Mercurial > repos > petr-novak > repeatrxplorer

comparison lib/tarean/tarean.R @ 0:1d1b9e1b2e2f draft

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author petr-novak
date Thu, 19 Dec 2019 10:24:45 -0500
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-1:000000000000 0:1d1b9e1b2e2f
1 #!/usr/bin/env Rscript
2 library(optparse, quiet = TRUE)
3 library(parallel)
4 if (interactive()){
5 ## define functions only and exit
6 ## assume that working directory was changes with source( chdir=TRUE)!!!
7 script.dir=normalizePath('.')
8 source('methods.R')
9 source('logo_methods.R')
10 source('htmlheader.R')
11 options(OGDF = paste0(script.dir,"/OGDF/runOGDFlayout"))
12
13 }else{
14 ## get options from command line
15 initial.options <- commandArgs(trailingOnly = FALSE)
16 file.arg.name <- "--file="
17 script.name <- sub(file.arg.name, "", initial.options[grep(file.arg.name, initial.options)])
18 script.dir <- normalizePath(dirname(script.name))
19 oridir=getwd()
20 ## parse arguments
21 option_list = list(
22 make_option(c('-i', '--input_sequences'),action='store',type='character',help='fasta file with input sequences',default=NA),
23 make_option(c('-o', '--output_dir'),action='store',type='character',help='output directory',default="./kmer_analysis"),
24 make_option(c('-m', '--min_kmer_length'),action='store',type='numeric',help='min kmer length',default=11),
25 make_option(c('-x', '--max_kmer_length'),action='store',type='numeric',help='min kmer length',default=27),
26 make_option(c('-n', '--cpu'),action='store',type='numeric',help='number of cpu to use',default=NULL),
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),
28 make_option(c('-r', '--reorient_reads'),action='store_true',type='logical',help='number of cpu to use',default=FALSE),
29 make_option(c('-l', '--no_layout'),action='store_true',type='logical',help='do not calculate graph layout',default=FALSE),
30 make_option(c('-p', '--paired'),action='store_true',type='logical',help='reads are paired',default=FALSE),
31 make_option(c('-t', '--tRNA_database='), action='store',type='character',help='path to tRNA database, is set PBS detection is performed',default=NULL)
32
33 )
34
35 description = paste (strwrap(" put decription here"), collapse ="\n")
36 epilogue = paste (strwrap(" put epilogue here"), collapse ="\n")
37 parser=OptionParser(
38 option_list=option_list,
39 epilogue=epilogue,
40 description=description,
41 )
42 opt = parse_args(parser, args=commandArgs(TRUE))
43 ## as Rscript
44 options(OGDF = paste0(script.dir,"/OGDF/runOGDFlayout"))
45 CPU = ifelse(is.null(opt$cpu), detectCores(), opt$cpu)
46 source(paste(script.dir,"/","methods.R", sep=''))
47 source(paste(script.dir,"/","logo_methods.R", sep=''))
48 source(paste(script.dir,"/","htmlheader.R", sep=''))
49 ## set number of CPU to use
50
51
52
53 ## run tarean:
54 tarean(
55 opt$input_sequences,
56 opt$output_dir,
57 opt$min_kmer_length,
58 opt$max_kmer_length,
59 CPU,
60 opt$sample_size,
61 opt$reorient_reads,
62 opt$tRNA_database,
63 !opt$no_layout,
64 paired = opt$paired
65 )
66 }