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comparison ideas_preprocessor.R @ 7:92bb33490bb4 draft

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Uploaded
author greg
date Wed, 24 Jan 2018 09:55:28 -0500
parents 2b4e1bd725f7
children 0cf23f33d13d
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6:6fe65d1379a8 7:92bb33490bb4
1 (.venv) [galaxy@IDEAS ideas_preprocessor]$ cat ideas_preprocessor.R
2 #!/usr/bin/env Rscript 1 #!/usr/bin/env Rscript
3 2
4 suppressPackageStartupMessages(library("data.table")) 3 suppressPackageStartupMessages(library("data.table"))
5 suppressPackageStartupMessages(library("optparse")) 4 suppressPackageStartupMessages(library("optparse"))
6 5
86 for (i in 1:length(tmp_files)) { 85 for (i in 1:length(tmp_files)) {
87 from_path = paste(tmp_dir, tmp_files[i], sep="/"); 86 from_path = paste(tmp_dir, tmp_files[i], sep="/");
88 to_path = paste(output_tmp_dir, tmp_files[i], sep="/"); 87 to_path = paste(output_tmp_dir, tmp_files[i], sep="/");
89 file.rename(from_path, to_path); 88 file.rename(from_path, to_path);
90 } 89 }
91 if (!is.nulll(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) { 90 if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) {
92 # Rename chrom_bed_input to chromosomes.txt 91 # Rename chrom_bed_input to chromosomes.txt
93 # and move it to the output directory. 92 # and move it to the output directory.
94 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/"); 93 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
95 file.rename(opt$chrom_bed_input, to_path) 94 file.rename(opt$chrom_bed_input, to_path)
96 # Move chromosome_windows.txt to the output directory. 95 # Move chromosome_windows.txt to the output directory.