diff options
Diffstat (limited to 'scripts/rqtl_wrapper.R')
| -rw-r--r-- | scripts/rqtl_wrapper.R | 16 |
1 files changed, 7 insertions, 9 deletions
diff --git a/scripts/rqtl_wrapper.R b/scripts/rqtl_wrapper.R index ea2c345..2ac8faa 100644 --- a/scripts/rqtl_wrapper.R +++ b/scripts/rqtl_wrapper.R @@ -3,8 +3,6 @@ library(qtl) library(stringi) library(stringr) -tmp_dir = Sys.getenv("TMPDIR") - option_list = list( make_option(c("-g", "--geno"), type="character", help=".geno file containing a dataset's genotypes"), make_option(c("-p", "--pheno"), type="character", help="File containing two columns - sample names and values"), @@ -18,7 +16,7 @@ option_list = list( make_option(c("--pstrata"), action="store_true", default=NULL, help="Use permutation strata (stored as final column/vector in phenotype input file)"), make_option(c("-s", "--scale"), type="character", default="mb", help="Mapping scale - Megabases (Mb) or Centimorgans (cM)"), make_option(c("--control"), type="character", default=NULL, help="Name of marker (contained in genotype file) to be used as a control"), - make_option(c("-o", "--outdir"), type="character", default=file.path(tmp_dir, "output"), help="Directory in which to write result file"), + make_option(c("-o", "--outdir"), type="character", default=NULL, help="Directory in which to write result file"), make_option(c("-f", "--filename"), type="character", default=NULL, help="Name to use for result file"), make_option(c("-v", "--verbose"), action="store_true", default=NULL, help="Show extra information") ); @@ -58,7 +56,7 @@ geno_file = opt$geno pheno_file = opt$pheno # Generate randomized filename for cross object -cross_file = file.path(tmp_dir, "cross", paste(stri_rand_strings(1, 8), ".cross", sep = "")) +cross_file = file.path(opt$outdir, "cross", paste(stri_rand_strings(1, 8), ".cross", sep = "")) trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) } @@ -258,9 +256,9 @@ if (!is.null(opt$pairscan)) { # Calculate permutations if (opt$nperm > 0) { if (!is.null(opt$filename)){ - perm_out_file = file.path(opt$outdir, paste("PERM_", opt$filename, sep = "" )) + perm_out_file = file.path(opt$outdir, "output", paste("PERM_", opt$filename, sep = "" )) } else { - perm_out_file = file.path(opt$outdir, paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = "")) + perm_out_file = file.path(opt$outdir, "output", paste(pheno_name, "_PERM_", stri_rand_strings(1, 8), sep = "")) } if (!is.null(opt$addcovar) || !is.null(opt$control)){ @@ -284,9 +282,9 @@ if (opt$nperm > 0) { } if (!is.null(opt$filename)){ - out_file = file.path(opt$outdir, opt$filename) + out_file = file.path(opt$outdir, "output", opt$filename) } else { - out_file = file.path(opt$outdir, paste(pheno_name, "_", stri_rand_strings(1, 8), sep = "")) + out_file = file.path(opt$outdir, "output", paste(pheno_name, "_", stri_rand_strings(1, 8), sep = "")) } if (!is.null(opt$addcovar) || !is.null(opt$control)){ @@ -299,7 +297,7 @@ if (!is.null(opt$addcovar) || !is.null(opt$control)){ verbose_print('Writing results to CSV file\n') if (!is.null(opt$pairscan)) { - map_out_file = file.path(opt$outdir, paste("MAP_", opt$filename, sep = "" )) + map_out_file = file.path(opt$outdir, "output", paste("MAP_", opt$filename, sep = "" )) write.csv(qtl_results[1], out_file) write.csv(qtl_results[2], map_out_file) } else { |