)
if (all(!grepl("fastq.gz", fastq2) || !grepl("fastq", fastq2))) {
stop("S1_fastq2_usable_dir: ", InArg$S1_fastq2_usable_dir, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
#----------------
# preliminary fastq check:
#----------------
cat("Preliminary fastq checking...")
# count fast1 lines:
Lines_fastq = ShortRead::countLines(dirPath = c(InArg$S1_fastq1_usable_dir,
InArg$S1_fastq2_usable_dir))
if (Lines_fastq[[1]] != Lines_fastq[[2]]) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " and S1_fastq2_usable_dir: ",
InArg$S1_fastq2_usable_dir, " files are not of same length.", call. = FALSE)
}
cat("OK\n")
Totfastqreads = Lines_fastq[[1]]/4 #four lines per entry
} else {
# then the fastq files will be found in stage 0, so return their names
S0_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S0_results")
S1_fastq1_usable_dir = paste(InArg$SA_prefix, "_usable_1.fastq.gz", sep = "")
InArg$S1_fastq1_usable_dir = file.path(S0_AnalysisDir, S1_fastq1_usable_dir)
S1_fastq2_usable_dir = paste(InArg$SA_prefix, "_usable_2.fastq.gz", sep = "")
InArg$S1_fastq2_usable_dir = file.path(S0_AnalysisDir, S1_fastq2_usable_dir)
}
futile.logger::flog.info("Correct Stage 1 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 1:
#------------
# new variable for stage 1:
InArg$S1_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S1_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S2- pet classification
Input_check_S2_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 2 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the S2_image:
#------------
if (!methods::is(InArg$S2_image, "logical")) {
stop("S2_image: ", InArg$S2_image, " has to be logical!", call. = FALSE)
} else if (InArg$S2_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S2_image==TRUE. Please install it.", call. = FALSE)
}
}
#------------
# check the S2_BlackList:
#------------
if (!methods::is(InArg$S2_BlackList, "logical") && !methods::is(InArg$S2_BlackList,
"GRanges")) {
stop("S2_BlackList: has to be logical or a GRanges object!", call. = FALSE)
}
#------------
# give name to savedir for stage 2:
#------------
InArg$S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
#------------
# check S2_PairedEndBAMpath:
#------------
if (!c(1) %in% InArg$SA_stages) {
# then S2_PairedEndBAMpath is given as input and it has to be the paired end bam
# file it can be both bam and sam format:
if (!methods::is(InArg$S2_PairedEndBAMpath, "character")) {
stop("S2_PairedEndBAMpath: ", InArg$S2_PairedEndBAMpath, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S2_PairedEndBAMpath)) {
stop("S2_PairedEndBAMpath: ", InArg$S2_PairedEndBAMpath, " file does not exist!",
call. = FALSE)
}
# check format:
PairedDataName = basename(InArg$S2_PairedEndBAMpath)
PairedDataName = strsplit(PairedDataName, ".", fixed = TRUE)
PairedDataName = unlist(PairedDataName)
Format = PairedDataName[length(PairedDataName)]
if (all(!c("bam", "sam") %in% Format)) {
stop("S2_PairedEndBAMpath: ", InArg$S2_PairedEndBAMpath, " has to be of .bam or .sam format!",
call. = FALSE)
}
# else load the data now:, note SA_AnalysisDir is needed in case BAM is SAM and
# needs to be saved there
S2_PairedData = LoadBAM_FromInputChecks_fun(SA_AnalysisDir = InArg$SA_AnalysisDir,
S2_AnalysisDir = InArg$S2_AnalysisDir, SA_prefix = InArg$SA_prefix, S2_PairedEndBAMpath = InArg$S2_PairedEndBAMpath,
Format = Format, S2_BlackList = InArg$S2_BlackList, S2_image = InArg$S2_image)
# save:
InArg$S2_PairedData = S2_PairedData
InArg$S2_PairedEndBAMpath = NULL
InArg$S2_BlackList = NULL
} else {
# it will be created with the following directory:
S1_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S1_results")
PairedEndBAMfile = paste(InArg$SA_prefix, "_Paired_end.bam", sep = "")
PairedEndBAMpath = file.path(S1_AnalysisDir, PairedEndBAMfile)
InArg$S2_PairedEndBAMpath = PairedEndBAMpath
}
futile.logger::flog.info("Correct Stage 2 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# return:
#------------
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S3
Input_check_S3_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 3 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the S3_image:
#------------
if (!methods::is(InArg$S3_image, "logical")) {
stop("S3_image: ", InArg$S3_image, " has to be logical!", call. = FALSE)
} else if (InArg$S3_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S3_image==TRUE. Please install it.", call. = FALSE)
}
}
#------------
# check the S3_method:
#------------
if (!InArg$S3_method %in% stats::p.adjust.methods) {
stop("S3_method: ", InArg$S3_method, " is wrong! See ??stats::p.adjust.methods.",
call. = FALSE)
}
#------------
# check the S3_fileSelfDir:
#------------
if (!c(2) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if (!methods::is(InArg$S3_fileSelfDir, "character")) {
stop("S3_fileSelfDir: ", InArg$S3_fileSelfDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S3_fileSelfDir)) {
stop("S3_fileSelfDir: ", InArg$S3_fileSelfDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S3_fileSelfDir)
if (!exists(paste(InArg$SA_prefix, "_pselfData", sep = ""))) {
stop("If S3_fileSelfDir is used to load PSelf class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_pselfData", sep = ""), call. = FALSE)
}
S3_Selfobject = get(paste(InArg$SA_prefix, "_pselfData", sep = ""))
# check class:
if (!methods::is(S3_Selfobject, "PSelf")) {
stop("The file loaded from S3_fileSelfDir: ", InArg$S3_fileSelfDir, " is not of PSelf class!",
call. = FALSE)
}
InArg$S3_Selfobject = S3_Selfobject
InArg$S3_fileSelfDir = NULL
