Nothing
read.GB <-
function(access.nb, seq.names = access.nb, species.names = TRUE, gene=TRUE, access=TRUE, as.character = FALSE) {
N <- length(access.nb)
nrequest <- N%/%400 + as.logical(N%%400)
X <- character(0)
for (i in 1:nrequest) {
a <- (i - 1) * 400 + 1
b <- 400 * i
if (i == nrequest)
b <- N
URL <- paste("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=",
paste(access.nb[a:b], collapse = ","), "&rettype=gb&retmode=text",
sep = "")
X <- c(X, scan(file = URL, what = "", sep = "\n", quiet = TRUE))
}
FI <- grep("^ {0,}ORIGIN", X) + 1
LA <- which(X == "//") - 1
obj <- list()
length(obj) <- N
for (i in 1:N) {
tmp <- gsub("[[:digit:] ]", "", X[FI[i]:LA[i]])
obj[[i]] <- unlist(strsplit(tmp, NULL))
}
names(obj) <- seq.names
if (!as.character)
obj <- as.DNAbin(obj)
if (species.names) {
tmp <- character(N)
sp <- grep("ORGANISM", X)
for (i in 1:N) tmp[i] <- unlist(strsplit(X[sp[i]], " +ORGANISM +"))[2]
attr(obj, "species") <- gsub(" ", "_", tmp)
if (gene) {
tmp2 <- character(N)
def <- grep("DEFINITION", X)
for (i in 1:N) tmp2[i] <- unlist(strsplit(X[def[i]], "DEFINITION +"))[2]
attr(obj, "gene") <- gsub(" ", "_", tmp2)
if (access) {
tmp3 <- character(N)
def <- grep("ACCESSION", X)
for (i in 1:N) tmp3[i] <- unlist(strsplit(X[def[i]], "ACCESSION +"))[2]
attr(obj, "accession_num") <- gsub(" ", "_", tmp3)
}
names(obj)<-paste(attr(obj,"accession_num"), "|", attr(obj,"species"), sep = "")
obj
}
}
}
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