ENCODExplorer-release: A compilation of ENCODE metadata

#' Produce a subset of data following predefined criteria
#'
#' After running the \code{prepare_ENCODEDb} function, this function will allow 
#' you to extract a subset of data encording to the following criteria : 
#' accession, assay name, biosample, dataset accession, file accession, 
#' file format, laboratory, donor organism, target and treatment.
#' 
#' By default, the query can be made on an exact match term. This behaviour can 
#' be modified by setting the \code{fixed} argument at \code{TRUE}
#' 
#' @param  df \code{list} of two \code{data.frame} containing ENCODE 
#' experiment and dataset metadata 
#' @param  set_accession character string to select the experiment or dataset accession
#' @param  assay character string to select the assay type
#' @param  biosample character string to select the biosample name
#' @param  dataset_accession character string to select the dataset accession
#' @param  file_accession character string to select the file accesion
#' @param  file_format character string to select the file format
#' @param  lab character string to select the laboratory 
#' @param  organism character string to select the donor organism
#' @param  target character string to select the experimental target
#' @param  treatment character string to select the treatment
#' @param  file_status character string to select the file status 
#' ("released", "revoked", "all"). Default "released"
#' @param  status character string to select the dataset/experiment status
#' @param  fixed logical. If TRUE, pattern is a string to be matched as it is.
#'
#' @return a \code{list} of two \code{data.frame}s containing data about ENCODE 
#' experiments and datasets
#'
#' @examples
#'   queryEncode(biosample = "A549", file_format = "bam")
#'
#' @export
queryEncode <- function(df = NULL, set_accession = NULL, assay = NULL, biosample = NULL,
                  dataset_accession = NULL, file_accession = NULL, file_format = NULL, 
                  lab = NULL, organism = NULL, target = NULL, treatment = NULL,
                  file_status = "released", status = "released", fixed = TRUE) {
  if(is.null(df)) {data(encode_df, envir = environment())} else {encode_df = df}
  
  if(is.null(set_accession) && is.null(assay) && is.null(biosample) && is.null(dataset_accession) &&
       is.null(file_accession) && is.null(file_format) && is.null(lab) && is.null(organism) &&
       is.null(target) && is.null(treatment))
  {
    warning("Please provide at least one valid criteria", call. = FALSE)
    NULL
    
  } else {
    s1 = encode_df$experiment
    s2 = encode_df$dataset
    
    ac = set_accession
    as = assay
    bs = biosample
    da = dataset_accession
    fa = file_accession
    ff = file_format
    lb = lab
    og = organism
    tg = target
    tr = treatment
    es = status
    fs = file_status
    
    if(fixed) {
      
      if(!is.null(ac)) {
        s1 <- subset(s1, s1$accession == ac)
        s2 <- subset(s2, s2$accession == ac)
      }
      
      if(!is.null(as)) {
        s1 <- subset(s1, s1$assay == as)
        s2 <- subset(s2, s2$assay == as)
      }
      
      if(!is.null(bs)) {
        s1 <- subset(s1, s1$biosample_name == bs)
        s2 <- subset(s2, s2$biosample_name == bs)
      }
      
      if(!is.null(da)) {
        s1 <- subset(s1, s1$dataset_accession == da)
        s2 <- subset(s2, s2$accession == da)
      }
      
      if(!is.null(fa)) {
        s1 <- subset(s1, s1$file_accession == fa)
        s2 <- subset(s2, s2$file_accession == fa)
      }
      
      if(!is.null(ff)) {
        s1 <- subset(s1, s1$file_format == ff)
        s2 <- subset(s2, s2$file_format == ff)
      }
      
      if(!is.null(lb)) {
        s1 <- subset(s1, s1$lab == lb)
        s2 <- subset(s2, s2$lab == lb)
      }
      
      if(!is.null(og)) {
        s1 <- subset(s1, s1$organism == og)
        s2 <- subset(s2, s2$organism == og)
      }
      
      if(!is.null(tg)) {
        s1 <- subset(s1, s1$target == tg)
        s2 <- subset(s2, s2$target == tg)
      }
      
      if(!is.null(tr)) {
        s1 <- subset(s1, s1$treatment == tr)
        s2 <- subset(s2, s1$treatment == tr)
      }
      
      if(fs != "all") {
        s1 <- subset(s1, s1$file_status == fs)
        s2 <- subset(s2, s2$file_status == fs)
      }
      
      if(es != "all") {
        s1 <- subset(s1, s1$status == es)
        s2 <- subset(s2, s2$status == es)
      }
      
    } else {
      # retirer ignorer les espaces, les tirets et la casse
      # m cf 7 = MCf7 = mcf-7 = MCF-7 ... etc
      
      if(!is.null(ac)) {
        query.transfo = query_transform(ac)
        select.entries = grepl(x = s1$accession, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$accession, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(as)) {
        query.transfo = query_transform(as)
        select.entries = grepl(x = s1$assay, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$assay, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(bs)) {
        query.transfo = query_transform(bs)
        select.entries = grepl(x = s1$biosample_name, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$biosample_name, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(da)) {
        query.transfo = query_transform(da)
        select.entries = grepl(x = s1$dataset_accession, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$accession, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(fa)) {
        query.transfo = query_transform(fa)
        select.entries = grepl(x = s1$file_accession, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$file_accession, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(ff)) {
        query.transfo = query_transform(ff)
        select.entries = grepl(x = s1$file_format, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$file_format, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(lb)) {
        query.transfo = query_transform(lb)
        select.entries = grepl(x = s1$lab, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$lab, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(og)) {
        query.transfo = query_transform(og)
        select.entries = grepl(x = s1$organism, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$organism, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(tg)) {
        query.transfo = query_transform(tg)
        select.entries = grepl(x = s1$target, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$target, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(!is.null(tr)) {
        query.transfo = query_transform(tr)
        select.entries = grepl(x = s1$treatment, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$treatment, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(fs != "all") {
        query.transfo = query_transform(fs)
        select.entries = grepl(x = s1$file_status, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$file_status, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
      if(es != "all") {
        query.transfo = query_transform(es)
        select.entries = grepl(x = s1$status, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s1 = s1[select.entries,]
        
        select.entries = grepl(x = s2$status, pattern = query.transfo, 
                               ignore.case =TRUE, perl =TRUE)
        s2 = s2[select.entries,]
      }
      
    }
    
    
    
    if((nrow(s1) + nrow(s2)) == 0) {
      warning("No result found. You can try the <searchEncode> function or set the fixed option to FALSE", call. = FALSE)
      NULL
    }
    else
    {
      query_results = list(experiment = s1, dataset = s2)
      print(paste0("experiment results : ",nrow(query_results$experiment)," files in ",length(unique(query_results$experiment$accession))," experiments ; dataset results : ",nrow(query_results$dataset), " files"))
      query_results
    }
    
  }
}

query_transform <- function(my.term) {
  my.term = gsub(my.term, pattern = " ", replacement = "", fixed =TRUE)
  my.term = gsub(my.term, pattern = "-", replacement = "", fixed =TRUE)
  my.term = gsub(my.term, pattern = ",", replacement = "", fixed =TRUE)
  my.term = strsplit(my.term, split = "")[[1]]
  my.term.4.grep = paste0("^",paste(my.term, collapse = "[ ,-]?"))
  
  my.term.4.grep
}