Mercurial > repos > greg > ideas_preprocessor

comparison ideas_preprocessor.R @ 29:3b3001355f44 draft

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Uploaded
author greg
date Tue, 06 Feb 2018 08:24:35 -0500
parents 19881f817d25
children 0cb6ff8ba6df
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28:55d264cd49e8 29:3b3001355f44
100 system(cmd); 100 system(cmd);
101 # Move the tmp archive to the output directory. 101 # Move the tmp archive to the output directory.
102 to_path = paste(opt$output_files_path, "tmp.tar.gz", sep="/"); 102 to_path = paste(opt$output_files_path, "tmp.tar.gz", sep="/");
103 file.rename("tmp.tar.gz", to_path); 103 file.rename("tmp.tar.gz", to_path);
104 # Handle file names for display in the primary dataset if necessary. 104 # Handle file names for display in the primary dataset if necessary.
105 if (!is.null(opt$chrom_bed_input) && !is.null(opt$chromosome_windows)) { 105 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/");
106 # Renane opt$chrom_bed_input to be chromosomes.bed 106 if (is.null(opt$chrom_bed_input) {
107 # and make a copy of it in the output directory. 107 # Move cbi_file to the output directory,
108 to_path = paste(opt$output_files_path, "chromosomes.bed", sep="/"); 108 # naming it chromosomes.bed.
109 file.rename(cbi_file, to_path);
110 } else {
111 # Copy opt$chrom_bed_input to the output
112 # directory, naming it chromosomes.bed.
109 file.copy(opt$chrom_bed_input, to_path); 113 file.copy(opt$chrom_bed_input, to_path);
114 }
115 if (!is.null(opt$chromosome_windows)) {
110 # Move chromosome_windows.txt to the output directory. 116 # Move chromosome_windows.txt to the output directory.
111 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/"); 117 to_path = paste(opt$output_files_path, opt$chromosome_windows, sep="/");
112 file.rename(opt$chromosome_windows, to_path); 118 file.rename(opt$chromosome_windows, to_path);
113 } 119 }