two tables

dge_workflow/cutadapt_summary.R

+#!/usr/bin/env Rscript
+#' # First try
+##+ echo=FALSE, message=FALSE
+
+## Note This script is supposed to be knitr::spin'ed
+
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/core_commons.R")
+devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/ggplot_commons.R")
+
+## can we access variables from the parent spin.R process?
+#echo("rscript is ", r_script)
+
+argv = commandArgs(TRUE)
+#echo("argv is ", argv)
+
+#if(str_detect(argv[1], "fastqc_summary")) argv <- argv[-1]
+
+if(length(argv) != 1){
+  stop("Usage: First_try.R <directory with cutadapt log files>")
+  echo
+}
+
+baseDir=argv[1]
+
+
+if(is.na(file.info(baseDir)$isdir)){
+  stop(paste("directory '", baseDir,"'does not exist"))
+}
+
+baseDir="/home/mel/MPI-Bioinf/Project1_reads/141126_cutadapt_logs"
+
+
+logDataFiles <- list.files(path=baseDir, pattern="ca.fastq.gz.ca.log", full.names=TRUE, recursive=T)
+
+#echo("files are", logDataFiles)
+
+#' ## Title
+echo("Quality Control Summary")
+#' ## General information
+info1=readLines(pipe( paste("grep -F 'cutadapt' ", logDataFiles[1]) ))
+echo(info1)
+info2=readLines(pipe( paste("grep -F 'Maximum error rate' ", logDataFiles[1]) ))
+echo(info2)
+info3=readLines(pipe( paste("grep -F 'No. of adapters' ", logDataFiles[1]) ))
+echo(info3)
+
+#' ## cutadapt parameters:
+parameters=readLines(pipe( paste("grep -F 'Command line parameters' ", logDataFiles[1]) ))
+echo(parameters)
+
+echo("Some explanation:")
+if (grepl("-a", parameters) ==TRUE)
+  echo("-a indicates that the following is a 3' adapter.")
+if (grepl("-g", parameters) ==TRUE)
+  echo("-g indicates that the following is a 5' adapter.")
+if (grepl("-b", parameters) ==TRUE)
+  echo("-b indicates that the adapter is 3' or 5' (both possible).")
+if (grepl("-m", parameters) ==TRUE)
+  echo("Reads shorter than -m bases are thrown away.")
+if (grepl("-q", parameters) ==TRUE)
+  echo("Quality trimming is done with a threshold specified after -q.")
+if (grepl("-p", parameters) ==TRUE)
+  echo("option 'paired output' is used.")
+if (grepl("-e", parameters) ==TRUE)
+  echo("-e changes the error tolerance. (The default maximum error rate is 0.1)")
+if (grepl("-O", parameters) ==TRUE)
+  echo("The minimum overlap length is changed using -O.")
+if (grepl("-N", parameters) ==TRUE)
+  echo("Wildcard characters in the adapter are enabled by -N.")
+
+echo("For more detailed information on cutadapt go to https://cutadapt.readthedocs.org/en/latest/index.html")
+
+
+#' ## Table 1: information of each run
+genTable1 <- function(logFile){
+  data.frame(
+    run=sub("^([^.]*).*", "\\1", basename(logFile)),
+    num_proReads=(paste("grep -F 'Processed reads' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9]+") %>% unlist() %>% as.numeric())[2],
+    num_proBases=(paste("grep -F 'Processed bases' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9]+") %>% unlist() %>% as.numeric())[2],
+    trim_reads=(paste("grep -F 'Trimmed reads' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[3],
+    qual_trimmed=(paste("grep -F 'Quality-trimmed' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[4],
+    trim_bases=(paste("grep -F 'Trimmed bases' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[4],
+    too_short=(paste("grep -F 'Too short reads' ", logFile )  %>% pipe() %>% readLines() %>% strsplit( "[^0-9\\.]+") %>% unlist() %>% as.numeric())[3]
+  )
+}
+table1 <- logDataFiles %>% ldply(genTable1) %>% print_head()
+
+#' ## Table 2: adapter information (of each run)
+genTable2 <- function(logFile){
+  #browser()
+  data.frame(
+    run=sub("^([^.]*).*", "\\1", basename(logFile)),
+    adapter=(paste("grep -F '=== Adapter ' ", logFile )  %>% pipe() %>% readLines() %>% str_split_fixed("'", 3))[,2],
+    trimmed=(paste("grep -F '; Trimmed: ' ", logFile )  %>% pipe() %>% readLines() %>% str_split_fixed( "[^0-9]+", 6))[,5] %>% as.numeric(),
+    overlapped5=(paste("grep -F 'overlapped the 5' ", logFile )  %>% pipe() %>% readLines() %>% str_split_fixed( "[^0-9]+", 2) )[,1] %>% as.numeric(),
+    overlapped3=(paste("grep -F 'overlapped the 3' ", logFile )  %>% pipe() %>% readLines() %>% str_split_fixed( "[^0-9]+", 2) )[,1] %>% as.numeric()
+  )
+}
+table2 <- logDataFiles %>% ldply(genTable2) %>% print_head()
+