R/utility_installtool_rnaseqpipline.R

In HowardChao/RNA-seq_pipeline:

#' #' Choose the location where 'gene_data' and 'RNAseq_bin' will be installed
#' #' @export
#' SetPrefixPath <- function(path.prefix = "NOT_SET_YET", print = TRUE) {
#'   # Check the prefix exist
#'   if (isTRUE(dir.exists(path.prefix))){
#'     if (substr(path.prefix, nchar(path.prefix), nchar(path.prefix)) != '/') {
#'       pkg.global.path.prefix$data_path <- paste0(path.prefix, '/')
#'     } else {
#'       pkg.global.path.prefix$data_path <- path.prefix
#'     }
#'     if (print) {
#'       cat(c("************** Setting prefix path ************\n"))
#'       cat(paste0("(\u270e) : The following files will be installed under '", pkg.global.path.prefix$data_path, "'\n\n"))
#'     }
#'     return(TRUE)
#'   } else if (path.prefix == "NOT_SET_YET") {
#'     stop("(\u2718) Please give value to prefix path.\n\n")
#'     return(FALSE)
#'   } else {
#'     stop(paste0("(\u2718) Prefix path '", path.prefix, "' is invalid. Please try another one.\n\n"))
#'     return(FALSE)
#'   }
#' }

#' #' Checking the absolute path
#' #' @export
#' CheckPrefixPath <- function(path.prefix = pkg.global.path.prefix$data_path, print = TRUE) {
#'   if (print) {
#'     cat(c("************** Checking prefix path ************\n"))
#'   }
#'   if (path.prefix == "NOT_SET_YET") {
#'     stop("(\u2718) You haven't set the prefix directory for the following steps.\n       Please run 'SetPrefixPath()' first to set the prefix directory.\n\n")
#'     return(FALSE)
#'   } else {
#'     if (print) {
#'       cat(paste0("(\u2714) :Prefix directory: '", pkg.global.path.prefix$data_path, "'\n\n"))
#'     }
#'     return(TRUE)
#'   }
#' }

#' Check input files directory
#' @export
CheckInputDirFiles <- function(input.path.prefix = "NOT_SET_YET", gene.name = "NO_DATA", sample.pattern = "NO_DATA", print=TRUE) {
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))){
    if (input.path.prefix == "NOT_SET_YET" ||gene.name == "NO_DATA" || sample.pattern == "NO_DATA"){
      if (input.path.prefix == "NOT_SET_YET") {
        cat("(\u2718) : 'input.path.prefix' is missing.\n     Can't check input file directory.\n\n")
      }
      if (gene.name == "NO_DATA") {
        cat("(\u2718) : 'gene.name' is missing.\n\n")
      }
      if (sample.pattern == "NO_DATA") {
        cat("(\u2718) : 'sample.pattern' is missing.\n\n")
      }
      return(FALSE)
    } else {
      if (substr(input.path.prefix, nchar(input.path.prefix), nchar(input.path.prefix)) != '/') {
        pkg.global.path.prefix$input.files <- paste0(input.path.prefix, '/')
      } else {
        pkg.global.path.prefix$input.files <- input.path.prefix
      }
      input.file.dir <- dir.exists(paste0(pkg.global.path.prefix$input.files, "input_files/"))
      if(!isTRUE(input.file.dir)){
        cat(c("(\u2718) : ", paste0("'",pkg.global.path.prefix$input.files, "input_files/'"), "is not exit. Please check whether prefix absolute path of 'input_files' is valid.\n\n"))
        return(FALSE)
      }
      if (print) {
        cat(c("************** Checking hierarchy of", paste0("'", pkg.global.path.prefix$input.files, 'input_files/\''), "************\n"))
        cat(c("(\u2714) : Prefix of input_files", paste0("'",pkg.global.path.prefix$input.files, "'"), "is valid\n\n"))
      }
      # only check whether exist
      gtf.file <- file.exists(paste0(pkg.global.path.prefix$input.files, "input_files/",gene.name, ".gtf"))
      # only check whether exist
      fa.file <- file.exists(paste0(pkg.global.path.prefix$input.files, "input_files/",gene.name, ".fa"))
      # check exist and rules
      raw.fastq.dir <- dir.exists(paste0(pkg.global.path.prefix$input.files, "input_files/raw_fastq.gz/"))
      # check exist and rules
      phenodata.file <- file.exists(paste0(pkg.global.path.prefix$input.files, "input_files/phenodata.csv"))
      # check exist and rules