} else {
# give the path directory where it will be saved:
S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
fileSelDir = paste(InArg$SA_prefix, "_pselfData", sep = "")
fileSelDir = file.path(S2_AnalysisDir, fileSelDir)
InArg$S3_fileSelfDir = fileSelDir
}
futile.logger::flog.info("Correct Stage 3 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 3:
#------------
InArg$S3_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S3_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S4
Input_check_S4_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 4 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the S4_image:
#------------
if (!methods::is(InArg$S4_image, "logical")) {
stop("S4_image: ", InArg$S4_image, " has to be logical!", call. = FALSE)
} else if (InArg$S4_image) {
if ((!requireNamespace("ggplot2", quietly = TRUE))|(!requireNamespace("reshape2", quietly = TRUE))) {
stop("ggplot2 and reshape2 packages are needed if S4_image==TRUE. Please install it.", call. = FALSE)
}
}
#------------
# check the S4_PeakExt:
#------------
if (!methods::is(InArg$S4_PeakExt, "numeric")) {
stop("S4_PeakExt: ", InArg$S4_PeakExt, " has to be a numeric!", call. = FALSE)
} else if (InArg$S4_PeakExt < 0) {
stop("S4_PeakExt: ", InArg$S4_PeakExt, " should be positive!", call. = FALSE)
} else {
# round it:
InArg$S4_PeakExt = round(InArg$S4_PeakExt)
}
#------------
# check the S4_minPETs:
#------------
if (!methods::is(InArg$S4_minPETs, "numeric")) {
stop("S4_minPETs: ", InArg$S4_minPETs, " has to be a numeric!", call. = FALSE)
} else if (InArg$S4_minPETs < 1) {
stop("S4_minPETs: ", InArg$S4_minPETs, " has to be at least = 1!", call. = FALSE)
} else {
# round it:
InArg$S4_minPETs = round(InArg$S4_minPETs)
}
#------------
# check the S4_FDR_peak:
#------------
if (!methods::is(InArg$S4_FDR_peak, "numeric")) {
stop("S4_FDR_peak: ", InArg$S4_FDR_peak, " has to be a numeric!", call. = FALSE)
} else if (InArg$S4_FDR_peak > 1) {
stop("S4_FDR_peak: ", InArg$S4_FDR_peak, " has to be a numeric smaller than 1!",
call. = FALSE)
} else if (InArg$S4_FDR_peak < 0) {
stop("S4_FDR_peak: ", InArg$S4_FDR_peak, " has to be a positive numeric!",
call. = FALSE)
}
#------------
# check the S4_method:
#------------
if (!InArg$S4_method %in% stats::p.adjust.methods) {
stop("S4_method: ", InArg$S4_method, " is wrong! See ??stats::p.adjust.methods.",
call. = FALSE)
}
#------------
# check the S4_filePSFitDir:
#------------
if (!c(3) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if (!methods::is(InArg$S4_filePSFitDir, "character")) {
stop("S4_filePSFitDir: ", InArg$S4_filePSFitDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S4_filePSFitDir)) {
stop("S4_filePSFitDir: ", InArg$S4_filePSFitDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S4_filePSFitDir)
if (!exists(paste(InArg$SA_prefix, "_psfitData", sep = ""))) {
stop("If S4_filePSFitDir is used to load PSFit class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_psfitData", sep = ""), call. = FALSE)
}
S4_FitObject = get(paste(InArg$SA_prefix, "_psfitData", sep = ""))
# check class:
if (!methods::is(S4_FitObject, "PSFit")) {
stop("The file loaded from S4_filePSFitDir: ", InArg$S4_filePSFitDir,
" is not of PSFit class!", call. = FALSE)
}
InArg$S4_FitObject = S4_FitObject
InArg$S4_filePSFitDir = NULL
} else {
# give the path directory where it will be saved:
S3_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S3_results")
filefitDir = paste(InArg$SA_prefix, "_psfitData", sep = "")
filefitDir = file.path(S3_AnalysisDir, filefitDir)
InArg$S4_filePSFitDir = filefitDir
}
#------------
# check the S4_filePIntraDir:
#------------
if (!c(2) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if(!is.null(InArg$S4_filePIntraDir)){
if (!methods::is(InArg$S4_filePIntraDir, "character")) {
stop("S4_filePIntraDir: ", InArg$S4_filePIntraDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S4_filePIntraDir)) {
stop("S4_filePIntraDir: ", InArg$S4_filePIntraDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S4_filePIntraDir)
if (!exists(paste(InArg$SA_prefix, "_pintraData", sep = ""))) {
stop("If S4_filePIntraDir is used to load PIntra class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_pintraData", sep = ""), call. = FALSE)
}
S4_IntraObject = get(paste(InArg$SA_prefix, "_pintraData", sep = ""))
# check class:
if (!methods::is(S4_IntraObject, "PIntra")) {
stop("The file loaded from S4_filePIntraDir: ", InArg$S4_filePIntraDir,
" is not of PIntra class!", call. = FALSE)
}
InArg$S4_IntraObject = S4_IntraObject
}else{# else it is null
InArg$S4_IntraObject = NULL
}
InArg$S4_filePIntraDir = NULL #for both null and not
} else {
# give the path directory where it will be saved:
S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
fileIntraDir = paste(InArg$SA_prefix, "_pintraData", sep = "")
fileIntraDir = file.path(S2_AnalysisDir, fileIntraDir)
InArg$S4_filePIntraDir = fileIntraDir
}
#------------
# check the S4_filePInterDir:
#------------
if (!c(2) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if(!is.null(InArg$S4_filePInterDir)){
if (!methods::is(InArg$S4_filePInterDir, "character")) {
stop("S4_filePInterDir: ", InArg$S4_filePInterDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S4_filePInterDir)) {
stop("S4_filePInterDir: ", InArg$S4_filePInterDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S4_filePInterDir)
if (!exists(paste(InArg$SA_prefix, "_pinterData", sep = ""))) {
stop("If S4_filePInterDir is used to load PInter class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_pinterData", sep = ""), call. = FALSE)
