#' Run HISAT2
#'
#' @description Runs the HISAT2 tool, can be used for single end and paired end reads
#'
#' @import parallel
#'
#' @param input1 List of the paths to files containing to the forward reads, required
#' @param input2 List of the paths to files containing to the reverse reads, required for paired end sequence data
#' @param index Path to the reference genome hisat2 index, required
#' @param sample.name List of the sample names, required
#' @param strandedness Strand-specific information
#' @param no_splice Disable spliced alignment, use for Trypanosomes
#' @param known_splice File with known splice sites
#' @param assembly Reports alignments tailored for transcript assemblers
#' @param threads Number of threads for hisat2 to use, default set to 10
#' @param phred Quality score offsets, default set to illumina/sanger standard of 33
#' @param out.dir Name of the directory from the HISAT2 output. If NULL,
#' which is the default, a directory named "hisat2_alignments" is created in the current
#' working directory.
#' @param parallel Run in parallel, default set to FALSE
#' @param cores Number of cores/threads to use for parallel processing, default set to 4
#' @param execute Whether to execute the commands or not, default set to TRUE
#' @param hisat2 Path to the HISAT2 program, required
#' @param version Returns the version number
#'
#' @examples
#' \dontrun{
#' trimmed_reads_dir <- "trimmed_reads"
#' mate1 <- list.files(path = trimmed_reads_dir, pattern = "*_R1_001.fastq$", full.names = TRUE)
#' mate2 <- list.files(path = trimmed_reads_dir, pattern = "*_R2_001.fastq$", full.names = TRUE)
#'
#' sample_names <- unlist(lapply(strsplit(list.files(path = trimmed_reads_dir,
#' pattern = "*_R1_001.fastq$",
#' full.names = FALSE),"_"), `[[`, 1))
#'
#' index <- "/export/buzz1/Genome/Homo_sapiens/Ensembl/GRCH38_p7/Sequence/Transcriptome/
#' KallistoIndex/GRCh38_p7.kall"
#'
#' # Paired End example
#' strandedness <- "RF"
#' hisat2.cmds <- run_hisat2(input1 = mate1,
#' input2 = mate2,
#' index = genome,
#' sample.name = sample.names,
#' strandedness = strandedness,
#' assembly = TRUE,
#' out.dir = hisat.alignments.dir,
#' hisat2 = "/software/hisat_v2-2.1.0/hisat2")
#'
#' # Single End example
#' strandedness <- "R"
#' hisat2.cmds <- run_hisat2(input1 = mate1,
#' index = genome,
#' sample.name = sample.names,
#' strandedness = strandedness,
#' assembly = TRUE,
#' out.dir = hisat.alignments.dir,
#' hisat2 = "/software/hisat_v2-2.1.0/hisat2")
#' }
#'
#' @return A list with the HISAT2 commands
#' @export
#'
run_hisat2 <- function(input1 = NULL,
input2 = NULL,
index = NULL,
sample.name = NULL,
strandedness = NULL,
no_splice = FALSE,
known_splice = NULL,
assembly = FALSE,
phred = 33,
threads = 10,
out.dir = NULL,
parallel = FALSE,
cores = 4,
execute = TRUE,
hisat2 = NULL,
version = FALSE){
# Check hisat2 program can be found
sprintf("type -P %s &>//dev//null && echo 'Found' || echo 'Not Found'", hisat2)
# Version
if (isTRUE(version)){
hisat2_run <- sprintf('%s --version',
hisat2)
result <- system(hisat2_run, intern = TRUE)
return(result)
}
# Create the directory to write the data, if it is not present
if (is.null(out.dir)){
out.dir <- "hisat2_alignments"
dir.create(out.dir, showWarnings = FALSE, recursive = TRUE)
}
# Create the sample directories for the per sample HISAT2 results
lapply(paste(out.dir,sample.name, sep = "/"), function(cmd) dir.create(cmd, showWarnings = FALSE, recursive = TRUE))
# Set the additional arguments
args <- ""
# Strandedness
if (!is.null(strandedness)){
args <- paste(args,"--rna-strandness",strandedness,sep = " ")
}
# No spliced alignment
if (isTRUE(no_splice)){
args <- paste(args,"--no-spliced-alignment",sep = " ")
}
# Assembly
if (isTRUE (assembly)){
args <- paste(args,"--dta",sep = " ")
}
# Threads
if (!is.null(threads)){
args <- paste(args,paste("--threads",threads,sep = "="),sep = " ")
}
# Phred score
if (phred != 33){
args <- paste(args,"--phred64",sep = " ")
}else{
args <- paste(args,"--phred33",sep = " ")
}
# Known splice
if (!is.null(known_splice)){
args <- paste(args,"--known-splicesite-infile",known_splice,sep = " ")
}
# Set the names for the alignment and logfiles
logfile <- paste(out.dir,sample.name,paste(sample.name,"log",sep = "."),sep = "/")
samfile <- paste(out.dir,sample.name,paste(sample.name,"sam",sep = "."),sep = "/")
# Create the HISAT2 commands
# Paired end
if (!is.null(input2)){
hisat2.run <- sprintf('%s %s -x %s -1 %s -2 %s -S %s > %s 2>&1',
hisat2,args,index,input1,input2,samfile,logfile)
}
# Single end
else if (is.null(input2)){
hisat2.run <- sprintf('%s %s -x %s -U %s -S %s > %s 2>&1',
hisat2,args,index,input1,samfile,logfile)
}
# Run the HISAT2 commands
if (isTRUE(execute)){
if (isTRUE(parallel)){
cluster <- makeCluster(cores)
parLapply(cluster, hisat2.run, function (cmd) system(cmd))
stopCluster(cluster)
}else{
lapply(hisat2.run, function (cmd) system(cmd))
}
}
# Return the list of HISAT2 commands
return(hisat2.run)
}
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