diff fastqc_report_render_ori.R @ 14:2efa46ce2c4c draft

upgrade fastqc_report

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fastqc_report_render_ori.R	Wed Oct 18 22:06:39 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()
+