}
S4_InterObject = get(paste(InArg$SA_prefix, "_pinterData", sep = ""))
# check class:
if (!methods::is(S4_InterObject, "PInter")) {
stop("The file loaded from S4_filePInterDir: ", InArg$S4_filePInterDir,
" is not of PInter class!", call. = FALSE)
}
InArg$S4_InterObject = S4_InterObject
}else{# else it is null
InArg$S4_InterObject = NULL
}
InArg$S4_filePInterDir = NULL #common for both null and not null
} else {
# give the path directory where it will be saved:
S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
fileInterDir = paste(InArg$SA_prefix, "_pinterData", sep = "")
fileInterDir = file.path(S2_AnalysisDir, fileInterDir)
InArg$S4_filePInterDir = fileInterDir
}
#------------
# check if the S4_IntraObject/S4_InterObject are NULL in case they are given as input:
#------------
if (is.null(InArg$S4_IntraObject) & is.null(InArg$S4_InterObject) &
(!c(2) %in% InArg$SA_stages)) {
stop("No Intra/Inter-ligated data is found (both NULL)!", call. = FALSE)
}
futile.logger::flog.info("Correct Stage 4 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 4:
#------------
InArg$S4_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S4_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for breaking the output:
Break_output_fun = function(InArg) {
#--------------
# Stage 0 output:
#--------------
S0names = c("S0_AnalysisDir", "SA_prefix", "S0_fastq1", "S0_fastq2", "S0_LinkerA",
"S0_LinkerB", "S0_MinReadLength", "S0_MaxReadLength", "S0_LinkerOccurence",
"S0_image", "S0_fastqStream", "S0_Totfastqreads")
InArgS0 = InArg[which(names(InArg) %in% S0names)]
#--------------
# Stage 1 output:
#--------------
S1names = c("S1_AnalysisDir", "SA_prefix", "S1_fastq1_usable_dir", "S1_fastq2_usable_dir",
"S1_image", "S1_makeSam", "S1_genome", "S1_RbowtieIndexBuild", "S1_RbowtieIndexDir",
"S1_RbowtieIndexPrefix", "S1_RbowtieRefDir", "S1_BAMStream")
InArgS1 = InArg[which(names(InArg) %in% S1names)]
#--------------
# Stage 2 output:
#--------------
S2names = c("S2_AnalysisDir", "S2_PairedEndBAMpath", "S2_image", "S2_BlackList",
"S2_PairedData", "SA_prefix")
InArgS2 = InArg[which(names(InArg) %in% S2names)]
#--------------
# Stage 3 output:
#--------------
S3names = c("S3_AnalysisDir", "S3_fileSelfDir", "S3_method", "S3_Selfobject",
"SA_prefix", "S3_image")
InArgS3 = InArg[which(names(InArg) %in% S3names)]
#--------------
# Stage 4 output:
#--------------
S4names = c("S4_AnalysisDir", "S4_filePSFitDir", "S4_filePIntraDir", "S4_filePInterDir",
"S4_FDR_peak", "S4_method", "S4_FitObject", "S4_IntraObject", "S4_InterObject",
"SA_prefix", "S4_image", "S4_minPETs", "S4_PeakExt")
InArgS4 = InArg[which(names(InArg) %in% S4names)]
return(list(InArgS0 = InArgS0, InArgS1 = InArgS1, InArgS2 = InArgS2, InArgS3 = InArgS3,
InArgS4 = InArgS4))
}
# done
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MACPET documentation built on Nov. 8, 2020, 5:47 p.m.
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Defines functions Break_output_fun Input_check_S4_fun Input_check_S3_fun Input_check_S2_fun Input_check_S1_fun Input_check_S0_fun Input_check_SA_fun InputCheckMACPETUlt
#' @importFrom stats p.adjust.methods
#' @importFrom methods is
#' @importFrom ShortRead countLines
#' @importFrom futile.logger flog.appender flog.layout layout.format appender.tee flog.info flog.warn
#------------------------------------
# input check for MACPETUlt.R
#------------------------------------
# main function for checking the inputs:
InputCheckMACPETUlt = function(InArg) {
LogFile = list() #for the log file.
LogFile[1] = "|%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%|"
LogFile[2] = "|-------------MACPET analysis input checking------------|"
LogFile[3] = "|%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%|"
#------------------------------------
# all stages input:
#------------------------------------
Input_check_SA_fun(InArg = InArg)
LogFile[4] = "Common stage inputs...OK"
LogFile[5] = paste("Stages to run: ", paste((InArg$SA_stages), collapse = "-"),
sep = "")
# write in log and print:
for (lf in seq_len(5)) futile.logger::flog.info(LogFile[[lf]], name = "SA_LogFile",
capture = FALSE)
#------------------------------------
# 0 stage input:
#------------------------------------
if (c(0) %in% InArg$SA_stages) {
InArg = Input_check_S0_fun(InArg)
}
#------------------------------------
# 1 stage input:
#------------------------------------
if (c(1) %in% InArg$SA_stages) {
InArg = Input_check_S1_fun(InArg)
}
#------------------------------------
# 2 stage input:
#------------------------------------
if (c(2) %in% InArg$SA_stages) {
InArg = Input_check_S2_fun(InArg)
}
#------------------------------------
# 3 stage input:
#------------------------------------
if (c(3) %in% InArg$SA_stages) {
InArg = Input_check_S3_fun(InArg)
}
#------------------------------------
# 4 stage input:
#------------------------------------
if (c(4) %in% InArg$SA_stages) {
InArg = Input_check_S4_fun(InArg)
}
#--------------------------
# Break output:
#--------------------------
InArg = Break_output_fun(InArg = InArg)
#--------------------------
# Finallize
#--------------------------
futile.logger::flog.info("All inputs correct! Starting MACPET analysis...", name = "SA_LogFile",
capture = FALSE)
return(InArg)
}
# Done
#---------------------
#---------------------
# function for checking inputs for stage SA
Input_check_SA_fun = function(InArg) {
#------------
# check directory:
#------------
if (!methods::is(InArg$SA_AnalysisDir, "character")) {
