R/buildAnntationHub.R

In guokai8/bioAnno: Build Annotation From Online Database

#' @title extract annotation database by using AnnotationHub
#' @importFrom AnnotationHub AnnotationHub
#' @importFrom AnnotationHub query
#' @importFrom AnnotationDbi select
#' @importFrom AnnotationDbi keys
#' @importFrom AnnotationDbi columns
#' @importFrom AnnotationForge makeOrgPackage
#' @importFrom RSQLite dbGetQuery
#' @importFrom utils remove.packages
#' @importFrom utils install.packages
#' @importFrom stats na.omit
#' @param species species name(common name,kegg.species.code or scientifc name)
#' @param author author for the annotation package
#' @param maintainer maintainer for the annotation package
#' @param tax_id taxonomy id for the species
#' @param genus genus for the species
#' @param version version for the annotation package
#' @param install install the package or not
#' @param pkgname package name you want to choose
#' @param outputDir temporary file path
#' @param rebuild rebuild the package or not(default: FALSE)
#' @examples
#' ## build annoataion package for c elegans
#' fromAnnHub(species = "celegans", install = FALSE)
#' @author Kai Guo
#' @return annotation package
#' @export
fromAnnHub<-function(species, author = NULL,
        maintainer = NULL, tax_id = NULL, genus = NULL,
        version = NULL,install = TRUE, pkgname=NULL, outputDir = NULL, 
        rebuild = FALSE){
    dbi <- .getdbname(species)
    if(is.null(dbi)){
        dbi <- tryCatch({
                .get.species.info(species = species);
                dbi <- dbi["scientific.name"];
                dbi <- paste0(unlist(strsplit(dbi, ' '))[c(1,2)], collapse = " ")},
                        error = function(e){
                                return(NA)
                                })
    }
    species <- gsub(' .*', '', species)
    if(!is.null(pkgname)){
      dbname <- paste0('org.', pkgname, '.eg.db')
    }else{
      dbname <- paste0('org.', species, '.eg.db')
    }
    if(isTRUE(rebuild)){
        suppressMessages(remove.packages(dbname))
    }
    if(is_installed(dbname)){
        suppressMessages(requireNamespace(dbname, quietly = TRUE))
        cat("You alreay had the annotation package: ", dbname, " \n")
    }else{
        # create the temp cache for AnnotationHub
        dir.create(paste0(tempdir(),"/AnnotationHub/"))
        ah <- AnnotationHub(cache = paste0(tempdir(),"/AnnotationHub/"), ask = FALSE)
        if(is.na(dbi)){
             dbi<-species   
        }
        ah <- query(ah, dbi)
        ahdb <- ah$title
        names(ahdb) <- ah$ah_id
        ### only need ors.xxx.eg.xxx or org.xxx.db.sqlite
        idx<-grep('^org', grep('\\.[eg|db]', ahdb, value = TRUE), value = TRUE)
         #idx <- grep(sub(' .*','',sub(' ','_',dbi)),ahdb,value=T)
        if(length(idx) > 1){
            cat("Please select which database you want to use (1,2,3,...): \n")
            for(i in seq_len(length(idx))){
                cat(i, ":", idx[i], "\n")
            }
            idd <- readidx()
            idx <- idx[idd]
        }
    idn <- names(idx)
    res <- ah[[idn]]
    packinfo <- dbGetQuery(res$conn, "select * from metadata;")
    geneinfo <- select(res,keys = keys(res), columns = c("GENENAME"))
    geneinfo <- na.omit(geneinfo)
    colnames(geneinfo)[1] <- "GID"
    gene2entrezid <- data.frame("GID"=geneinfo$GID,"ENTREZID"= geneinfo$GID)
    gene2refseq <- select(res, keys = keys(res), columns = c("REFSEQ"))
    gene2refseq <- na.omit(gene2refseq)
    colnames(gene2refseq)[1] <- "GID"
    gene2symbol <- select(res, keys = keys(res), columns = c("SYMBOL"))
    gene2symbol <- na.omit(gene2symbol)
    colnames(gene2symbol)[1] <- "GID"
    gene2go <- select(res, keys = keys(res), columns = c("GOALL", "EVIDENCEALL"))
    gene2go <- gene2go[, c(1, 2, 3)]
    gene2go <- gene2go[!duplicated(gene2go), ]
    gene2go <- na.omit(gene2go)
    colnames(gene2go) <- c("GID", "GO", "EVIDENCE")
    pathway = FALSE
    if("PATH" %in% columns(res)){
        gene2path <- select(res, keys = keys(res), columns = c("PATH"))
        colnames(gene2path) <- c("GID", "PATH")
        gene2path <- gene2path[!duplicated(gene2path), ]
        gene2path <- na.omit(gene2path)
        pathway <- TRUE
    }
    gene2ensembl <- data.frame("GID"=keys(res)[1],"ENSEMBL"="")
    if("ENSEMBL" %in% columns(res)){
      gene2ensembl <- select(res, keys = keys(res), columns = c("ENSEMBL"))
      colnames(gene2ensembl) <- c("GID", "ENSEMBL")
      gene2ensembl <- gene2ensembl[!duplicated(gene2ensembl), ]
      gene2ensembl <- na.omit(gene2ensembl)
    }
    if(is.null(version)){
        version <- "0.0.1"
    }
    if(is.null(tax_id)){
        tax_id <- packinfo[6,2]
    }
    if(is.null(author)){
        author <- "myself"
    }
    if(is.null(maintainer)){
        maintainer <- "myself<myself@email.com>"
    }
    if(is.null(genus)){
        genus <- ""
    }
    if(is.null(species)){
        species <- species
    }
    if(!is.null(pkgname)){
      species <- pkgname
    }
    if(is.null(outputDir)){
        outputDir <- tempdir()
    }
    if(isTRUE(pathway)){
        package <- suppressWarnings(makeOrgPackage(
            gene_info = geneinfo,
            entrezid = gene2entrezid,
            refseq = gene2refseq,
            symbol = gene2symbol,
            ensembl = gene2ensembl,
            go = gene2go,
            path = gene2path,
            maintainer = maintainer,
            author = author,
            outputDir = outputDir,
            tax_id = "tax_id",
            genus = "",
            species = species,
            version = version,
            verbose = FALSE,
            goTable = "go"))
    }else{
        package <- suppressWarnings(makeOrgPackage(
        gene_info = geneinfo,
        refseq = gene2refseq,
        symbol = gene2symbol,
        ensembl = gene2ensembl,
        entrezid = gene2entrezid,
        go = gene2go,
        maintainer = maintainer,
        author = author,
        outputDir = outputDir,
        tax_id = "tax_id",
        genus = "",
        species = species,
        version = version,
        verbose = FALSE,
        goTable = "go"))
    }
    if(isTRUE(install)){
        install.packages(package, repos = NULL, type = "source")
        unlink(package, recursive = TRUE)
    }else{
        .show.path(package)
        .show.tables(package)
        #return(package)
    }
    }
}