      ht2.dir <- dir.exists(paste0(pkg.global.path.prefix$input.files, "input_files/indexes/"))
      if (isTRUE(raw.fastq.dir)) {
        raw.fastq <- list.files(path = paste0(pkg.global.path.prefix$input.files, 'input_files/raw_fastq.gz/'), pattern = sample.pattern, all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
        raw.fastq.number <- length(raw.fastq)
      }
      if (isTRUE(ht2.dir)) {
        ht2.files <- list.files(path = paste0(pkg.global.path.prefix$input.files, 'input_files/indexes/'), pattern = paste0("^", gene.name, "_tran.[0-9]*.ht2$"), all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
        ht2.files.number <- length(ht2.files)
      }
      if (!isTRUE(gtf.file)) {
        grab.gtf.file <- Sys.glob(file.path(path = paste0(pkg.global.path.prefix$input.files, 'input_files'), "*.gtf"))
        cat(paste0("(\u2718) : '", gene.name, ".gtf (user input)' and '", grab.gtf.file, " (find in directory)' ", " are mismatched.\n"))
      } else {
        if (print) {
          cat(paste0("(\u2714) : '", gene.name, ".gtf'", " is in 'input_files'\n"))
        }
      }
      if (!isTRUE(fa.file)) {
        grab.fa.file <- Sys.glob(file.path(path = paste0(pkg.global.path.prefix$input.files, 'input_files'), "*.fa"))
        cat(paste0("(\u2718) : '", gene.name, ".fa (user input)' and '", grab.fa.file, " (find in directory)' ", " are mismatched.\n"))
      } else {
        if (print) {
          cat(paste0("(\u2714) : '", gene.name, ".fa'", " is in 'input_files'\n"))
        }
      }
      if (!isTRUE(raw.fastq.dir)) {
        cat(c("(\u2718) : 'raw_fastq.gz/' is missing.\n"))
      } else {
        if (print) {
          cat(paste0("(\u2714) : 'raw_fastq.gz/' is in 'input_files'\n"))
        }
      }
      if (isTRUE(raw.fastq.dir) && raw.fastq.number == 0) {
        cat(paste0("(\u2718) : Sample pattern \"", sample.pattern ,"\" is not found in 'raw_fastq.gz/'.\n"))
      } else if (isTRUE(raw.fastq.dir) && raw.fastq.number >= 0) {
        if (print){
          for (i in raw.fastq) {
            cat(paste0("(\u2714) : 'raw_fastq.gz/", i, "'"), "is in 'input_files/'\n")
          }
        }
      }
      if (!isTRUE(phenodata.file)) {
        cat(paste0("(\u2718) : '", "phenodata.csv is missing.\n"))
      } else {
        if (print) {
          cat(paste0("(\u2714) : '", "phenodata.csv is in 'input_files'\n"))
        }
      }
      invalid.column.number <- -1
      pheno_data <- read.csv(paste0(pkg.global.path.prefix$input.files, "/input_files/phenodata.csv"))
      sample.table <- as.data.frame(table(pheno_data[1]))
      compare.sample.table <- as.data.frame(table(pheno_data[2]))
      extract.fastq.gz.sample.names <- unique(gsub("_[1-2]*.fastq.gz", "", raw.fastq))
      if(length(extract.fastq.gz.sample.names) == length(row.names(sample.table))){
        # check the number of sample(rows) in 'phenodata.csv' is same as the number of unique samples in 'fastq.gz.files'
        if(identical(sort(extract.fastq.gz.sample.names), sort(as.character(sample.table[1][,1])))){
          # check all the name in bath 'phenodata.csv' and 'fastq.gz.files' are same
          if (length(row.names(compare.sample.table)) == 2) {
            ## only two groups are allowed
            invalid.column.number <- 0
            for( i in 1:length(pheno_data) ){
              if(length(pheno_data[i][is.na(pheno_data[i]) == TRUE]) != 0) {
                invalid.column.number <- invalid.column.number + 1
                cat(paste0("(\u2718) : There are missing values in column '", names(pheno_data[i]), "'\n" ))
              }
            }
            if (invalid.column.number != 0) {
              cat(paste0("(\u2718) : ", invalid.column.number, " columns are invalid. Please fix 'phenodata.csv'\n\n" ))
            }
          }
        } else {
          cat(paste0("(\u2718) : Sample names in 'phenodata.csv' and 'XXX.fastq.gz' are different. Please check 'phenodata.csv' matches the 'XXX.fastq.gz'\n\n" ))