stop("SA_AnalysisDir:", InArg$SA_AnalysisDir, " is not a directory!", call. = FALSE)
} else if (!dir.exists(InArg$SA_AnalysisDir)) {
stop("SA_AnalysisDir:", InArg$SA_AnalysisDir, " directory does not exist!",
call. = FALSE)
}
#------------
# check stages:
#------------
if (!methods::is(InArg$SA_stages, "numeric")) {
stop("SA_stages: ", InArg$SA_stages, " variable has to be a numeric or numeric vector!",
call. = FALSE)
} else if (any(!InArg$SA_stages %in% c(0, 1, 2, 3, 4))) {
stop("SA_stages: ", InArg$SA_stages, " variable has to be a numeric or numeric vector with values c(0,1,2,3,4)!",
call. = FALSE)
} else {
stageseq = seq(from = min(InArg$SA_stages), to = max(InArg$SA_stages))
if (any(!stageseq %in% InArg$SA_stages)) {
stop("SA_stages: ", InArg$SA_stages, " cannot have skipped intermediate stages!",
call. = FALSE)
}
}
#------------
# check prefix:
#------------
if (!methods::is(InArg$SA_prefix, "character")) {
stop("SA_prefix: ", InArg$SA_prefix, " variable has to be a string!", call. = FALSE)
} else if (nchar(InArg$SA_prefix) == 0) {
stop("SA_prefix: ", InArg$SA_prefix, " variable has to be a non-empty string!",
call. = FALSE)
}
#------------
# create log file
#------------
SA_LogFile.dir = file.path(InArg$SA_AnalysisDir, paste(InArg$SA_prefix, "_analysis.log",
sep = ""))
if (file.exists(SA_LogFile.dir))
unlink(SA_LogFile.dir, recursive = TRUE, force = TRUE)
# create the log file:
futile.logger::flog.appender(futile.logger::appender.tee(SA_LogFile.dir), "SA_LogFile")
futile.logger::flog.layout(futile.logger::layout.format("~m"), name = "SA_LogFile")
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S0- fastq split
Input_check_S0_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 0 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check fastq files:
#------------
# 1:
if (!methods::is(InArg$S0_fastq1, "character")) {
stop("S0_fastq1: ", InArg$S0_fastq1, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S0_fastq1)) {
stop("S0_fastq1: ", InArg$S0_fastq1, " file does not exist!", call. = FALSE)
} else {
fastq1 = basename(InArg$S0_fastq1)
if (!grepl(".fastq.gz", fastq1) & !grepl(".fastq", fastq1)) {
stop("S0_fastq1: ", InArg$S0_fastq1, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
# 2:
if (!methods::is(InArg$S0_fastq2, "character")) {
stop("S0_fastq2: ", InArg$S0_fastq2, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S0_fastq2)) {
stop("S0_fastq2: ", InArg$S0_fastq2, " file does not exist!", call. = FALSE)
} else {
fastq2 = basename(InArg$S0_fastq2)
if (!grepl(".fastq.gz", fastq2) & !grepl(".fastq", fastq2)) {
stop("S0_fastq2: ", InArg$S0_fastq2, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
#----------------
# preliminary fastq check:
#----------------
cat("Preliminary fastq checking...")
# count fast1 lines:
Lines_fastq = ShortRead::countLines(dirPath = c(InArg$S0_fastq1, InArg$S0_fastq2))
if (Lines_fastq[[1]] != Lines_fastq[[2]]) {
stop("S0_fastq1: ", InArg$S0_fastq1, " and S0_fastq2: ", InArg$S0_fastq2,
" files are not of same length.", call. = FALSE)
}
cat("OK\n")
S0_Totfastqreads = Lines_fastq[[1]]/4 #four lines per entry
# new variable to use in stage 0:
InArg$S0_Totfastqreads = S0_Totfastqreads
#----------------
# check linkers
#----------------
if (!methods::is(InArg$S0_LinkerA, "character")) {
stop("S0_LinkerA: ", InArg$S0_LinkerA, " has to be a string!", call. = FALSE)
} else if (nchar(InArg$S0_LinkerA) == 0) {
stop("S0_LinkerA: ", InArg$S0_LinkerA, " has to be a non-empty string!",
call. = FALSE)
}
futile.logger::flog.info(paste("Linker A sequence chosen:", InArg$S0_LinkerA),
name = "SA_LogFile", capture = FALSE)
if (!methods::is(InArg$S0_LinkerB, "character")) {
stop("S0_LinkerB: ", InArg$S0_LinkerB, " has to be a string!", call. = FALSE)
} else if (nchar(InArg$S0_LinkerB) == 0) {
stop("S0_LinkerB: ", InArg$S0_LinkerB, " has to be a non-empty string!",
call. = FALSE)
}
futile.logger::flog.info(paste("Linker B sequence chosen:", InArg$S0_LinkerB),
name = "SA_LogFile", capture = FALSE)
# linker match:
if (nchar(InArg$S0_LinkerA) != nchar(InArg$S0_LinkerB)) {
LogFile = paste("WARNING: S0_LinkerA:", InArg$S0_LinkerA, "and S0_LinkerB:",
InArg$S0_LinkerB, " lengths do not match.")
futile.logger::flog.warn(LogFile, name = "SA_LogFile", capture = FALSE)
}
#----------------
# check S0_LinkerOccurence:
#----------------
if (!methods::is(InArg$S0_LinkerOccurence, "numeric")) {
stop("S0_LinkerOccurence: ", InArg$S0_LinkerOccurence, " has to be an integer!",
call. = FALSE)
} else if (!InArg$S0_LinkerOccurence %in% c(0, 1, 2, 3, 4)) {
stop("S0_LinkerOccurence: ", InArg$S0_LinkerOccurence, " has to be one of 0, 1, 2, 3, 4!",
call. = FALSE)
}
if (InArg$S0_LinkerOccurence == 0) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with any read with no linker will be moved to ambiguous class.")
} else if (InArg$S0_LinkerOccurence == 1) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with left read with no linker, but right read with linker, will be moved to usable class.")
} else if (InArg$S0_LinkerOccurence == 2) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with right read with no linker, but left read with linker, will be moved to usable class.")
} else if (InArg$S0_LinkerOccurence == 3) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with any or both reads without linkers, will be moved to usable class.")
} else if (InArg$S0_LinkerOccurence == 4) {
LogFile = paste("Linker mode chosen:", InArg$S0_LinkerOccurence, "\n ==> PETs with both reads without linkers, will be moved to usable class.")
