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1 #!/usr/bin/env Rscript
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2 library(optparse, quiet = TRUE)
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3 library(parallel)
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4 if (interactive()){
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5 ## define functions only and exit
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6 ## assume that working directory was changes with source( chdir=TRUE)!!!
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7 script.dir=normalizePath('.')
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8 source('methods.R')
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9 source('logo_methods.R')
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10 source('htmlheader.R')
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11 options(OGDF = paste0(script.dir,"/OGDF/runOGDFlayout"))
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12
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13 }else{
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14 ## get options from command line
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15 initial.options <- commandArgs(trailingOnly = FALSE)
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16 file.arg.name <- "--file="
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17 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
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18 script.dir <- normalizePath(dirname(script.name))
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19 oridir=getwd()
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20 ## parse arguments
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21 option_list = list(
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22 make_option(c('-i', '--input_sequences'),action='store',type='character',help='fasta file with input sequences',default=NA),
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23 make_option(c('-o', '--output_dir'),action='store',type='character',help='output directory',default="./kmer_analysis"),
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24 make_option(c('-m', '--min_kmer_length'),action='store',type='numeric',help='min kmer length',default=11),
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25 make_option(c('-x', '--max_kmer_length'),action='store',type='numeric',help='min kmer length',default=27),
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26 make_option(c('-n', '--cpu'),action='store',type='numeric',help='number of cpu to use',default=NULL),
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27 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),
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28 make_option(c('-r', '--reorient_reads'),action='store_true',type='logical',help='number of cpu to use',default=FALSE),
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29 make_option(c('-l', '--no_layout'),action='store_true',type='logical',help='do not calculate graph layout',default=FALSE),
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30 make_option(c('-p', '--paired'),action='store_true',type='logical',help='reads are paired',default=FALSE),
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31 make_option(c('-t', '--tRNA_database='), action='store',type='character',help='path to tRNA database, is set PBS detection is performed',default=NULL)
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32
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33 )
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34
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35 description = paste (strwrap(" put decription here"), collapse ="\n")
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36 epilogue = paste (strwrap(" put epilogue here"), collapse ="\n")
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37 parser=OptionParser(
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38 option_list=option_list,
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39 epilogue=epilogue,
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40 description=description,
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41 )
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42 opt = parse_args(parser, args=commandArgs(TRUE))
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43 ## as Rscript
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44 options(OGDF = paste0(script.dir,"/OGDF/runOGDFlayout"))
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45 CPU = ifelse(is.null(opt$cpu), detectCores(), opt$cpu)
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46 source(paste(script.dir,"/","methods.R", sep=''))
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47 source(paste(script.dir,"/","logo_methods.R", sep=''))
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48 source(paste(script.dir,"/","htmlheader.R", sep=''))
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49 ## set number of CPU to use
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50
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51
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52
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53 ## run tarean:
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54 tarean(
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55 opt$input_sequences,
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56 opt$output_dir,
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57 opt$min_kmer_length,
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58 opt$max_kmer_length,
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59 CPU,
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60 opt$sample_size,
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61 opt$reorient_reads,
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62 opt$tRNA_database,
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63 !opt$no_layout,
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64 paired = opt$paired
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65 )
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66 }
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