        }
      } else {
        cat(paste0("(\u2718) : The sample's numbers in 'phenodata.csv' and 'XXX.fastq.gz' are different. Please check 'phenodata.csv' matches the 'XXX.fastq.gz'\n\n" ))
      }
      if (!isTRUE(ht2.dir)) {
        ## not exist
        if (print) {
          cat(c("(\u26A0) : 'indexes/' is optional. You can download the corresponding 'XXX.ht2' from 'https://ccb.jhu.edu/software/hisat2/index.shtml' to speed up the process.\n"))
        }
      } else {
        if (print) {
          ## exist
          cat(paste0("(\u2714) : 'indexes/' is in 'input_files'\n"))
        }
      }
      if (isTRUE(ht2.dir) && ht2.files.number == 0) {
        cat(c("(\u26A0) : 'indexes/' directory has been created but there are no samples in 'indexes/' or files' names", paste0("\"^", gene.name, "_tran.[0-9]*.ht2$\""), "in 'indexes/' are not found.\n      No files will be copied.\n      (1). Check whether files name", paste0("'", gene.name, "_tran.[0-9]*.ht2'"), "matches the files in 'indexes' directory.\n      (2). If you don't have", paste0("'", gene.name, "_tran.[0-9].ht2'"), "files, remove 'indexes' directory\n\n"))
        return(FALSE)
      } else if (isTRUE(ht2.dir) && ht2.files.number >= 0) {
        pkg.global.ht2$logic <- TRUE
        if (print){
          for (i in ht2.files) {
            cat(paste0("(\u2714) : 'indexes/", i, "'"), "is in 'input_files/'\n")
          }
        }
      }
      if (isTRUE(gtf.file) && isTRUE(raw.fastq.dir) && isTRUE(raw.fastq.dir) && raw.fastq.number != 0 && isTRUE(phenodata.file) && invalid.column.number == 0 ) {
        if (print) {
          cat(c(paste0("\n(\u2714) : '", pkg.global.path.prefix$input.files,"input_files/", "'"), "is valid !\n"))
          if (isTRUE(ht2.dir) && ht2.files.number != 0) {
            cat(paste0("(\u2714) : optional directory 'indexes/' is valid !\n\n"))
          }
        }
        return(TRUE)
      } else {
        cat("\n")
        return(FALSE)
      }
    }
  }
}

#' Copy input files directory
#' @export
CopyInputDir <- function(input.path.prefix = "NOT_SET_YET", gene.name = "NO_DATA", sample.pattern = "NO_DATA", optional = pkg.global.ht2$logic) {
  if (isTRUE(CheckInputDirFiles(input.path.prefix = input.path.prefix, gene.name = gene.name, sample.pattern = sample.pattern, print=FALSE))) {
    if (isTRUE(CheckDirAll(print = FALSE))){
      current.path <- getwd()
      setwd(paste0(pkg.global.path.prefix$data_path, "gene_data/"))
      cat(c("************** Copying", paste0("'", pkg.global.path.prefix$input.files, "input_files/'"), "************\n"))
      cat(c("Copying From :", paste0(pkg.global.path.prefix$input.files, "input_files/", gene.name, ".gtf"), "\n"))
      file.copy(paste0(pkg.global.path.prefix$input.files, "input_files/", gene.name, ".gtf"), paste0(getwd(), "/ref_genes/", gene.name, ".gtf"))
      cat(c("          To :"), paste0(getwd(), "/ref_genes/", gene.name, ".gtf", "\n"))
      cat(c("Copying From :", paste0(pkg.global.path.prefix$input.files, "input_files/", gene.name, ".fa"),  "\n"))
      file.copy(paste0(pkg.global.path.prefix$input.files, "input_files/", gene.name, ".fa"), paste0(getwd(), "/ref_genome/", gene.name, ".fa"))
      cat(c("          To :"), paste0(getwd(), "/ref_genome/", gene.name, ".fa", "\n"))
      cat(c("Copying From :", paste0(pkg.global.path.prefix$input.files, "input_files/", "raw_fastq.gz/"),  "\n"))
      file.copy(paste0(pkg.global.path.prefix$input.files, "input_files/", "raw_fastq.gz/"), paste0(getwd(), "/"), overwrite = TRUE, recursive = TRUE)
      cat(c("          To :", paste0(getwd(),"/raw_fastq.gz/"), "\n"))
      cat(c("Copying From :", paste0(pkg.global.path.prefix$input.files, "input_files/phenodata.csv"),  "\n"))
      file.copy(paste0(pkg.global.path.prefix$input.files, "input_files/phenodata.csv"), paste0(getwd(), "/phenodata.csv"))
      cat(c("          To :"), paste0(getwd(), "/phenodata.csv\n"))
      on.exit(setwd(current.path))