}
futile.logger::flog.info(LogFile, name = "SA_LogFile", capture = FALSE)
#----------------
# check lengths
#----------------
if (!methods::is(InArg$S0_MinReadLength, "numeric")) {
stop("S0_MinReadLength: ", InArg$S0_MinReadLength, " has to be an integer!",
call. = FALSE)
} else if (InArg$S0_MinReadLength < 0) {
stop("S0_MinReadLength: ", InArg$S0_MinReadLength, " has to be >=0!", call. = FALSE)
} else {
InArg$S0_MinReadLength = ceiling(InArg$S0_MinReadLength)
}
if (!methods::is(InArg$S0_MaxReadLength, "numeric")) {
stop("S0_MaxReadLength: ", InArg$S0_MaxReadLength, " has to be an integer!",
call. = FALSE)
} else if (InArg$S0_MaxReadLength < 0) {
stop("S0_MaxReadLength: ", InArg$S0_MaxReadLength, " has to be >=0!", call. = FALSE)
} else {
InArg$S0_MaxReadLength = ceiling(InArg$S0_MaxReadLength)
}
if (InArg$S0_MinReadLength >= InArg$S0_MaxReadLength) {
stop("S0_MinReadLength: ", InArg$S0_MinReadLength, " has to be < S0_MaxReadLength: ",
InArg$S0_MaxReadLength, " !", call. = FALSE)
}
futile.logger::flog.info(paste("Maximum read length after linker trimming:",
InArg$S0_MaxReadLength), name = "SA_LogFile", capture = FALSE)
futile.logger::flog.info(paste("Minimum read length after linker trimming:",
InArg$S0_MinReadLength), name = "SA_LogFile", capture = FALSE)
#----------------
# checkimage and fastqStream:
#----------------
if (!methods::is(InArg$S0_image, "logical")) {
stop("S0_image ", InArg$S0_image, " has to be logical!", call. = FALSE)
} else if (InArg$S0_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S0_image==TRUE. Please install it.", call. = FALSE)
}
}
if (!methods::is(InArg$S0_fastqStream, "numeric")) {
stop("S0_fastqStream: ", InArg$S0_fastqStream, " has to be a numeric!", call. = FALSE)
} else if (InArg$S0_fastqStream <= 0) {
stop("S0_fastqStream: ", InArg$S0_fastqStream, " has to be a positive numeric!",
call. = FALSE)
} else {
InArg$S0_fastqStream = ceiling(InArg$S0_fastqStream)
}
futile.logger::flog.info("Correct Stage 0 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 0:
#------------
# new variable for stage 0:
InArg$S0_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S0_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S1- mapping and paired-end bam creation
Input_check_S1_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 1 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the logical:
#------------
if (!methods::is(InArg$S1_image, "logical")) {
stop("S1_image: ", InArg$S1_image, " has to be logical!", call. = FALSE)
} else if (InArg$S1_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S1_image==TRUE. Please install it.", call. = FALSE)
}
}
if (!methods::is(InArg$S1_RbowtieIndexBuild, "logical")) {
stop("S1_RbowtieIndexBuild: ", InArg$S1_RbowtieIndexBuild, " has to be logical!",
call. = FALSE)
}
futile.logger::flog.info(paste("Building bowtie index?", InArg$S1_RbowtieIndexBuild),
name = "SA_LogFile", capture = FALSE)
if (!methods::is(InArg$S1_makeSam, "logical")) {
stop("S1_makeSam: ", InArg$S1_makeSam, " has to be logical!", call. = FALSE)
}
#------------
# check S1_BAMStream:
#------------
if (!methods::is(InArg$S1_BAMStream, "numeric")) {
stop("S1_BAMStream: ", InArg$S1_BAMStream, " has to be a numeric!", call. = FALSE)
} else if (InArg$S1_BAMStream <= 0) {
stop("S1_BAMStream: ", InArg$S1_BAMStream, " has to be a positive numeric!",
call. = FALSE)
} else {
InArg$S1_BAMStream = ceiling(InArg$S1_BAMStream)
}
#------------
# check S1_genome:
#------------
if (!methods::is(InArg$S1_genome, "character")) {
stop("S1_genome: ", InArg$S1_genome, " has to be a character!", call. = FALSE)
} else if (!InArg$S1_genome %in% names(sysdata)) {
LogFile = paste("WARNING: S1_genome: ", InArg$S1_genome, ", is not a part of ",
paste(names(sysdata), collapse = "/"), ". If S2_BlackList==TRUE, then no black-listed regions will be removed from the data.",
sep = "")
futile.logger::flog.warn(LogFile, name = "SA_LogFile", capture = FALSE)
}
futile.logger::flog.info(paste("Genome chosen:", InArg$S1_genome), name = "SA_LogFile",
capture = FALSE)
#------------
# check S1_RbowtieIndexPrefix:
#------------
if (!methods::is(InArg$S1_RbowtieIndexPrefix, "character")) {
stop("S1_RbowtieIndexPrefix: ", InArg$S1_RbowtieIndexPrefix, " has to be a string!",
call. = FALSE)
} else if (nchar(InArg$S1_RbowtieIndexPrefix) == 0) {
stop("S1_RbowtieIndexPrefix: ", InArg$S1_RbowtieIndexPrefix, " has to be a non-empty string!",
call. = FALSE)
}
#------------
# check S1_RbowtieIndexDir:
#------------
if (!InArg$S1_RbowtieIndexBuild) {
# if the bowtie index is built already:
if (!methods::is(InArg$S1_RbowtieIndexDir, "character")) {
stop("S1_RbowtieIndexDir: ", InArg$S1_RbowtieIndexDir, " variable has to be a directory!",
call. = FALSE)
} else if (!dir.exists(InArg$S1_RbowtieIndexDir)) {
stop("S1_RbowtieIndexDir: ", InArg$S1_RbowtieIndexDir, " directory does not exist!",
call. = FALSE)
}
# check the directory files:
BowtieIndexes = file.path(InArg$S1_RbowtieIndexDir, InArg$S1_RbowtieIndexPrefix)
BowtieIndexes = paste(BowtieIndexes, c(".1.ebwt", ".1.ebwtl", ".2.ebwt",
".2.ebwtl", ".3.ebwt", ".3.ebwtl", ".4.ebwt", ".4.ebwtl", ".rev.1.ebwt",
".rev.1.ebwtl", ".rev.2.ebwt", ".rev.2.ebwtl"), sep = "")
for (i in seq_len(length(BowtieIndexes)/2)) {
if (!file.exists(BowtieIndexes[i]) && !file.exists(BowtieIndexes[i +
1])) {
stop(basename(BowtieIndexes[i]), " or ", basename(BowtieIndexes[i +
