R/GRangesINinteractionSubsetFASTA.R

In vitkl/SLIMFinderR: Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference

##' Check if proteins in GRanges were used for motif search using QSLIMFinder (SLIMFinder)
##' @rdname GRangesINinteractionSubsetFASTA
##' @name GRangesINinteractionSubsetFASTA
##' @author Vitalii Kleshchevnikov
##' @param GRanges object containing instances of linear motifs or domains in proteins (identified by UniProtKB accession)
##' @param interactionSubsetFASTA object of class InteractionSubsetFASTA_list containing: FASTA sequences for interacting proteins, molecular interaction data they correspond to. Each element of a list contains input for individual QSLIMFinder run.
##' @param query_only return only GRanges for query proteins
##' @return list containing 2 vectors: which GRanges are in InteractionSubsetFASTA_list and seqlengths vector for these GRanges
##' @import data.table
##' @import GenomicRanges
##' @export GRangesINinteractionSubsetFASTA
##' @seealso \code{\link{ELMdb2GRanges}}, \code{\link{runQSLIMFinder}}, \code{\link{SLIMFinderOcc2GRanges}}, \code{\link{listInteractionSubsetFASTA}}, \code{\link{randomGRanges}}
GRangesINinteractionSubsetFASTA = function(grange, interactionSubsetFASTA, query_only = F, clustermq = F) {
  if(class(interactionSubsetFASTA) != "InteractionSubsetFASTA_list") stop("interactionSubsetFASTA should be of class InteractionSubsetFASTA_list returned by listInteractionSubsetFASTA()")
  fasta_subset_list = interactionSubsetFASTA$fasta_subset_list

  sequences_Searched = lapply(fasta_subset_list, function(fasta_subset) {
    x = width(fasta_subset)
    names(x) = names(fasta_subset)
    x
  })

  sequences_Searched = unlist(sequences_Searched, use.names = TRUE)
  sequences_Searched_names = names(sequences_Searched)
  names(sequences_Searched) = gsub("^.+\\.\\.", "", sequences_Searched_names)
  sequences_Searched = sequences_Searched[unique(names(sequences_Searched))]




  if(query_only){
    interaction_subset = interactionSubsetFASTA$interaction_subset
    query_Names = vapply(interaction_subset, function(interaction_sub) {
      interaction_sub$ids_set2
    }, FUN.VALUE = character(1), USE.NAMES = FALSE)

    sequences_Searched = sequences_Searched[unique(query_Names)]
    sequences_Searched = sequences_Searched[unique(names(sequences_Searched))]
  }

  list(granges_in_sequences_Searched = as.character(seqnames(grange)) %in% names(sequences_Searched), seqlengths = sequences_Searched)
}