R/getMgrastAnnotation.R

In mmnet: A metagenomic pipeline for systems biology

getMgrastAnnotation <- function(MetagenomeID, evalue = 5, identity = 60, length = 15,
                                resource = c(source = "KO", type = "ontology"), login.info = NULL) 
{
    if (!is.null(login.info))
      public <- FALSE
    else
      public <- TRUE
    status <- checkMgrastMetagenome(metagenome.id = MetagenomeID, login.info = login.info, public = public)
    if (status){
      MetagenomeID <- paste0("mgm", MetagenomeID)
      server.resource <- "http://api.metagenomics.anl.gov/1/annotation/similarity/"
      server.resource <- paste0(server.resource,MetagenomeID)
      message(paste("Loading the annotations form MG-RAST of", MetagenomeID), domain = NA)
      message("The time spent in this step is proportional to the total amount of remote data...")
      if (!is.null(login.info)){
        webkey <- login.info["webkey"]
        param <- list(source = resource["source"], type = resource["type"], evalue = evalue, 
             identity = identity, length = length, auth = webkey)
      }else{
        param <- list(source = resource["source"], type = resource["type"], evalue = evalue, 
                      identity = identity, length = length)
      }
      anno <- tryCatch(
        getForm(server.resource,
                .params = param,
                .opts=list(noprogress = FALSE, 
                           progressfunction = function(down,up){
                             cat(paste('\r', "loading", paste0(round(down[2]/1024^2, 2),"MB"),"..."))
                             flush.console()
                           })
        ),
        error = function(e) {
          msg <- conditionMessage(e)
          structure(msg, class = "try-error")
        }
      )
      if (inherits(anno, "try-error")){
        warning(anno)
        return(FALSE)
      }
      invalid.source <- which(grepl("Invalid\\s+ontology\\s+source", anno))
      if (length(invalid.source)) 
        stop("invalid ontology source")
      if (length(which(grepl("insufficient\\s+permissions", anno)))) 
        stop("invalid webkey")
      anno <- read.delim(textConnection(anno), header = FALSE, sep = "\t", stringsAsFactor = F)
      return(anno)
      cat("\n",MetagenomeID, "annotation data loading completed")      
    }else{
      return(NULL)
    }   
}