R/methyl_startplugin_parse.R

In NCI-CGR/TypeSeqHPV-Methyl: HPV methylation analysis Workflows

#'
meth_startplugin_parse <- function(args_df){
  require(jsonlite)
  require(tidyverse)
  
  if ( args_df$is_torrent_server == "yes") {
    
    plugin_json = fromJSON(file("./startplugin.json"), simplifyDataFrame = TRUE, simplifyMatrix = TRUE)
    
    #manifest
    data_frame(values = plugin_json$pluginconfig$typing_manifest) %>%
      mutate(values = str_replace(values, "\n", "" )) %>%
      separate(col = values, sep = ",", into = unlist(str_split(.$values[1], ","))) %>%
      slice(2:n()) %>%
      glimpse() %>%
      write_csv("manifest.csv")
    
    #control_defs
    data_frame(values = plugin_json$pluginconfig$control_definitions) %>%
      mutate(values = str_replace(values, "\n", "" )) %>%
      separate(col = values, sep = ",", into = unlist(str_split(.$values[1], ","))) %>%
      slice(2:n()) %>%
      write_csv("control_defs.csv")
    
    #barcode_file
 #   data_frame(values = plugin_json$pluginconfig$barcode_file) %>%
  #    mutate(values = str_replace(values, "\n", "" )) %>%
   #   separate(col = values, sep = ",", into = unlist(str_split(.$values[1], ","))) %>%
    #  slice(2:n()) %>%
    #  glimpse() %>%
    #  write_csv("barcodes.csv")
    
    #grouping
    # data_frame(values = plugin_json$pluginconfig$grouping_defs) %>%
    #    mutate(values = str_replace(values, "\n", "" )) %>%
    #   separate(col = values, sep = ",", into = unlist(str_split(.$values[1], ","))) %>%
    #  slice(2:n()) %>%
    # glimpse() %>%
    #  write_csv("grouping_defs.csv")
    
    
    #control freq
    data_frame(values = plugin_json$pluginconfig$control_freq) %>%
       mutate(values = str_replace(values, "\n", "" )) %>%
       separate(col = values, sep = ",", into = unlist(str_split(.$values[1], ","))) %>%
       slice(2:n()) %>%
       glimpse() %>%
       write_csv("control_freq.csv")
    
    
  }
  
  manifest = read_csv(args_df$manifest) %>%
    map_if(is.factor, as.character) %>%
    as_tibble() %>%
    glimpse() %>%
    write_csv("manifest.csv") # csv needed for ADAM demux part
  
  control_defs = read_csv(args_df$control_definitions) %>%
    map_if(is.factor, as.character) %>%
    as_tibble()  %>%
    drop_na() %>%
    glimpse()
  
 # barcode_file = read_csv(args_df$barcode_file) %>%
#    map_if(is.factor, as.character) %>%
 #   as_tibble() %>%
#    glimpse() %>%
#    write_csv("barcodes.csv") # csv needed for ADAM demux part
  
  
  #grouping_defs = read_csv(args_df$grouping_defs) %>%
  #    map_if(is.factor, as.character) %>%
  #   as_tibble() %>%
  #  glimpse() %>%
  # write_csv("grouping_defs.csv")
  
  control_freq = read_csv(args_df$control_freq) %>%
        map_if(is.factor, as.character) %>%
        as_tibble() %>%
        glimpse() %>%
     write_csv("control_freq.csv")
  
  
  
  
  #return list output
  
  return(list(manifest = manifest,
             # barcode_file = barcode_file,
              control_definitions = control_defs,
              control_freq = control_freq
              #  grouping_defs = grouping_defs
  ))
  
  
  
}