comparison add_protein_features.R @ 11:8df559ad14a7 draft

planemo upload commit 27f7b6a4a0139ca47ae874fe2fe6de4bd40ffbcf-dirty

10:4de4f6359820

protein_features = function() {

  args <- get_args()  
  
  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
  
  #setting variables
  inputtype = args$inputtype
  if (inputtype == "copy_paste") {
    input = get_list_from_cp(args$input)

  } else {
    res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info)
    res = res[!duplicated(res$NextprotID),]
    output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T)
    output_content = order_columns(output_content,ncol,id_type,file)
    output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
    write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
  } 
  
}

11:8df559ad14a7

protein_features = function() {

  args <- get_args()  
  
  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features/args.rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features/args.rda")
  
  #setting variables
  inputtype = args$inputtype
  if (inputtype == "copy_paste") {
    input = get_list_from_cp(args$input)

  } else {
    res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info)
    res = res[!duplicated(res$NextprotID),]
    output_content = merge(file, res,by.x=ncol,by.y="NextprotID",incomparables = NA,all.x=T)
    output_content = order_columns(output_content,ncol,id_type,file)
    output_content = output_content[,-which(colnames(output_content)=="NextprotID")]      #remove nextprotID column
    output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
    write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
  } 
  
}