      if (isTRUE(optional)) {
        cat(c("Copying From :", paste0(pkg.global.path.prefix$input.files, "input_files/", "indexes/"),  "\n"))
        file.copy(paste0(pkg.global.path.prefix$input.files, "input_files/", "indexes/"), paste0(getwd(), "/"), overwrite = TRUE, recursive = TRUE)
        cat(c("          To :", paste0(getwd(),"/indexes/"), "\n\n"))
      } else {
        cat("\n")
      }
    }
  }
}

#' Create sample gene directory
#' @export
MkdirGeneDir <- function() {
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))){
    cat("************** Creating 'gene-data/' directory ************\n")
    gene_data.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/')), showWarnings = FALSE) == 0
    if (!isTRUE(gene_data.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/'.\n     Please check whether the directory is already exit.\n"))
    }
    ref.genome.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/ref_genome/')), showWarnings = FALSE) == 0
    if (!isTRUE(ref.genome.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/ref_genome/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/ref_genome/'.\n     Please check whether the directory is already exit.\n"))
    }
    ref.genes.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/ref_genes/')), showWarnings = FALSE) == 0
    if (!isTRUE(ref.genes.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/ref_genes/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/ref_genes/'.\n     Please check whether the directory is already exit.\n"))
    }
    indexes.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/indexes/')), showWarnings = FALSE) == 0
    if (!isTRUE(indexes.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/indexes/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/indexes/'.\n     Please check whether the directory is already exit.\n"))
    }
    samples.fastq.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/raw_fastq.gz')), showWarnings = FALSE) == 0
    if (!isTRUE(samples.fastq.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/raw_fastq.gz/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/raw_fastq.gz/'.\n     Please check whether the directory is already exit.\n"))
    }
    samples.sam.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/raw_sam')), showWarnings = FALSE) == 0
    if (!isTRUE(samples.sam.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/raw_sam/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/raw_sam/'.\n     Please check whether the directory is already exit.\n"))
    }
    samples.bam.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/raw_bam')), showWarnings = FALSE) == 0
    if (!isTRUE(samples.bam.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/raw_bam/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/raw_bam/'.\n     Please check whether the directory is already exit.\n"))
    }
    samples.gtf.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'gene_data/raw_gtf')), showWarnings = FALSE) == 0
    if (!isTRUE(samples.gtf.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "gene_data/raw_gtf/'.\n\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "gene_data/raw_gtf/'.\n     Please check whether the directory is already exit.\n\n"))
    }
  }
}

#' Make RNAseq_bin/ directory
#' @export
MkdirRNAseq_bin <- function() {
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))){
    cat("************** Creating 'RNAseq_bin/' directory ************\n")
    RNAseq_bin.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'RNAseq_bin/')), showWarnings = FALSE) == 0
    if (!isTRUE(RNAseq_bin.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "RNAseq_bin/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "RNAseq_bin/'.\n     Please check whether the directory is already exit.\n"))
    }
    download.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'RNAseq_bin/Download/')), showWarnings = FALSE) == 0
