#'Database download
#'
#'Downloads database from EBI ftp server.
#'
#'@param URL URL to database on EBI
#'@param type type of sequences (nuc for nucletide, prot for aminoacid)
#'@param directory directory to which the database is saved
#'@param mergeIntoOneFasta TRUE: merge all FASTA files to a single FASTA file
#'@param name name of the merged FASTA file
#'
#'@return None
#'
#'@examples
#'download_DB('ftp://ftp.ebi.ac.uk/pub/databases/ipd/mhc/nhp/')
#'
#'@export
downloadDb <- function(URL, type='nuc', directory=getwd(), mergeIntoOneFasta=FALSE, name='database'){
download.file(URL, 'html.csv')
tabulka <- read.table("html.csv" , fill = TRUE ,row.names=NULL)
file.remove('html.csv')
tabulka<-tabulka[5]
tabulka<-unlist(tabulka)
r_vyraz<- paste('.*_', type, '.fasta"', sep='')
linky <- sub(r_vyraz,'\\1',tabulka[grepl(r_vyraz, tabulka)])
linky <- gsub('</A>', '',linky)
linky <- gsub('>', URL, linky)
stara_wd<-getwd()
setwd(directory)
sek<-DNAStringSet()
if (mergeIntoOneFasta==FALSE){
for (i in 1:length(linky)){
download.file(linky[i], substring(linky[i], width(URL)+1))
}
}
else {
for (i in 1:length(linky)){
download.file(linky[i], substring(linky[i], width(URL)+1))
sek<-DNAStringSet(c(sek,readDNAStringSet(substring(linky[i], width(URL)+1))))
file.remove(substring(linky[i], width(URL)+1))
}
}
writeXStringSet(sek, paste(name,'.fasta'))
setwd(stara_wd)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.