1]), " files are missing from S1_RbowtieIndexDir or the S1_RbowtieIndexPrefix is wrong!",
call. = FALSE)
}
}
} else {
# you will build the index, check the fasta files
#------------
# check S1_RbowtieRefDir:
#------------
if (!methods::is(InArg$S1_RbowtieRefDir, "character")) {
stop("S1_RbowtieRefDir: ", InArg$S1_RbowtieRefDir, " has to be a character vector with the paths of the .fa files for building the bowtie index!",
call. = FALSE)
} else if (any(!file.exists(InArg$S1_RbowtieRefDir))) {
Famissing = which(!file.exists(InArg$S1_RbowtieRefDir))
Famissing = InArg$S1_RbowtieRefDir[Famissing]
Famissing = paste(basename(Famissing), collapse = "/")
stop("S1_RbowtieRefDir contains the following missing .fa files: ", Famissing,
call. = FALSE)
}
# give the S1_RbowtieIndexDir, where to save the index:
InArg$S1_RbowtieIndexDir = file.path(InArg$SA_AnalysisDir, "S1_results",
"BowtieIndex")
}
#------------
# check S1_fastq1_usable_dir and S1_fastq2_usable_dir:
#------------
if (!c(0) %in% InArg$SA_stages) {
# then the fastq files are given as input so they have to be checked: 1:
if (!methods::is(InArg$S1_fastq1_usable_dir, "character")) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S1_fastq1_usable_dir)) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " file does not exist!",
call. = FALSE)
} else {
fastq1 = basename(InArg$S1_fastq1_usable_dir)
if (all(!grepl("fastq.gz", fastq1) || !grepl("fastq", fastq1))) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
# 2:
if (!methods::is(InArg$S1_fastq2_usable_dir, "character")) {
stop("S1_fastq2_usable_dir: ", InArg$S1_fastq2_usable_dir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S1_fastq2_usable_dir)) {
stop("S1_fastq2_usable_dir: ", InArg$S1_fastq2_usable_dir, " file does not exist!",
call. = FALSE)
} else {
fastq2 = basename(InArg$S1_fastq2_usable_dir)
if (all(!grepl("fastq.gz", fastq2) || !grepl("fastq", fastq2))) {
stop("S1_fastq2_usable_dir: ", InArg$S1_fastq2_usable_dir, " file is probably not fastq or fastq.gz format!",
call. = FALSE)
}
}
#----------------
# preliminary fastq check:
#----------------
cat("Preliminary fastq checking...")
# count fast1 lines:
Lines_fastq = ShortRead::countLines(dirPath = c(InArg$S1_fastq1_usable_dir,
InArg$S1_fastq2_usable_dir))
if (Lines_fastq[[1]] != Lines_fastq[[2]]) {
stop("S1_fastq1_usable_dir: ", InArg$S1_fastq1_usable_dir, " and S1_fastq2_usable_dir: ",
InArg$S1_fastq2_usable_dir, " files are not of same length.", call. = FALSE)
}
cat("OK\n")
Totfastqreads = Lines_fastq[[1]]/4 #four lines per entry
} else {
# then the fastq files will be found in stage 0, so return their names
S0_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S0_results")
S1_fastq1_usable_dir = paste(InArg$SA_prefix, "_usable_1.fastq.gz", sep = "")
InArg$S1_fastq1_usable_dir = file.path(S0_AnalysisDir, S1_fastq1_usable_dir)
S1_fastq2_usable_dir = paste(InArg$SA_prefix, "_usable_2.fastq.gz", sep = "")
InArg$S1_fastq2_usable_dir = file.path(S0_AnalysisDir, S1_fastq2_usable_dir)
}
futile.logger::flog.info("Correct Stage 1 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 1:
#------------
# new variable for stage 1:
InArg$S1_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S1_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S2- pet classification
Input_check_S2_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 2 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the S2_image:
#------------
if (!methods::is(InArg$S2_image, "logical")) {
stop("S2_image: ", InArg$S2_image, " has to be logical!", call. = FALSE)
} else if (InArg$S2_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S2_image==TRUE. Please install it.", call. = FALSE)
}
}
#------------
# check the S2_BlackList:
#------------
if (!methods::is(InArg$S2_BlackList, "logical") && !methods::is(InArg$S2_BlackList,
"GRanges")) {
stop("S2_BlackList: has to be logical or a GRanges object!", call. = FALSE)
}
#------------
# give name to savedir for stage 2:
#------------
InArg$S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
#------------
# check S2_PairedEndBAMpath:
#------------
if (!c(1) %in% InArg$SA_stages) {
# then S2_PairedEndBAMpath is given as input and it has to be the paired end bam
# file it can be both bam and sam format:
if (!methods::is(InArg$S2_PairedEndBAMpath, "character")) {
stop("S2_PairedEndBAMpath: ", InArg$S2_PairedEndBAMpath, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S2_PairedEndBAMpath)) {
stop("S2_PairedEndBAMpath: ", InArg$S2_PairedEndBAMpath, " file does not exist!",
call. = FALSE)
}
# check format:
PairedDataName = basename(InArg$S2_PairedEndBAMpath)
PairedDataName = strsplit(PairedDataName, ".", fixed = TRUE)
PairedDataName = unlist(PairedDataName)
Format = PairedDataName[length(PairedDataName)]
if (all(!c("bam", "sam") %in% Format)) {
stop("S2_PairedEndBAMpath: ", InArg$S2_PairedEndBAMpath, " has to be of .bam or .sam format!",
call. = FALSE)
}
# else load the data now:, note SA_AnalysisDir is needed in case BAM is SAM and
# needs to be saved there
S2_PairedData = LoadBAM_FromInputChecks_fun(SA_AnalysisDir = InArg$SA_AnalysisDir,
S2_AnalysisDir = InArg$S2_AnalysisDir, SA_prefix = InArg$SA_prefix, S2_PairedEndBAMpath = InArg$S2_PairedEndBAMpath,
Format = Format, S2_BlackList = InArg$S2_BlackList, S2_image = InArg$S2_image)
# save:
InArg$S2_PairedData = S2_PairedData
InArg$S2_PairedEndBAMpath = NULL
