Mercurial > repos > mingchen0919 > aurora_htseq
view htseq_count_render.R @ 1:cc33706a1d4b draft
update
author | mingchen0919 |
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date | Tue, 06 Mar 2018 17:38:58 -0500 |
parents | 10a460f61ac2 |
children | db9da9716914 |
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##============ Sink warnings and errors to a file ============== ## use the sink() function to wrap all code within it. ##============================================================== zz = file('warnings_and_errors.txt') sink(zz) sink(zz, type = 'message') #------------import libraries-------------------- options(stringsAsFactors = FALSE) library(getopt) library(rmarkdown) #------------------------------------------------ #------------get arguments into R-------------------- # library(dplyr) # getopt_specification_matrix(extract_short_flags('htseq_count.xml')) %>% # write.table(file = 'spec.txt', sep = ',', row.names = FALSE, col.names = TRUE, quote = FALSE) spec_matrix = as.matrix( data.frame(stringsAsFactors=FALSE, long_flags = c("X_e", "X_o", "X_d", "X_s", "X_t", "X_f", "X_r", "X_S", "X_a", "X_T", "X_i", "X_I", "X_m"), short_flags = c("e", "o", "d", "s", "t", "f", "r", "S", "a", "T", "i", "I", "m"), argument_mask_flags = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), data_type_flags = c("character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "character", "character") ) ) opt = getopt(spec_matrix) #---------------------------------------------------- #-----------using passed arguments in R # to define system environment variables--- do.call(Sys.setenv, opt[-1]) #---------------------------------------------------- #---------- often used variables ---------------- # OUTPUT_DIR: path to the output associated directory, which stores all outputs # TOOL_DIR: path to the tool installation directory OUTPUT_DIR = opt$X_d TOOL_DIR = opt$X_t RMD_NAME = 'htseq_count.Rmd' OUTPUT_REPORT = opt$X_o # create the output associated directory to store all outputs dir.create(OUTPUT_DIR, recursive = TRUE) #-----------------render Rmd-------------- render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT) #------------------------------------------ #==============the end============== ##--------end of code rendering .Rmd templates---------------- sink() ##=========== End of sinking output=============================