#' @title Check the hisat2 reports under the curent working directory.
#'
#' @param result_tail define what the tail of the hisat2 output is, default is "_hisat2.out".
#' @param Format whether format the returned output into a \code{data.frame}, default is TRUE.
#'
#' @examples
#' Check_hisat2_reports()
#'
#' @export
#'
Check_hisat2_reports <- function(result_tail="_hisat2.out",Format = T){
Hisat2_Output_filenames <- grep(paste0(result_tail,"$"),list.files(),value = T)
lst_result <- lapply(Hisat2_Output_filenames,readLines)
SRR_names = gsub(paste0(result_tail,"$"),"" ,Hisat2_Output_filenames )
names(lst_result) = SRR_names
if(!Format) {
return( lst_result )
}else{
lst_result_df = lapply( lst_result, function(x) data.frame(Total_Reads = gsub(" .*$","",x[1]),
Unpaired_Reads = paste0( gsub(").*$","",x[2]),")"),
No_alignment = paste0( gsub(").*$","",x[3]),")"),
Uniquely_alignment = paste0( gsub(").*$","",x[4]),")"),
Multiple_alignment = paste0( gsub(").*$","",x[5]),")"),
Mapping_efficiency = gsub(" .*$","",x[6]))
)
df_result = Reduce(rbind,lst_result_df)
df_result$Sample_ID = names(lst_result)
return(df_result[,c(7,1:6)])
}
}
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