InArg$S2_BlackList = NULL
} else {
# it will be created with the following directory:
S1_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S1_results")
PairedEndBAMfile = paste(InArg$SA_prefix, "_Paired_end.bam", sep = "")
PairedEndBAMpath = file.path(S1_AnalysisDir, PairedEndBAMfile)
InArg$S2_PairedEndBAMpath = PairedEndBAMpath
}
futile.logger::flog.info("Correct Stage 2 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# return:
#------------
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S3
Input_check_S3_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 3 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the S3_image:
#------------
if (!methods::is(InArg$S3_image, "logical")) {
stop("S3_image: ", InArg$S3_image, " has to be logical!", call. = FALSE)
} else if (InArg$S3_image) {
if (!requireNamespace("ggplot2", quietly = TRUE)) {
stop("ggplot2 is needed if S3_image==TRUE. Please install it.", call. = FALSE)
}
}
#------------
# check the S3_method:
#------------
if (!InArg$S3_method %in% stats::p.adjust.methods) {
stop("S3_method: ", InArg$S3_method, " is wrong! See ??stats::p.adjust.methods.",
call. = FALSE)
}
#------------
# check the S3_fileSelfDir:
#------------
if (!c(2) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if (!methods::is(InArg$S3_fileSelfDir, "character")) {
stop("S3_fileSelfDir: ", InArg$S3_fileSelfDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S3_fileSelfDir)) {
stop("S3_fileSelfDir: ", InArg$S3_fileSelfDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S3_fileSelfDir)
if (!exists(paste(InArg$SA_prefix, "_pselfData", sep = ""))) {
stop("If S3_fileSelfDir is used to load PSelf class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_pselfData", sep = ""), call. = FALSE)
}
S3_Selfobject = get(paste(InArg$SA_prefix, "_pselfData", sep = ""))
# check class:
if (!methods::is(S3_Selfobject, "PSelf")) {
stop("The file loaded from S3_fileSelfDir: ", InArg$S3_fileSelfDir, " is not of PSelf class!",
call. = FALSE)
}
InArg$S3_Selfobject = S3_Selfobject
InArg$S3_fileSelfDir = NULL
} else {
# give the path directory where it will be saved:
S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
fileSelDir = paste(InArg$SA_prefix, "_pselfData", sep = "")
fileSelDir = file.path(S2_AnalysisDir, fileSelDir)
InArg$S3_fileSelfDir = fileSelDir
}
futile.logger::flog.info("Correct Stage 3 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 3:
#------------
InArg$S3_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S3_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for checking inputs for stage S4
Input_check_S4_fun = function(InArg) {
futile.logger::flog.info("|---- Checking Stage 4 inputs ----|", name = "SA_LogFile",
capture = FALSE)
#------------
# check the S4_image:
#------------
if (!methods::is(InArg$S4_image, "logical")) {
stop("S4_image: ", InArg$S4_image, " has to be logical!", call. = FALSE)
} else if (InArg$S4_image) {
if ((!requireNamespace("ggplot2", quietly = TRUE))|(!requireNamespace("reshape2", quietly = TRUE))) {
stop("ggplot2 and reshape2 packages are needed if S4_image==TRUE. Please install it.", call. = FALSE)
}
}
#------------
# check the S4_PeakExt:
#------------
if (!methods::is(InArg$S4_PeakExt, "numeric")) {
stop("S4_PeakExt: ", InArg$S4_PeakExt, " has to be a numeric!", call. = FALSE)
} else if (InArg$S4_PeakExt < 0) {
stop("S4_PeakExt: ", InArg$S4_PeakExt, " should be positive!", call. = FALSE)
} else {
# round it:
InArg$S4_PeakExt = round(InArg$S4_PeakExt)
}
#------------
# check the S4_minPETs:
#------------
if (!methods::is(InArg$S4_minPETs, "numeric")) {
stop("S4_minPETs: ", InArg$S4_minPETs, " has to be a numeric!", call. = FALSE)
} else if (InArg$S4_minPETs < 1) {
stop("S4_minPETs: ", InArg$S4_minPETs, " has to be at least = 1!", call. = FALSE)
} else {
# round it:
InArg$S4_minPETs = round(InArg$S4_minPETs)
}
#------------
# check the S4_FDR_peak:
#------------
if (!methods::is(InArg$S4_FDR_peak, "numeric")) {
stop("S4_FDR_peak: ", InArg$S4_FDR_peak, " has to be a numeric!", call. = FALSE)
} else if (InArg$S4_FDR_peak > 1) {
stop("S4_FDR_peak: ", InArg$S4_FDR_peak, " has to be a numeric smaller than 1!",
call. = FALSE)
} else if (InArg$S4_FDR_peak < 0) {
stop("S4_FDR_peak: ", InArg$S4_FDR_peak, " has to be a positive numeric!",
call. = FALSE)
}
#------------
# check the S4_method:
#------------
if (!InArg$S4_method %in% stats::p.adjust.methods) {
stop("S4_method: ", InArg$S4_method, " is wrong! See ??stats::p.adjust.methods.",
call. = FALSE)
}
#------------
# check the S4_filePSFitDir:
#------------
if (!c(3) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if (!methods::is(InArg$S4_filePSFitDir, "character")) {
stop("S4_filePSFitDir: ", InArg$S4_filePSFitDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S4_filePSFitDir)) {
stop("S4_filePSFitDir: ", InArg$S4_filePSFitDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S4_filePSFitDir)
if (!exists(paste(InArg$SA_prefix, "_psfitData", sep = ""))) {
stop("If S4_filePSFitDir is used to load PSFit class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_psfitData", sep = ""), call. = FALSE)
}
S4_FitObject = get(paste(InArg$SA_prefix, "_psfitData", sep = ""))
# check class:
if (!methods::is(S4_FitObject, "PSFit")) {
stop("The file loaded from S4_filePSFitDir: ", InArg$S4_filePSFitDir,
" is not of PSFit class!", call. = FALSE)