    if (!isTRUE(download.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "RNAseq_bin/Download/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "RNAseq_bin/Download/'.\n     Please check whether the directory is already exit.\n"))
    }
    unpacked.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'RNAseq_bin/Unpacked/')), showWarnings = FALSE) == 0
    if (!isTRUE(unpacked.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "RNAseq_bin/Unpacked/'.\n\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "RNAseq_bin/Unpacked/'.\n     Please check whether the directory is already exit.\n\n"))
    }
  }
}

#' Make RNAseq_results/ directory
#' @export
MkdirRNAseq_results <- function(){
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))){
    cat("************** Creating 'RNAseq_results/' directory ************\n")
    RNAseq_results.dir <- dir.create(file.path(paste0(pkg.global.path.prefix$data_path, 'RNAseq_results/')), showWarnings = FALSE) == 0
    if (!isTRUE(RNAseq_results.dir)) {
      cat(paste0("(\u2714) : Create '", pkg.global.path.prefix$data_path, "RNAseq_results/'.\n"))
    } else {
      cat(paste0("(\u2718) : Fail to create '", pkg.global.path.prefix$data_path, "RNAseq_results/'.\n     Please check whether the directory is already exit.\n"))
    }
  }
}

#' Check sample gene and binary directory
#' @export
CheckDirAll <- function(print = TRUE) {
  if (print) {
    cat(c("************** Checking 'gene_data/' and 'RNAseq_bin/' directories ************\n"))
  }
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))) {
    gene.data.logic <- dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/ref_genes/")) &&
      dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/ref_genome/")) &&
      dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/indexes/")) &&
      dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/raw_fastq.gz/")) &&
      dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/raw_sam/")) &&
      dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/raw_bam/")) &&
      dir.exists(paste0(pkg.global.path.prefix$data_path, "gene_data/raw_gtf/"))
    rnaseq.bin.logic <- dir.exists(paste0(pkg.global.path.prefix$data_path, "RNAseq_bin/Download/")) && dir.exists(paste0(pkg.global.path.prefix$data_path, "RNAseq_bin/Unpacked/"))
    if (!isTRUE(gene.data.logic)){
      cat(c("There are directories missing in", paste0(pkg.global.path.prefix$data_path, "gene_data/.")), "\n")
    }
    if (!isTRUE(rnaseq.bin.logic)){
      cat(c("There are directories missing in", paste0(pkg.global.path.prefix$data_path, "RNAseq_bin/.")), "\n")
    }
    if (isTRUE(gene.data.logic) && isTRUE(rnaseq.bin.logic)){
      if (print) {
        cat(c("(\u2714) : Directories are all correct.\n\n"))
      }
      return(TRUE)
    } else {
      cat(c("(\u2718) : Please run 'MkdirAll()' to add the missing directories.\n\n"))
      return(FALSE)
    }
  }
}

#' Create sample gene and binary directory
#' @export
MkdirAll <- function() {
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))) {
    MkdirGeneDir()
    MkdirRNAseq_bin()
    MkdirRNAseq_results()
  }
}

#' check 'gene_data' and subdirectory files exit
#' @export
ProgressGenesFiles <- function(gene.name = "NO_DATA", sample.pattern = "NO_DATA", print = TRUE) {
  if (isTRUE(CheckDirAll(print = FALSE))){
    if (gene.name == "NO_DATA" || sample.pattern == "NO_DATA"){
      if (gene.name == "NO_DATA") {
        cat("(\u2718) : gene.name is missing.\n     Gene files checking fails\n\n")
      }
      if (sample.pattern == "NO_DATA"){
        cat("(\u2718) : sample.pattern is missing.\n     Gene files checking fails\n\n")
      }
      return(FALSE)
    } else {
      if (print) {
        cat(paste0("************** Current progress of RNA-seq files in '", paste0(pkg.global.path.prefix$data_path, "gene_data/'"), " **************\n"))
      }
      gtf.file <- file.exists(paste0(pkg.global.path.prefix$data_path, "gene_data", '/ref_genes/', gene.name, '.gtf'))
