#'  Fetch online genome annotations from Ensembldb database

#'

#' @param EnsDb_annotations (EndsDb object) - Ensembldb database (default: EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86

#'

#' @return gene_range (GRanges object) - Genome annotations

#' @export

#'

#' @examples gene_range = get_genome_annotations(EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86)

get_genome_annotations <- function(

  ensdb_annotations = EnsDb.Hsapiens.v86::EnsDb.Hsapiens.v86

  ) {

  # Get genome annotations from Ensembldb database

  gene_range <- Signac::GetGRangesFromEnsDb(ensdb_annotations)

  ucsc.levels <- stringr::str_replace(

    string = paste("chr", Signac::seqlevels(gene_range), sep = ""),

    pattern = "chrMT",

    replacement = "chrM") # Change chromosome names to UCSC format

  Signac::seqlevels(gene_range) <- ucsc.levels

  # check if Signac is the good package

  return(gene_range) # Return genome annotations

}

#' Fetch online TF motifs from JASPAR2020 and chromVARmotifs

#'

#' @param species (character) - Species name (default: "human")

#'

#' @return motifs_db (motifs_db object) - TF2motifs + motifs PWMs

#' @export

#'

#' @examples motifs_db = get_tf2motifs(species = "human")

get_tf2motifs <- function(species = "human") {

  #TF motifs using the union of databases: JASPAR and cis-BP

  # included in chromVAR

  getMatrixSet <- TFBSTools::getMatrixSet

  # If species is human or mouse

  if (species == "human") {

    # Parameters for JASPAR2020

    opts <- list(collection = "CORE",

              species    = "Homo sapiens",

              all_versions = FALSE)

    JASPAR_PWM <- TFBSTools::toPWM(getMatrixSet(JASPAR2020::JASPAR2020, opts))

    # Load data from JASPAR2020

    # Load data from chromVARmotifs

    # Original data accessible at https://github.com/GreenleafLab/chromVARmotifs

    data("human_pwms_v2")

    # Load data from chromVARmotifs

    motifs <- human_pwms_v2

    # Motifs from chromVARmotifs

  } else if (species == "mouse") {

    # Parameters for JASPAR2020

    opts <- list(collection = "CORE",

              species    = "Mus musculus",

              all_versions = FALSE)

    JASPAR_PWM <- TFBSTools::toPWM(getMatrixSet(JASPAR2020::JASPAR2020, opts))

    # Load data from JASPAR2020

    data("mouse_pwms_v2")

    # Load data from chromVARmotifs

    # Original data accessible at https://github.com/GreenleafLab/chromVARmotifs

    motifs <- mouse_pwms_v2

    # Motifs from chromVARmotifs

  }

  for (name in names(JASPAR_PWM)){

    # Combine motifs of JASPAR20202 and chromVARmotif

    motifs[name] <- JASPAR_PWM[name]

  }

  # Initiate final TF motifs table

  tf2motifs <- data.frame(motif = character(),

                          tf = character(),

                          stringsAsFactors = FALSE)

  for (i in seq_along(TFBSTools::name(motifs))){  # Fill TF motif table

  # TFBSTools::name(motifs) returns names of TFs associated to each PWMatrix

    tfs <- strsplit(TFBSTools::name(motifs)[i], "::")[[1]]

    # splitting TFs that are given as "name1::name2"

    for (tf in tfs){

      tf <- strsplit(tf, "(", fixed = TRUE)[[1]][1]

      # only keeping <NAME> in identifier "<NAME>(var.n)"

      tf2motifs <- rbind(tf2motifs, data.frame(motif = names(motifs)[i],

                                                             tf = tf))

    }

  }

  return(new("motifs_db",

             tf2motifs = tf2motifs,

             motifs = motifs,

             tfs = unique(tf2motifs$tf))) # Return motifs_db <- TF2motifs + motifs PWMs

}