R/clean_biopax.R

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

clean_biopax<-
  function(biopax){
    
    #' @export
    #' @title
    #' Clean BioPAX Object
    #' @description 
    #' 1) Strips hashes from property_value column.
    #' 2) Cleans a BioPAX object from html tags and garbled symbols. 
    #' 3) Unifies representation of some classes, common properties and property values.
    #' 4) Removes deadend references.
    #' @details 
    #'
    #' @param biopax BioPAX object.
    
    #' @author 
    #' Ivan Grishagin
    
    ################################ strip hashes from property value column
    biopax$dt$property_attr_value<-
      biopax$dt$property_attr_value %>% 
      striphash
    
    ################################ clean up property value column
    #1) removes html tags
    #2) removes eol chars
    #3) replaces entire uniprot (?) entries that start with "Recname:" with the recommended names
    biopax$dt$property_value<-
      biopax$dt$property_value %>%
      gsub(pattern="\n|<[^=]*?>|<[^-]*?>|<[^[:space:]]*?>"
           ,replacement = ""
           ,.)
    
    biopax$dt$property_value<-
      biopax$dt$property_value %>%
      gsub(pattern="^RecName: Full=(.*?);.*$"
           ,replacement = "\\1"
           ,.)
    biopax$dt$property_value[biopax$dt$property_value=="NA"]<-
      "UNKNOWN"
    
    ################################ garbled symbols
    dict<-
      data.table(from=c("\u201A\u00e0\u00f6\u221a\u00a9\u00ac\u00a8\u00ac\u00b5"
                        ,"\u00c3\u008e\u00c2\u00b2"
                        ,"\u00c3\u009f","&gt;","&apos;","&"
                        ,"\u00e2\u0080\u009c"
                        ,"\u00e2\u0080?"
                        ,"\u00c3\u00a2\u00e2\u0082\u00ac\u00e2\u0080\u009c"
                        ,"\u00c3\u00a2\u00e2\u0082\u00ac\u00e2"
                        ,"\u00e2\u0093"
                        ,"\u00e2\u0094"
                        ,"\u00c3\u00a2\u00e2\u0082\u00ac\u00e2\u0084\u00a2"
                        ,"\u00c3\u00a2\u00e2\u0082\u00ac\u00c2\u00b2"
                        ,"\u00c3\u00a2\u00e2\u0082\u00ac\u00c5\u0093"
                        ,"\u00c3\u00a2\u00e2\u0082\u00ac\u00c2?"
                        ,"\u0093"
                        ,"\u0094")
                 ,to=c("\u03b5"
                       ,"\u03b2"
                       ,"\u03b2",">","'","and"
                       ,""
                       ,""
                       ,"-"
                       ,"-"
                       ,"-"
                       ,"-"
                       ,"'"
                       ,"'"
                       ,"\""
                       ,"\""
                       ,"\""
                       ,"\""))
    
    #clean biopax object from utf tags
    #find affected rows
    badsymbol_rows<-
      biopax$dt[property_value!=""]$property_value %>% 
      grepl("[^[:graph:][:space:]]"
            ,.) 
    
    biopax$dt[property_value!=""][badsymbol_rows]$property_value<-
      biopax$dt[property_value!=""][badsymbol_rows]$property_value %>%
      mgsub(pattern = dict$from
            ,replacement = dict$to
            ,text.var = .)
    
    ################################ class
    class_dict<-
      data.table(from=c("Rna"
                        ,"RnaReference"
                        ,"Dna"
                        ,"DnaReference")
                 ,to=c("RNA"
                       ,"RNAReference"
                       ,"DNA"
                       ,"DNAReference"))
    
    biopax$dt$class<-
      biopax$dt$class %>% 
      mapvalues(from=class_dict$from
                ,to=class_dict$to
                ,warn_missing = FALSE)
    
    ################################ property
    property_dict<-
      data.table(from=c("dispName")
                 ,to=c("displayName"))
    
    biopax$dt$property<-
      biopax$dt$property %>% 
      mapvalues(from=property_dict$from
                ,to=property_dict$to
                ,warn_missing = FALSE)
    
    ################################ property_value
    property_value_dict<-
      data.table(from=c("LEFT_to_RIGHT")
                 ,to=c("LEFT-to-RIGHT"))
    
    biopax$dt$property_value<-
      biopax$dt$property_value %>% 
      mapvalues(from=property_value_dict$from
                ,to=property_value_dict$to
                ,warn_missing = FALSE)
    
    #unify database names
    db_dict<-
      system.file("extdata"
                  ,"unify_db_names.xlsx"
                  ,package="RIGbiopax") %>% 
      read_excel_astext(sheet = 1)
    
    biopax$dt$property_value<-
      biopax$dt$property_value %>% 
      mapvalues(from=db_dict$original_db_name
                ,to=db_dict$new_db_name
                ,warn_missing = FALSE)
    
    ################################ remove deadend references
    biopax<-
      biopax %>% 
      remove_deadend_refs
    
    
    return(biopax)
  }