      if (isTRUE(gtf.file)) {
        if(print){
          cat(c("(\u2714) :", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/ref_genes/', gene.name, '.gtf', "'"), "is exit\n\n"))
        }
      } else {
        cat(c("(\u2718) :", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/ref_genes/', gene.name, '.gtf', "'"), "is not exit\n"))
        cat(c("     Put the", paste0("'",gene.name,".gtf", "'"), "file in", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/ref_genes/', "'"), "to fix the error.\n\n"))
      }
      fa.file <- file.exists(paste0(pkg.global.path.prefix$data_path, "gene_data", '/ref_genome/', gene.name, '.fa'))
      if (isTRUE(fa.file)) {
        if(print){
          cat(c("(\u2714) :",paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/ref_genome/', gene.name, '.fa', "'"), "is exit\n\n"))
        }
      } else {
        cat(c("(\u2718) :",paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/ref_genome/', gene.name, '.fa', "'"), "is not exit\n"))
        cat(c("     Put the", paste0("'",gene.name,".fa", "'"), "file in", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/ref_genome/', "'"), "to fix the error.\n\n"))
      }
      fastq.gz.files <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/raw_fastq.gz/'), pattern = sample.pattern, all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      fastq.gz.files.number <- length(fastq.gz.files)
      if (fastq.gz.files.number != 0){
        if(print){
          for (i in fastq.gz.files){
            cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/raw_fastq.gz/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", fastq.gz.files.number, "files\n\n"))
        }
      }else {
        cat(c("(\u2718) :", paste0('\'',pkg.global.path.prefix$data_path, "gene_data", '/raw_fastq.gz/XXX_*.fastq.gz\''), "is not exit\n"))
        cat(c("     Put the", paste0('XXX_*.fastq.gz'), "file in", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/raw_fastq.gz/', "'"), "to fix the error.\n\n"))
      }
      phenodata.file <- file.exists(paste0(pkg.global.path.prefix$data_path, "gene_data", '/phenodata.csv'))
      invalid.column.number <- -1
      adjustvars <- c()
      pheno_data <- read.csv(paste0(pkg.global.path.prefix$data_path, "gene_data", "/phenodata.csv"))
      sample.table <- as.data.frame(table(pheno_data[1]))
      compare.sample.table <- as.data.frame(table(pheno_data[2]))
      extract.fastq.gz.sample.names <- unique(gsub("_[1-2]*.fastq.gz", "", fastq.gz.files))
      if(length(extract.fastq.gz.sample.names) == length(row.names(sample.table))){
        # check the number of sample(rows) in 'phenodata.csv' is same as the number of unique samples in 'fastq.gz.files'
        if(identical(sort(extract.fastq.gz.sample.names), sort(as.character(sample.table[1][,1])))){
          # check all the name in bath 'phenodata.csv' and 'fastq.gz.files' are same
          if (length(row.names(compare.sample.table)) == 2) {
            ## only two groups are allowed
            invalid.column.number <- 0
            adjustvars <- c()
            for( i in 1:length(pheno_data) ){
              if(length(pheno_data[i][is.na(pheno_data[i]) == TRUE]) != 0) {
                invalid.column.number <- invalid.column.number + 1
                cat(paste0("(\u2718) : There are missing values in column '", names(pheno_data[i]), "'\n" ))
              }
              if(i > 2){
                adjustvars <- append(adjustvars, names(pheno_data[i]))
              }
            }
            if (invalid.column.number != 0) {
              cat(paste0("(\u2718) : ", invalid.column.number, " columns are invalid. Please fix 'phenodata.csv'\n\n" ))
              adjustvars <- c()
            }
          }
        } else {
          cat(paste0("(\u2718) : Sample names in 'phenodata.csv' and 'XXX.fastq.gz' are different. Please check 'phenodata.csv' matches the 'XXX.fastq.gz'\n\n" ))
