R/get.palmSra.R

In palmid: RdRP Analysis Suite

# get.palmSra
#'
#' A wrapper of several get* functions to create a palm.sra data.frame
#'
#' @param pro.df   data.frame, imported diamond pro df. use get.pro()
#' @param con      pq-connection, use SerratusConnect()
#' @return palm.sra  data.frame
#' @keywords palmid sql geo biosample timeline Serratus Tantalus
#' @examples
#'
#' data("waxsys.pro.df")
#' con <- SerratusConnect()
#'
#' \donttest{
#' get.palmSra( waxsys.pro.df, con )
#' }
#'
#' @import dplyr ggplot2
#' @export
#'
get.palmSra <- function(pro.df, con = SerratusConnect()) {

  # Baseline rows from pro.df input
  palm.sra <- pro.df[ , c("qseqid", "sseqid", "pident", "evalue") ]

  # Retrieve each parent sOTU, keep 1 best match within an sOTU
  palm.sra$sOTU <- get.sOTU(palm.sra$sseqid, con, ordinal = TRUE)
    palm.sra <- palm.sra[order(palm.sra$pident, decreasing = TRUE), ]
    palm.sra <- palm.sra[ !duplicated(palm.sra$sOTU), ]

  # For each parent sOTU, retrieve a list of all children palm_id
  palm.sra$child_uid  <- get.sOTU(palm.sra$sOTU, con,
                                  get_childs = TRUE, ordinal = TRUE)

  # For each parent OR child palm_id, retrieve matching SRA runs
  sra.df <- get.sra(unlist(palm.sra$child_uid), con, ret_df = TRUE)

  # For each returned SRA-contig, merge-order to palm.sra
  # spagetti code incoming...
  list.contains <- function(child.list, palm_id){
    list.match <- (palm_id %in% child.list)
    return(list.match)
  }

  id.in.list <- function(palm_id, child.list){
    id.match <- which(unlist(lapply(palm.sra$child_uid, list.contains, palm_id)))
    return(id.match)
  }

  merge.order <- sapply( sra.df$palm_id, id.in.list, palm.sra$child_uid)
  palm.sra <- cbind( palm.sra[merge.order, ], sra.df)

  palm.sra <- palm.sra[ , c("run_id", "palm_id", "coverage",
                            "sOTU", "qseqid", "pident", "evalue",
                            "q_sequence")]

  colnames(palm.sra) <- c("run_id", "palm_id", "coverage",
                          "sOTU", "qseqid", "pident", "evalue",
                          "sra_sequence")

  palm.sra <- palm.sra[ order(palm.sra$evalue, decreasing = FALSE), ]
  palm.sra <- palm.sra[ order(palm.sra$pident, decreasing = TRUE), ]

  # Add BioSample, Geo data to palm.sra
  palm.sra$biosample_id <- get.sraBio(palm.sra$run_id, con, TRUE)

  # Add Organism/scientific_name of sra run
  palm.sra$scientific_name <- get.sraOrgn(palm.sra$run_id, con, TRUE)

  # Add time (release date) to palm.sra
  palm.sra$date <- get.sraDate(palm.sra$run_id, con, TRUE)

  # Add geo-data if available to palm.sra
  palm.geo.tmp <- get.sraGeo( run_ids = NULL,
                              biosample_ids = palm.sra$biosample_id, con = con, ordinal =  TRUE)

  if (!all(palm.geo.tmp$biosample_id == palm.sra$biosample_id)){
    stop("Error in geo lookup.")
  } else {
    palm.sra$lng <- palm.geo.tmp$lng
    palm.sra$lat <- palm.geo.tmp$lat
  }

  return(palm.sra)
}