R/EGAhtsgetResourceClient.R

In isglobal-brge/dsOmics: DataSHIELD server site Omic functions

#' EGA htsget resource client
#'
#' Build a GDS handler from a resource object describing access to a 
#' EGA valid credentials, pointing to a VCF or BAM file to be converted into a GDS file.
#'
#' @docType class
#' @format A R6 object of class EGAhtsgetResourceClient
#' @import resourcer
#' @export
EGAhtsgetResourceClient <- R6::R6Class(
  "EGAhtsgetResourceClient",
  inherit = FileResourceClient,
  public = list(
    initialize = function(resource) {
      super$initialize(resource)
    },
    getConnection = function() {
      conn <- super$getConnection()
      if (is.null(conn)) {
        resource <- super$getResource()
        format <- resource$format
        # if ("EGAhtsgetVCF" == format) {
        #   private$loadSNPRelate()
        #   private$loadRhtsget()
        #   private$loadGenomicRanges()
        #   private$loadVariantAnnotation()
        #   browser()
        #   private$.vcf.file.tmp <- tempfile(fileext = ".vcf")
        #   private$.gds.file.tmp <- tempfile(fileext = ".gds")
        #   url <- super$parseURL()
        #   token <- Rhtsget::htsget_get_token("https://ega.ebi.ac.uk:8443/ega-openid-connect-server/token",
        #                             resource$identity, resource$secret)
        #   method <- "biallelic.only"
        #   snpfirstdim <- FALSE
        #   private$.gr <- GenomicRanges::GRanges(paste0(url$query$referenceName, ":", url$query$start, "-", url$query$end))
        #   private$.sample_id <- substr(url$path, start = 24, stop = nchar(url$path))
        #   Rhtsget::htsget_variants(private$.gr, private$.sample_id, "https://ega.ebi.ac.uk:8052/elixir/tickets/tickets",
        #   #                          token, destination = private$.vcf.file.tmp)
        #   # Rhtsget::htsget_variants(private$.gr, private$.sample_id, "https://ega.ebi.ac.uk:8052/elixir/data/files",
        #                            token, destination = private$.vcf.file.tmp)
        #   # VariantAnnotation::readVcf(private$.vcf.file.tmp)
        #   SNPRelate::snpgdsVCF2GDS(private$.vcf.file.tmp, private$.gds.file.tmp)
        #   SNPRelate::snpgdsSummary(private$.gds.file.tmp)
        # }
        if("EGAhtsgetBAM" == format){
          private$loadgmapR()
          private$loadVariantTools()
          private$loadRhtsget()
          private$.vcf.file.tmp <- tempfile(fileext = ".vcf")
          private$.bam.file.tmp <- tempfile(fileext = ".bam")
          private$.gds.file.tmp <- tempfile(fileext = ".gds")
          token <- Rhtsget::htsget_get_token("https://ega.ebi.ac.uk:8443/ega-openid-connect-server/token",
                                    resource$identity, resource$secret)
          url <- super$parseURL()
          private$.gr <- GenomicRanges::GRanges(paste0(url$query$referenceName, ":", url$query$start, "-", url$query$end))
          private$.sample_id <- substr(url$path, start = 24, stop = nchar(url$path))
          bam <- Rhtsget::htsget_reads(private$.gr, private$.sample_id, "https://ega.ebi.ac.uk:8052/elixir/tickets/tickets", 
                              ega = TRUE, token, destination = private$.bam.file.tmp)
          sortedFile <- Rsamtools::sortBam(file = bam, destination = paste0(gsub('.{3}$', '', bam), "sorted"), byQname = FALSE)
          indexedFile <- Rsamtools::indexBam(sortedFile)
          bam <- Rsamtools::BamFile(sortedFile)

          BAM2VCF(bam, private$.gr, private$.vcf.file.tmp)
          method <- "biallelic.only"
          snpfirstdim <- FALSE
          SNPRelate::snpgdsVCF2GDS(private$.vcf.file.tmp, private$.gds.file.tmp, method = method, snpfirstdim = snpfirstdim)
          SNPRelate::snpgdsSummary(private$.gds.file.tmp)
          private$loadGWASTools()
          conn <- GWASTools::GdsGenotypeReader(private$.gds.file.tmp)
          super$setConnection(conn)
          return(conn)
        }
        else if("EGACSV" == format){
          browser()
          private$loadRhtsget()
          csv.file.tmp <- tempfile(fileext = ".csv")
          token <- Rhtsget::htsget_get_token("https://ega.ebi.ac.uk:8443/ega-openid-connect-server/token",
                                             resource$identity, resource$secret)
          url <- super$parseURL()
          private$.sample_id <- substr(url$path, start = 13, stop = nchar(url$path))
          Rhtsget::fetch_file(private$.sample_id, "https://ega.ebi.ac.uk:8052/elixir/data",
                              token, csv.file.tmp)
          return(read.csv(csv.file.tmp))
        }
        else {
          NULL
        }
      }
    },
    getValue = function() {
      self$getConnection()
    },
    close = function() {
      super$close()
      conn <- super$getConnection()
      if (!is.null(conn)) {
        GWASTools::close(conn)
        if (!is.null(private$.gds.file.tmp) && file.exists(private$.gds.file.tmp)) {
          # house keeping
          ignore <- tryCatch(file.remove(private$.gds.file.tmp), error = function(e) {})
        }
      }
    }
  ),
  private = list(
    .gds.file.tmp = NULL,
    .vcf.file.tmp = NULL,
    .bam.file.tmp = NULL,
    .gr = NULL,
    .sample_id = NULL,
    
    loadSNPRelate = function() {
      if (!require("SNPRelate")) {
        install.packages("SNPRelate", repos="http://R-Forge.R-project.org", dependencies = TRUE)
      }
    },
    loadGenomicRanges = function() {
      if (!require("GenomicRanges")) {
        if (!require("BiocManager")) {
          install.packages("BiocManager", repos = "https://cloud.r-project.org", dependencies = TRUE)
        }
        BiocManager::install("GenomicRanges", ask = FALSE)
      }
    },
    loadVariantAnnotation = function() {
      if (!require("VariantAnnotation")) {
        if (!require("BiocManager")) {
          install.packages("BiocManager", repos = "https://cloud.r-project.org", dependencies = TRUE)
        }
        BiocManager::install("VariantAnnotation", ask = FALSE)
      }
    },
    loadRhtsget = function() {
      if (!require("Rhtsget")) {
        devtools::install_github("ESCRI11/Rhtsget")
      }
    },
    loadGWASTools = function() {
      if (!require("GWASTools")) {
        if (!require("BiocManager")) {
          install.packages("BiocManager", repos = "https://cloud.r-project.org", dependencies = TRUE)
        }
        BiocManager::install("GWASTools", ask = FALSE)
      }
    },
    loadgmapR = function() {
      if (!require("gmapR")) {
        if (!require("BiocManager")) {
          install.packages("BiocManager", repos = "https://cloud.r-project.org", dependencies = TRUE)
        }
        BiocManager::install("gmapR", ask = FALSE)
      }
    },
    loadVariantTools = function() {
      if (!require("VariantTools")) {
        if (!require("BiocManager")) {
          install.packages("BiocManager", repos = "https://cloud.r-project.org", dependencies = TRUE)
        }
        BiocManager::install("VariantTools", ask = FALSE)
      }
    }
  )
)