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## package: megaptera
## called by:
## author: Christoph Heibl (at gmx.net)
## last update: 2014-08-20
esearch <- function(tax, db = "taxonomy", usehistory = FALSE, retmax = 10000){
id <- seq(from = 1, to = length(tax), by = 100)
id <- data.frame(from = id, to = c(id[-1] - 1, length(tax)))
webEnv <- NULL; queryKey <- NULL
for (i in 1:nrow(id) ){
cat("\niteration: ", i)
term <- unlist(tax)[id[i, 1]:id[i, 2]]
term <- paste(term, collapse = "+OR+")
## assemble URL
xml <- paste("http://eutils.ncbi.nlm.nih.gov/entrez/",
"eutils/esearch.fcgi?",
"tool=megaptera",
"&email=heibsta@gmx.net&",
"&usehistory=y&", sep = "")
if ( !is.null(webEnv) ) xml <- paste(xml, "&WebKey=", webEnv, sep = "")
xml <- paste(xml, "&db=", db, "&term=", term,
"&retmax=", retmax, sep = "")
## get and parse result
if ( is.null(webEnv) ){
xml <- xmlTreeParse(xml, useInternalNodes = TRUE)
webEnv <- xpathSApply(xml, fun = xmlToList,
path = "//eSearchResult/WebEnv")
queryKey <- xpathSApply(xml, fun = xmlToList,
path = "//eSearchResult/QueryKey")
} else {
browseURL(xml, browser = "false")
}
}
# s <- paste("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/",
# "esummary.fcgi?tool=megaptera&email=heibsta@gmx.net&",
# "db=nucleotide&query_key=", queryKey,
# "&WebEnv=", webEnv, sep = "")
# s <- xmlTreeParse(s, useInternalNodes = TRUE)
# ss <- xpathSApply(s, fun = xmlToList,
# path = "//DocSum/Id")
x <- paste("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/",
"efetch.fcgi?tool=megaptera&email=heibsta@gmx.net&",
"db=nucleotide&query_key=", queryKey,
"&WebEnv=", webEnv,
"&rettype=gb&retmode=xml", sep = "")
# xml <- scan(x, what = "c", quiet = TRUE, sep = "\n")
# write(xml, "test2.xml"); system("open -t test2.xml")
# x <- "test.xml"
obj <- xmlTreeParse(x, getDTD = FALSE, useInternalNodes = TRUE)
obj
}
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