R/reading_in.R

In georgedashen/zhcweek5: Extract the values for a specific test run by FastQC on a single fastq file

#' Function for parsing the text output of FastQC
#'
#' This functions extracts the values for a specific test run by Fast
#' QC on asingle fastq file.
#'
#' @param file string that specifies the path to an individual FastQC
#' result file (tyically named "fastqc_data.txt)"
#' @param sample A sample name that would be specified by user.
#' @param test Indicate which test results should be extracted. Default:
#' "Per base sequence quality". Other options are, for example, "Per
#'  tile sequence quality",
#' "Per sequence quality score" etc.
#'
#' @return data.frame with the values of a single FastQC test result.
#'
#' @examples \dontrun{
#' res <- reading_in(file =
#' "acinar-3_S9_L001_R1_001_fastqc/fastqc_data.txt")
#' }

reading_in <- function(file, sample = "",
                       test = "Per base sequence quality"){
## generate the string that will be used for the file parsing

syscommand <- paste0("sed -n '/", test, "/,/END_MODULE/p' ", file,
                     " | grep -v '^>>'")
## use the fread command, which can interpret UNIX commands
## on the fly to
## read in the correct portion of the FastQC result

dat <- data.table::fread( cmd = syscommand, header = TRUE) %>% as.data.frame

if(sample!=""){
sample_name <- rep(sample,nrow(dat))
dat$sample <- sample_name
}

return(dat)

}