R/remove_duplicate_biopax_components.R

In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

remove_duplicate_biopax_components<-
  function(biopax){
    #' @export
    #' @title 
    #' Remove Duplicate Components from BioPAX Object
    #' @description 
    #' BioPAX objects frequently have components that are identical in everything, but id. 
    #' This function removes all such duplicates, and changes all property_attr_values accordingly.
    #' @details 
    #' The biopax is processed iteratively.\cr
    #' First, two sets of properties are used to identify and remove:\cr
    #' 1) duplicate term-db-id, db-id, and position-status instances;\cr
    #' 2) duplicate instances that refer to instance listed in 1) -- 
    #' they have properties xref, term, evidenceCode, featureLocation, 
    #' modificationType, sequenceIntervalBegin, sequenceIntervalEnd. \cr\cr
    #' Second, two sets of classes are used to identify and remove:\cr
    #' 1) duplicate Protein, SmallMolecule, PhysicalEntity, RNA, DNA instances;\cr
    #' 2) duplicate Complex instances.\cr
    #' 
    #' @author 
    #' Ivan Grishagin
    
    #strip hashes from the biopax property attr value column
    biopax$dt$property_attr_value<-
      biopax$dt$property_attr_value %>% 
      striphash
    
    #first, clean-up entities by properties
    #then by class
    for(keep_list_name in c("property","class")){
      
      message("Removal of duplicate biopax components: using "
              ,toupper(keep_list_name)
              ," started...")
      
      #list of properties or classes to preserve
      keep_list<-
        internal_keep_property_class_list(keep_list_name=keep_list_name)
      
      #for each level of the element (property or class), 
      #perform the biopax component clean-up procedure
      for (keep_list_element in keep_list){
        #auxiliary biopax to compare to
        aux_biopax<-NULL
        iteration=0
        
        while(!identical(biopax,aux_biopax)){
          iteration<-
            iteration+1
          message("Removal of duplicate biopax components: iteration "
                  ,iteration
                  ," started...")
          
          #store old biopax in a new variable
          aux_biopax<-
            copy(biopax)
          
          #make a logical vector to subset the biopax
          #i.e. determine all instances to be processed
          logical_subset_vect<-
            switch(keep_list_name
                   ,property = biopax$dt[,.(logi=!id %in% id[!property %in% keep_list_element])]$logi
                   ,class = biopax$dt[,.(logi=class %in% keep_list_element)]$logi
            )
          
          #try function on "old" biopax
          #in the next iteration it will be compared to old self
          #and if different, the procedure will be repeated
          biopax<-
            biopax %>% 
            internal_rm_dupl_biopax_comp(logical_subset_vect)
          
          #if any other mods are avaialble, 
          #it will be different from the old one
          
          message("Removal of duplicate biopax components: iteration "
                  ,iteration
                  ," is over!")
        }
        #clean up
        rm(aux_biopax)
      }
      
      message("Removal of duplicate biopax components: using "
              ,toupper(keep_list_name)
              ," is over!")
    }
    
    return(biopax)
    
  }