        }
      } else {
        cat(paste0("(\u2718) : The sample's numbers in 'phenodata.csv' and 'XXX.fastq.gz' are different. Please check 'phenodata.csv' matches the 'XXX.fastq.gz'\n\n" ))
      }
      if (isTRUE(gtf.file)) {
        if(print){
          cat(c("(\u2714) :", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/phenodata.csv', "'"), "is exit\n\n"))
        }
      } else {
        cat(c("(\u2718) :", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/phenodata.csv', "'"), "is not exit\n"))
        cat(c("     Put the", paste0("'phenodata.csv'"), "file in", paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/', "'"), "to fix the error.\n\n"))
      }
      ht2.files <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/indexes/'), pattern = paste0("^", gene.name, "_tran.[0-9]*.ht2$"), all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      ht2.files.number <- length(ht2.files)
      if (ht2.files.number != 0) {
        if (print) {
          for (i in ht2.files){
            cat(c("(\u2714) :",paste0("'",pkg.global.path.prefix$data_path, "gene_data", '/indexes/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", ht2.files.number, "files\n\n"))
        }
      } else {
        cat(c("(\u231B) :", paste0('\'',pkg.global.path.prefix$data_path, "gene_data", '/indexes/', gene.name, '_tran.*.ht2\''), "is not exit\n"))
        cat("       Files haven't created yet. Run 'CreateHisat2Index()' to generate '*.ht2' files or download from 'https://ccb.jhu.edu/software/hisat2/index.shtml'\n\n")
      }
      sam.files <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/raw_sam/'), pattern = paste0( "^[A-Z, a-z]*", "[0-9]*", "[A-Z, a-z]*", ".sam$"), all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      sam.files.number <- length(sam.files)
      if (sam.files.number != 0){
        if (print) {
          for (i in sam.files){
            cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/raw_sam/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", sam.files.number, "files\n\n"))
        }
      }else {
        cat(c("(\u231B) :", paste0('\'', pkg.global.path.prefix$data_path, "gene_data", '/raw_sam/XXX.sam\''), "is not exit\n"))
        cat("       Files haven't created yet. Run 'Hisat2AlignmentDefault()' to generate 'XXX.sam' files\n\n")
      }
      bam.files <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/raw_bam/'), pattern = paste0( "^[A-Z, a-z]*", "[0-9]*", "[A-Z, a-z]*", ".bam$"), all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      bam.files.number <- length(bam.files)
      if (bam.files.number != 0){
        if (print) {
          for (i in bam.files){
            cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/raw_bam/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", bam.files.number, "files\n\n"))
        }
      }else {
        cat(c("(\u231B) :", paste0('\'', pkg.global.path.prefix$data_path, "gene_data", '/raw_sam/XXX.bam\''), "is not exit\n"))
        cat("       Files haven't created yet. Run 'SamtoolsToBam()' to generate 'XXX.bam' files\n\n")
      }
      gtf.files <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/raw_gtf/'), pattern = paste0("^[A-Z, a-z]*", "[0-9]*", "[A-Z, a-z]*", ".gtf$"), all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      gtf.files.number <- length(gtf.files)
      if (gtf.files.number != 0){
        if (print) {
          for (i in gtf.files){
            cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/raw_gtf/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", gtf.files.number, "files\n\n"))
        }
      }else {
        cat(c("(\u231B) :", paste0('\'',pkg.global.path.prefix$data_path, "gene_data", '/raw_gtf/XXX.gtf\''), "is not exit\n"))
        cat("       Files haven't created yet. Run 'StringTieAssemble()' to generate 'XXX.gtf' files\n\n")
      }
      stringtie_merged.gtf.file <- file.exists(paste0(pkg.global.path.prefix$data_path, "gene_data", '/merged/stringtie_merged.gtf'))
