#' Read sequences from .txt file
#'
#' Read sequence data saved in text file.
#'
#' @param connection a \code{\link{connection}} to the text (.txt) file.
#' @keywords manip
#' @return a list of sequences. Each element has class \code{\link[seqinr]{SeqFastaAA}}. If
#' connection contains no characters, function prompts warning and returns \code{NULL}.
#' @details The input file should contain one or more amino acid sequences separated by
#' empty line(s).
#' @export
#' @keywords manip
read_txt <- function(connection) {
content <- readLines(connection)
#test for empty content
if(content[1] != "" || length(content) > 1) {
if (sum(grepl(">", content, fixed = TRUE)) == 0) {
if (content[1] != "")
content <- c("", content)
#number of empty lines
nel <- 0
#content without too many empty lines
content2 <- c()
for (i in 1L:length(content)) {
if(content[i] == "") {
nel <- nel + 1
} else {
nel <- 0
}
if (nel <= 1)
content2 <- c(content2, content[i])
}
content <- content2
content_end <- length(content)
while(content[content_end] == "i")
content_end <- content_end - 1
prot_names <- sapply(1L:sum(content == ""), function(i)
paste0(">sequence", i))
content[content == ""] <- prot_names
}
read.fasta(textConnection(content), seqtype = "AA", as.string = FALSE)
} else {
warning("No text detected.")
NULL
}
}
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