--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/tarean/tarean.R	Thu Dec 19 10:24:45 2019 -0500
@@ -0,0 +1,66 @@
+#!/usr/bin/env Rscript
+library(optparse, quiet = TRUE)
+library(parallel)
+if (interactive()){
+  ## define functions only and exit
+  ## assume that working directory was changes with source( chdir=TRUE)!!!
+  script.dir=normalizePath('.')
+  source('methods.R')
+  source('logo_methods.R')
+  source('htmlheader.R')
+  options(OGDF = paste0(script.dir,"/OGDF/runOGDFlayout"))
+  
+}else{
+  ## get options from command line
+  initial.options <- commandArgs(trailingOnly = FALSE)
+  file.arg.name <- "--file="
+  script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
+  script.dir <- normalizePath(dirname(script.name))
+  oridir=getwd()
+  ## parse arguments
+  option_list = list(
+    make_option(c('-i', '--input_sequences'),action='store',type='character',help='fasta file with input sequences',default=NA),
+    make_option(c('-o', '--output_dir'),action='store',type='character',help='output directory',default="./kmer_analysis"),
+    make_option(c('-m', '--min_kmer_length'),action='store',type='numeric',help='min kmer length',default=11),
+    make_option(c('-x', '--max_kmer_length'),action='store',type='numeric',help='min kmer length',default=27),
+    make_option(c('-n', '--cpu'),action='store',type='numeric',help='number of cpu to use',default=NULL),
+    make_option(c('-s', '--sample_size'),action='store',type='numeric',help='number of sequences to use for analysis, is set to 0 all sequences are used',default=10000),
+    make_option(c('-r', '--reorient_reads'),action='store_true',type='logical',help='number of cpu to use',default=FALSE),
+    make_option(c('-l', '--no_layout'),action='store_true',type='logical',help='do not calculate graph layout',default=FALSE),
+    make_option(c('-p', '--paired'),action='store_true',type='logical',help='reads are paired',default=FALSE),
+    make_option(c('-t', '--tRNA_database='), action='store',type='character',help='path to tRNA database, is set PBS detection is performed',default=NULL)
+    
+  )
+
+  description = paste (strwrap(" put decription here"), collapse ="\n")
+  epilogue = paste (strwrap(" put epilogue here"), collapse ="\n")
+  parser=OptionParser(
+    option_list=option_list,
+    epilogue=epilogue,
+    description=description,
+    )
+  opt = parse_args(parser, args=commandArgs(TRUE))
+  ## as Rscript
+  options(OGDF = paste0(script.dir,"/OGDF/runOGDFlayout"))
+  CPU = ifelse(is.null(opt$cpu), detectCores(), opt$cpu)
+  source(paste(script.dir,"/","methods.R", sep=''))
+  source(paste(script.dir,"/","logo_methods.R", sep=''))
+  source(paste(script.dir,"/","htmlheader.R", sep=''))
+  ## set number of CPU to use
+
+
+  
+  ## run tarean:
+  tarean(
+    opt$input_sequences,
+    opt$output_dir,
+    opt$min_kmer_length,
+    opt$max_kmer_length,
+    CPU,
+    opt$sample_size,
+    opt$reorient_reads,
+    opt$tRNA_database,
+    !opt$no_layout,
+    paired = opt$paired
+    )
+}