Mercurial > repos > petr-novak > repeatrxplorer
view lib/tarean/tarean.R @ 0:1d1b9e1b2e2f draft
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author | petr-novak |
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date | Thu, 19 Dec 2019 10:24:45 -0500 |
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#!/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 ) }