R/load_biopax_file.R

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

load_biopax_file<-
  function(source_name=NULL
           ,source_dir=NULL){
    #' @export
    #' @title 
    #' Load BioPAX from OWL File
    #' @description 
    #' Tries to load a BioPAX object from an OWL file.
    #' @details 
    #' This function tries to perform a fuzzy search for a directory 
    #' that contains \code{source_name} inside a \code{source_dir}. 
    #' This is useful when you have several "sources" of pathways, 
    #' i.e. SciSig, Biocarta, etc., with only one OWL file per directory.
    #' @param source_name Name of a BioPAX source.
    #' Used to search for a directory with the source OWL file.
    #' @param source_dir Directory with BioPAX files (optional).   
    #'  
    #' @author 
    #' Ivan Grishagin
    
    
    require(rBiopaxParser)
    if(is.null(source_name)){
      stop("Provide source_name!")
    }
    if (is.null(source_dir)){
      source_dir<-getwd()
    }
    
    #find owl directory
    owl_dirs<-list.dirs(source_dir
                        ,recursive = FALSE)
    owl_num<-agrep(source_name
                   ,owl_dirs
                   ,max.distance = 0.2)
    
    owl.filename<-list.files(owl_dirs[owl_num]
                             ,pattern = "\\.owl"
                             ,full.names = TRUE)
    #check if only one filename has been fetched
    if(length(owl.filename)!=1){
      stop("There's not just one biopax file in the following folder:\n",owl_dirs[owl_num])
    }
    #read in the owl file
    owl_biopax<-readBiopax(owl.filename)
  }