New functions to UniProt.ws

# Setting general options to store the location of temporary speclist file

options("tempspecfile"=tempfile("specfile."))

# specfileloc

specfileloc <- function(){
  specfile <- system.file("extdata/speclist.txt")

  # Check if speclist.txt is available online, if yes, download, if not, fall back to local copy
  localfile <- getOption("tempspecfile")
  if(require(RCurl)){
    if(!file.exists(localfile)){
      specurl <- 'http://www.uniprot.org/docs/speclist.txt'
      test <- getBinaryURL(specurl)
      if(length(test)>1){
        writeBin(test,localfile)
        specfile <- localfile
      }
    }else{
      specfile <- localfile
    }
  }

  # Check if specfile exists or throw error

  if(!file.exists(specfile)){
    stop("speclist.txt cannot be downloaded from UniProt.org, and it is not found locally")
  }

  return(specfile)

}

# digest specfile

digestspecfile <- function(specfile = specfileloc()){
  my.text <- readLines(specfile)
  codetable <- my.text[grep("^[A-Z0-9]+ +[ABEVO]", my.text, perl=TRUE, value=FALSE)]

  codes <- data.frame(domain = substr(codetable,7,7),
                      taxId = as.numeric(substr(codetable,8,15)),
                      taxname = sapply(strsplit(codetable, ": N="), '[', 2),
                      row.names = sapply(strsplit(codetable, " +[ABEVO] +",perl=TRUE), '[', 1))

  codes$species <- gsub("^([^ ]* [^ ]*) .*$","\\1",codes$taxname, perl=TRUE)


  return(codes)
}

# taxname2species

taxname2species <- function(taxname){
  codetable <- digestspecfile()
  specnames <- codetable[taxname,"species"]
  return(specnames)
}

# taxname2taxid

taxname2taxid  <- function(taxname){
  codetable <- digestspecfile()
  taxids <- codetable[taxname,"taxId"]
  return(taxids)
}

#taxname2domain

taxname2domain <- function(taxname){
  codetable <- digestspecfile()
  domains <- codetable[taxname,"domain"]
  return(domains)
}