      if (isTRUE(stringtie_merged.gtf.file)) {
        if (print) {
          cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", "/merged/stringtie_merged.gtf", "'"), "is exit\n\n"))
        }
      } else {
        cat(c("(\u231B) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", "/merged/stringtie_merged.gtf", "'"), "is not exit\n"))
        cat("       Files haven't created yet. Run 'StringTieMergeTrans()' to generate 'stringtie_merged.gtf' files\n\n")
      }
      gffcompare.related.dirs <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/merged/'), pattern = "^merged.", all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      gffcompare.related.dirs.number <- length(gffcompare.related.dirs)
      if (gffcompare.related.dirs.number != 0){
        if (print) {
          for (i in gffcompare.related.dirs){
            cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/merged/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", gffcompare.related.dirs.number, "files\n\n"))
        }
      }else {
        cat(c("(\u231B) :", paste0('\'', pkg.global.path.prefix$data_path, "gene_data", '/merged/', "merged.", "XXX/"), "is not exit\n"))
        cat("       Directories haven't created yet. Run 'GffcompareRefSample()' to generate", paste0("merged/", "merged.XXX/"), "files\n\n")
      }
      ballgown.dirs <- list.files(path = paste0(pkg.global.path.prefix$data_path, "gene_data", '/ballgown/'), pattern = sample.pattern, all.files = FALSE, full.names = FALSE, recursive = FALSE, ignore.case = FALSE)
      ballgown.dirs.number <- length(ballgown.dirs)
      if (ballgown.dirs.number != 0){
        if (print) {
          for (i in ballgown.dirs){
            cat(c("(\u2714) :", paste0("'", pkg.global.path.prefix$data_path, "gene_data", '/ballgown/', i, "'"), "is exit\n"))
          }
          cat(c("Total:", ballgown.dirs.number, "directories\n\n"))
        }
      }else {
        cat(c("(\u231B) :", paste0('\'',pkg.global.path.prefix$data_path, "gene_data", '/ballgown/', gsub(".fastq.gz", replace = "", sample.pattern), "/"), "is not exit\n"))
        cat("       Directories haven't created yet. Run 'StringTieToBallgown()' to generate", paste0("ballgown/", sample.pattern, "/"), "directories\n\n")
      }
      return(list(gtf.file.logic.df = gtf.file, fa.file.logic.df = fa.file,
                  fastq.gz.files.number.df = fastq.gz.files.number,
                  fastq.gz.files.df = fastq.gz.files,
                  phenodata.file.df = phenodata.file,
                  phenodata.invalid.column.number.df = invalid.column.number,
                  phenodata.adjustvars.df = adjustvars,
                  ht2.files.number.df = ht2.files.number,
                  ht2.files.df = ht2.files,
                  sam.files.number.df = sam.files.number,
                  sam.files.df = sam.files,
                  bam.files.number.df = bam.files.number,
                  bam.files.df = bam.files,
                  gtf.files.number.df = gtf.files.number,
                  gtf.files.df = gtf.files,
                  stringtie_merged.gtf.file.df = stringtie_merged.gtf.file,
                  gffcompare.related.dirs.df = gffcompare.related.dirs,
                  gffcompare.related.dirs.number.df = gffcompare.related.dirs.number,
                  ballgown.dirs.number.df = ballgown.dirs.number,
                  ballgown.dirs.df = ballgown.dirs))
    }
  }
}

#' Add '~/RNAseq_bin/ to R environment "PATH"
#' @export
ExportPath <- function() {
  if (isTRUE(CheckPrefixPath(pkg.global.path.prefix$data_path, print = FALSE))){
    cat("************** Adding PATH to R environment ************\n")
    old.path <- Sys.getenv("PATH")
    Sys.setenv(
      PATH = paste(old.path, paste0(pkg.global.path.prefix$data_path, "RNAseq_bin"), sep = ":")
    )
    cat("\u27a4\u27a4 R environment 'PATH' : ", Sys.getenv("PATH"), "\n\n")
  }
}