}
InArg$S4_FitObject = S4_FitObject
InArg$S4_filePSFitDir = NULL
} else {
# give the path directory where it will be saved:
S3_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S3_results")
filefitDir = paste(InArg$SA_prefix, "_psfitData", sep = "")
filefitDir = file.path(S3_AnalysisDir, filefitDir)
InArg$S4_filePSFitDir = filefitDir
}
#------------
# check the S4_filePIntraDir:
#------------
if (!c(2) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if(!is.null(InArg$S4_filePIntraDir)){
if (!methods::is(InArg$S4_filePIntraDir, "character")) {
stop("S4_filePIntraDir: ", InArg$S4_filePIntraDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S4_filePIntraDir)) {
stop("S4_filePIntraDir: ", InArg$S4_filePIntraDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S4_filePIntraDir)
if (!exists(paste(InArg$SA_prefix, "_pintraData", sep = ""))) {
stop("If S4_filePIntraDir is used to load PIntra class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_pintraData", sep = ""), call. = FALSE)
}
S4_IntraObject = get(paste(InArg$SA_prefix, "_pintraData", sep = ""))
# check class:
if (!methods::is(S4_IntraObject, "PIntra")) {
stop("The file loaded from S4_filePIntraDir: ", InArg$S4_filePIntraDir,
" is not of PIntra class!", call. = FALSE)
}
InArg$S4_IntraObject = S4_IntraObject
}else{# else it is null
InArg$S4_IntraObject = NULL
}
InArg$S4_filePIntraDir = NULL #for both null and not
} else {
# give the path directory where it will be saved:
S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
fileIntraDir = paste(InArg$SA_prefix, "_pintraData", sep = "")
fileIntraDir = file.path(S2_AnalysisDir, fileIntraDir)
InArg$S4_filePIntraDir = fileIntraDir
}
#------------
# check the S4_filePInterDir:
#------------
if (!c(2) %in% InArg$SA_stages) {
# means the data is given as it is, so load it and check class check if directory
# exists:
if(!is.null(InArg$S4_filePInterDir)){
if (!methods::is(InArg$S4_filePInterDir, "character")) {
stop("S4_filePInterDir: ", InArg$S4_filePInterDir, " variable has to be a file directory!",
call. = FALSE)
} else if (!file.exists(InArg$S4_filePInterDir)) {
stop("S4_filePInterDir: ", InArg$S4_filePInterDir, " file does not exist!",
call. = FALSE)
}
# load data:
load(InArg$S4_filePInterDir)
if (!exists(paste(InArg$SA_prefix, "_pinterData", sep = ""))) {
stop("If S4_filePInterDir is used to load PInter class data, the object loaded should be named: ",
paste(InArg$SA_prefix, "_pinterData", sep = ""), call. = FALSE)
}
S4_InterObject = get(paste(InArg$SA_prefix, "_pinterData", sep = ""))
# check class:
if (!methods::is(S4_InterObject, "PInter")) {
stop("The file loaded from S4_filePInterDir: ", InArg$S4_filePInterDir,
" is not of PInter class!", call. = FALSE)
}
InArg$S4_InterObject = S4_InterObject
}else{# else it is null
InArg$S4_InterObject = NULL
}
InArg$S4_filePInterDir = NULL #common for both null and not null
} else {
# give the path directory where it will be saved:
S2_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S2_results")
fileInterDir = paste(InArg$SA_prefix, "_pinterData", sep = "")
fileInterDir = file.path(S2_AnalysisDir, fileInterDir)
InArg$S4_filePInterDir = fileInterDir
}
#------------
# check if the S4_IntraObject/S4_InterObject are NULL in case they are given as input:
#------------
if (is.null(InArg$S4_IntraObject) & is.null(InArg$S4_InterObject) &
(!c(2) %in% InArg$SA_stages)) {
stop("No Intra/Inter-ligated data is found (both NULL)!", call. = FALSE)
}
futile.logger::flog.info("Correct Stage 4 inputs given.", name = "SA_LogFile",
capture = FALSE)
#------------
# create savedir for stage 4:
#------------
InArg$S4_AnalysisDir = file.path(InArg$SA_AnalysisDir, "S4_results")
return(InArg)
}
# done
#---------------------
#---------------------
# function for breaking the output:
Break_output_fun = function(InArg) {
#--------------
# Stage 0 output:
#--------------
S0names = c("S0_AnalysisDir", "SA_prefix", "S0_fastq1", "S0_fastq2", "S0_LinkerA",
"S0_LinkerB", "S0_MinReadLength", "S0_MaxReadLength", "S0_LinkerOccurence",
"S0_image", "S0_fastqStream", "S0_Totfastqreads")
InArgS0 = InArg[which(names(InArg) %in% S0names)]
#--------------
# Stage 1 output:
#--------------
S1names = c("S1_AnalysisDir", "SA_prefix", "S1_fastq1_usable_dir", "S1_fastq2_usable_dir",
"S1_image", "S1_makeSam", "S1_genome", "S1_RbowtieIndexBuild", "S1_RbowtieIndexDir",
"S1_RbowtieIndexPrefix", "S1_RbowtieRefDir", "S1_BAMStream")
InArgS1 = InArg[which(names(InArg) %in% S1names)]
#--------------
# Stage 2 output:
#--------------
S2names = c("S2_AnalysisDir", "S2_PairedEndBAMpath", "S2_image", "S2_BlackList",
"S2_PairedData", "SA_prefix")
InArgS2 = InArg[which(names(InArg) %in% S2names)]
#--------------
# Stage 3 output:
#--------------
S3names = c("S3_AnalysisDir", "S3_fileSelfDir", "S3_method", "S3_Selfobject",
"SA_prefix", "S3_image")
InArgS3 = InArg[which(names(InArg) %in% S3names)]
#--------------
# Stage 4 output:
#--------------
S4names = c("S4_AnalysisDir", "S4_filePSFitDir", "S4_filePIntraDir", "S4_filePInterDir",
"S4_FDR_peak", "S4_method", "S4_FitObject", "S4_IntraObject", "S4_InterObject",
"SA_prefix", "S4_image", "S4_minPETs", "S4_PeakExt")
InArgS4 = InArg[which(names(InArg) %in% S4names)]
return(list(InArgS0 = InArgS0, InArgS1 = InArgS1, InArgS2 = InArgS2, InArgS3 = InArgS3,
InArgS4 = InArgS4))
}
# done
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