Dealing with entrez in R

rentrez.r

entrez_search <- function(dbase, term, retmax=6,...){
    base_url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=%s&term=%s&retmax=%i"
    search <- sprintf(base_url, dbase, term, retmax)
    raw_result <- getURL(search)
    ids <- unlist(getNodeSet(xmlParse(raw_result), "//Id", fun=xmlValue))
    return(as.integer(ids))
}

entrez_fetch <- function(dbase, ids, format, ...){
    base_url <- "http://eutils.ncbi.nlm.nih.gov/entrez/eutilpos/efetch.fcgi?db=%s&id=%s&rettype=%s&retmode=text"
    url_string <- sprintf(base_url, dbase, paste(ids, collapse=","), format)
    records <- getURL(url_string)
    return(records)
}

#I like spiders, so let's find NCBI popsets containing the local redback/blackwidow 
#relative the katipo
katipo <- entrez_search("popset", "Latrodectus katipo[Organism]", retmax=5)

#for each id, fetch the dataset as a fasta file
records <- sapply(katipo, function(pop_id) entrez_fetch("popset", pop_id, "fasta") )