#' bs
#'
#' bs2
#'
#' @param fastq_file_path ffp
#'
#' @return a val
#' @export
#'
read_fastq <- function(fastq_file_path) {
con <- file(fastq_file_path, open="r")
records <- readLines(con)
close(con)
quality_scores <- records[seq_along(records) %% 4 == 0]
fastq_sequences <- records[seq_along(records) %% 4 == 2]
sequence_ids <- records[seq_along(records) %% 4 == 1]
sequence_ids <- sapply(sequence_ids,
FUN = function(d){substring(d, regexpr('@',d) + 1, nchar(d))},
USE.NAMES=FALSE)
fastq_data <- data.frame(id=sequence_ids,
sequence=fastq_sequences,
quality_score=quality_scores,
stringsAsFactors = FALSE)
return(fastq_data)
}
#fastq_data <- read_fastq('~/Downloads/SP1.fq')
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