####
# Get the desired distribution of iRefIndex from the web repository:
####
get_irefindex = function(tax_id="All", iref_version="current", data_folder=getwd()) {
# 1. Get data folder:
if (data_folder == "data") {
datafolder = system.file("data", package = "iRefR")
} else if (data_folder == "home") {
datafolder = R.home()
} else {
datafolder = data_folder
}
# 2. Get release dates and full URLs:
if (iref_version == "current") {
iref_version = "15.0"
release_date = "22012018"
url = paste("http://irefindex.org/download/irefindex/data/current/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
} else {
if (iref_version == "7.0") {
release_date = "11042010"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psimi_tab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "8.0") {
release_date = "01192011"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psimi_tab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "9.0") {
release_date = "10182011"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psimi_tab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "10.0") {
release_date = "03022013"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "11.0") {
release_date = "05192013"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "12.0") {
release_date = "06062013"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "13.0") {
release_date = "08122013"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "14.0") {
release_date = "07042015"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
if (iref_version == "15.0") {
release_date = "22012018"
url = paste("http://irefindex.org/download/irefindex/data/archive/release_", iref_version, "/psi_mitab/MITAB2.6/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
}
}
# 3. Check if file already exists. Otherwise, download and save:
if (iref_version == "14.0") {
txt_date_fix = "04072015"
} else if (iref_version == "15.0") {
txt_date_fix = "01-22-2018"
} else {
txt_date_fix = release_date
}
file_location = paste(datafolder, "/", tax_id,".mitab.", txt_date_fix,".txt",sep="")
if (file.exists(file_location) == TRUE) {
cat("Reading available iRefIndex file...\n")
irefindex_tab = unique(read.table(file_location, header=TRUE, comment.char="", sep='\t', quote=""))
} else {
cat("Downloading iRefIndex file...\n")
zipfile = paste(datafolder, "/", tax_id, ".mitab.", release_date, ".txt.zip", sep="")
download.file(url, destfile=zipfile)
unzip(zipfile, exdir=datafolder)
#file.remove(zipfile)
cat("Reading downloaded file...\n")
txtfile = paste(datafolder, "/", tax_id,".mitab.", txt_date_fix,".txt", sep="")
irefindex_tab = unique(read.table(txtfile, header=TRUE, comment.char="", sep='\t', quote=""))
cat("File has been saved as:\n")
cat(paste(txtfile, "\n"))
#save(file = paste(datafolder, "/", tax_id,".mitab.", release_date,".RData",sep=""), list = "irefindex_tab")
}
irefindex_tab
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.