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## read.GenBank.R (2024-02-13)
## Read DNA Sequences and Annotations from GenBank
## Copyright 2002-2022 Emmanuel Paradis and Klaus Schliep 2024
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
read.GenBank <- function(access.nb, seq.names = access.nb, species.names = TRUE,
as.character = FALSE, chunk.size = 400, quiet = TRUE,
type = "DNA")
{
type <- match.arg(type, c("DNA", "AA"))
db <- ifelse(type == "DNA", "nucleotide", "protein")
chunk.size <- as.integer(chunk.size)
N <- length(access.nb)
## if more than 400 sequences, we break down the requests
a <- 1L
b <- if (N > chunk.size) chunk.size else N
fl <- paste0(tempfile(), ".fas")
if (!quiet)
cat("Note: chunk.size =", chunk.size, "(max nb of sequences downloaded together)\n")
repeat {
if (!quiet) cat("\rDownloading sequences:", b, "/", N, "...")
URL <- paste0("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=", db, "&id=",
paste(access.nb[a:b], collapse = ","), "&rettype=fasta&retmode=text")
X <- scan(file = URL, what = "", sep = "\n", quiet = TRUE)
cat(X, sep = "\n", file = fl, append = TRUE)
if (b == N) break
a <- b + 1L
b <- b + chunk.size
if (b > N) b <- N
}
if (!quiet) {
cat(" Done.\nNote: the downloaded sequences are in file:", fl)
cat("\nReading sequences...")
}
res <- read.FASTA(fl, type = type)
if (is.null(res)) return(NULL)
attr(res, "description") <- names(res)
if (length(access.nb) != length(res)) {
names(res) <- gsub("\\..*$", "", names(res))
failed <- paste(access.nb[! access.nb %in% names(res)], collapse = ", ")
warning(paste0("cannot get the following sequence(s):\n", failed))
} else names(res) <- access.nb
if (as.character) res <- as.character(res)
if (!quiet) cat("\n")
if (species.names) {
a <- 1L
b <- if (N > chunk.size) chunk.size else N
sp <- character(0)
repeat {
if (!quiet) cat("\rDownloading species names:", b, "/", N)
URL <- paste("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=", db, "&id=",
paste(access.nb[a:b], collapse = ","), "&rettype=gb&retmode=text", sep = "")
X <- scan(file = URL, what = "", sep = "\n", quiet = TRUE, n = -1)
sp <- c(sp, gsub(" +ORGANISM +", "", grep("ORGANISM", X, value = TRUE)))
if (b == N) break
a <- b + 1L
b <- b + chunk.size
if (b > N) b <- N
}
if (!quiet) cat(".\n")
attr(res, "species") <- gsub(" ", "_", sp)
}
if (!quiet) cat("Done.\n")
res
}
.parse.annotations.file <- function(file) {
get.product.others.gene <- function(a, b) {
res <- rep(NA_character_, 3L)
if (a > b) return(res)
y <- x[a:b]
li <- length(i <- grep("product\t", y))
lj <- length(j <- grep("gene\t", y))
if (li) res[1L] <- gsub("product\t", "", y[i])
if (lj) res[2L] <- gsub("gene\t", "", y[j])
if (length(y) > li + lj) res[3L] <- paste(y[-c(i, j)], collapse = "; ")
res
}
convert.with.incomplete <- function(vec) {
i <- grep("<|>", vec)
if (length(i)) {
incomplete <<- c(incomplete, i)
vec[i] <- gsub("<|>", "", vec[i])
}
as.integer(vec)
}
x <- scan(file, what = "", sep = "\n", quiet = TRUE, skip = 1)
n <- length(x)
i <- grep("^\t\t\t", x)
i2 <- seq_len(n)[-i]
Y <- strsplit(x[i2], "\t")
incomplete <- NULL
start <- convert.with.incomplete(sapply(Y, "[", 1L))
end <- convert.with.incomplete(sapply(Y, "[", 2L))
if (!is.null(incomplete)) {
incomplete <- sort(unique(incomplete))
warning(paste("features were incomplete in row(s):",
paste(incomplete, collapse = ", ")))
}
res <- data.frame(start, end)
sel <- which(!duplicated.data.frame(res))
res <- res[sel, ]
res$type <- sapply(Y, "[", 3L)[sel]
i3 <- i2[sel]
from <- i3 + 1L
to <- c(i3[-1L] - 1L, n)
x[i] <- gsub("^\t\t\t", "", x[i])
Z <- mapply(get.product.others.gene, from, to)
res$product <- Z[1L, ]
gene <- Z[2L, ]
res$others <- gsub("\t", ": ", Z[3L, ])
if (!all(is.na(gene))) res$gene <- gene
row.names(res) <- as.character(seq_len(nrow(res)))
res
}
getAnnotationsGenBank <- function(access.nb, quiet = TRUE)
{
N <- length(access.nb)
res <- setNames(vector("list", N), access.nb)
notfound <- NULL
s1 <- "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id="
s3 <- "&rettype=ft&retmode=text"
for (i in 1:N) {
if (!quiet) cat("\rDownloading annotations:", i, "/", N)
URL <- paste0(s1, access.nb[i], s3)
fl <- tempfile()
ans <- try(download.file(URL, fl, quiet = TRUE), silent = TRUE)
if (inherits(ans, "try-error")) {
notfound <- c(notfound, access.nb[i])
next
}
res[[i]] <- .parse.annotations.file(fl)
}
if (!quiet) cat(". Done.\n")
if (!is.null(notfound)) {
warning(paste0("cannot get features for the following accession(s):\n",
paste(notfound, collapse = ", ")))
if (length(notfound) == N) return(NULL)
}
if (N == 1) res[[1L]] else res
}
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