R/airenApp.R

In alberto-rodriguezizquierdo/airen_r: A R package to optimize the performance of Restriction digestion to improve the resolution of GBS

#' @title AppLauncher
#' @name airenApp
#' @description hands-on airenbox
#' @param root working directory
#' @import dplyr
#' @import SimRAD
#' @import XML
#' @author Alberto Rodriguez-Izquierdo, 2021

airenApp <- function(root){


  configFile <- getConfigFile(root)

  #########---------Restriction Enzyme simulation----------#########
  if (configFile$parameters$typeAnalysis == 'restriction'){

    resultsRestriction <- restrictionSimulation(dnaseq = paste0(configFile$data$dataPath,'/',configFile$data$genome),
                                                enzyme_db = paste0(configFile$data$dataPath,'/',configFile$data$enzyme_db),
                                                min.size = configFile$parameters$min.size,
                                                max.size = configFile$parameters$max.size,
                                                type_analysis = configFile$parameters$ifRestriction,
                                                enzyme_selection = configFile$parameters$combination$enzyme_selection,
                                                nb_repeat=configFile$parameters$replicate_enzyme$nb_repeat,
                                                use_output = configFile$output$use_output,
                                                outputDir = configFile$output$outputDir,
                                                wd=root)



  }

  ##########---------Random genome fragmentation------------##########

  if (configFile$parameters$typeAnalysis == 'random'){

    for(x in 1:configFile$parameters$random_genome_fragmentation$nb_repeat){

      eval(parse(text=paste0('results', x,' <- randomGenomeFragmentation(configFile$data$genome, configFile$parameters$min_size, configFile$parameters$max_size, configFile$parameters$random_genome_fragmentation$nb_fragments)')))

      eval(parse(text=paste0("write.fasta(as.list(results",x,"$fragmentRes), results",x,"$V1, file.out=paste0(root,'/output/random_genome_fragmentation/results',x,'.fasta'))")))

      eval(parse(text=paste0('rm(results',x,')')))

    }

  }

  if (configFile$parameters$typeAnalysis == 'position'){

    calculatePositionFragment(count_dir=configFile$parameters$calculatePosition$outputPath,
                              alignment_path=configFile$parameters$calculatePosition$alignment_path,
                              gffPath=configFile$parameters$calculatePosition$gffFile,
                              category=configFile$parameters$calculatePosition$category)

  }



  print('App finished successfully!')
}