diff fastqc_report_render.R @ 1:22cd2369354b draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_report_render.R	Mon Aug 07 21:40:45 2017 -0400
@@ -0,0 +1,87 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+        error=function(){
+          cat(geterrmessage(), file=stderr())
+          quit("no", 1, F)
+        })
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+  library(getopt)
+  library(tools)
+})
+
+# column 1: the long flag name
+# column 2: the short flag alias. A SINGLE character string
+# column 3: argument mask
+#           0: no argument
+#           1: argument required
+#           2: argument is optional
+# column 4: date type to which the flag's argument shall be cast.
+#           possible values: logical, integer, double, complex, character.
+spec_list=list()
+spec_list$READS = c('reads', 'r', '1', 'character')
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+spec_list$FASTQC_TPL = c('fastqc_tpl', 'p', 1, 'character')
+spec_list$REPORT = c('report', 'o', '1', 'character')
+spec_list$REPORT_OUTPUT_DIR = c('report_output_dir', 'd', '1', 'character')
+
+
+spec = t(as.data.frame(spec_list))
+
+opt = getopt(spec)
+# arguments are accessed by long flag name (the first column in the spec matrix)
+#                        NOT by element name in the spec_list
+# example: opt$help, opt$expression_file
+##====== End of arguments handling ==========
+
+
+mgsub = function(pattern, replacement, x) {
+  if(length(pattern) != length(replacement) ) {
+    stop("pattern and replacement have to be the same in length")
+  }
+  
+  result = x
+  
+  for(i in 1:length(pattern)) {
+    result = try( gsub(pattern[i], replacement[i], x = result) )
+  }
+  
+  result
+}
+
+
+##====== replace variables in tpl file ======
+p = c('READS', 
+      'ECHO',
+      'FASTQC_TPL',
+      'REPORT_OUTPUT_DIR',
+      'REPORT')
+r = c(opt$reads,
+      opt$echo,
+      opt$fastqc_tpl,
+      opt$report_output_dir,
+      opt$report)
+
+fastqc_report_tpl = mgsub(p, r, readLines(opt$fastqc_tpl))
+
+##====== write replaced text into Rmd file ===
+fileConn = file('fastqc_report.Rmd')
+writeLines(fastqc_report_tpl, con=fileConn)
+close(fileConn)
+
+##====== render Rmd files ====================
+rmarkdown::render('fastqc_report.Rmd')
+file.copy('fastqc_report.html', opt$report, recursive=TRUE)
+paste0('cp -r ./* ', opt$report_output_dir) %>%
+  system()
+