Nothing
uniprot <- function(accid) {
oops <- requireNamespace("XML", quietly = TRUE)
if(!oops)
stop("Please install the XML package from CRAN")
url <- paste('http://www.uniprot.org/uniprot/', accid, '.xml', sep="")
tmpfile <- tempfile()
download.file(url, tmpfile) ##, method="wget")
xml <- XML::xmlRoot(XML::xmlParse(tmpfile))
node.names <- XML::xmlSApply(xml[[1]], XML::xmlName)
## acession
inds <- which(node.names=="accession")
accession <- NULL
for(i in 1:length(inds))
accession <- c(accession, XML::xmlValue(xml[[1]][[inds[i]]]))
## and name
inds <- which(node.names=="name")
name <- NULL
for(i in 1:length(inds))
name <- c(name, XML::xmlValue(xml[[1]][[inds[i]]]))
## sequence
inds <- which(node.names=="sequence")
sequence <- gsub("\n", "", XML::xmlValue(xml[[1]][[inds]]))
## organism
inds <- which(node.names=="organism")
node <- xml[[1]][[inds]]
organism <- NULL
tmpl <- unlist(XML::xmlApply(node, XML::xmlAttrs))
if("scientific" %in% tmpl)
organism <- XML::xmlValue(node[[which(tmpl %in% "scientific")]])
if("common" %in% tmpl)
organism <- c(organism, XML::xmlValue(node[[which(tmpl %in% "common")]]))
## taxon
inds <- which(node.names=="organism")
node <- xml[[1]][[inds]]
taxon <- NULL
for ( i in 1:XML::xmlSize(node[['lineage']]) ) {
taxon <- c(taxon, XML::xmlValue(node[['lineage']][[i]]))
}
## protein
node <- xml[[1]][['protein']]
fullName <- XML::xmlValue(node[['recommendedName']][['fullName']])
shortName <- XML::xmlValue(node[['recommendedName']][['shortName']])
## gene
node <- xml[[1]][['gene']]
gene <- XML::xmlValue(node[[1]])
## dbReference
inds <- which(node.names=="dbReference")
dbref <- list()
for(i in 1:length(inds)) {
node <- xml[[1]][[inds[i]]]
dbref[[i]] <- XML::xmlAttrs(node)
}
dbref <- unlist(dbref)
type.inds <- names((dbref)) == "type"
id.inds <- names((dbref)) == "id"
dbref <- data.frame(type=dbref[type.inds], id=dbref[id.inds],
stringsAsFactors=FALSE)
out <- list(accession = accession, name = name,
fullName = fullName, shortName = shortName,
sequence = sequence, gene = gene,
organism = organism, taxon = taxon,
dbref=dbref)
return(out)
}
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