comparison id_converter.py @ 17:1e45ea50f145 draft

planemo upload commit 640429adac783e2354f5caf12d7b6b81b8ddf54f-dirty

16:b6607b7e683f

    ids_list=[]

    for line in input_file :
        if line != [] and set(line) != {''}: 
            line[nb_col] = re.sub(r"\s+","",line[nb_col])
            if ";" in line[nb_col] :
                ids = line[nb_col].split(";")
                for id in ids :
                    new_file.append(line[:nb_col]+[id]+line[nb_col+1:])
                    ids_list.append(id)

    header=False
    if args.id_type in target_ids : target_ids.remove(args.id_type)
    if args.input_type=="file" :
        args.column_number = nb_col_to_int(args.column_number)
        header = str2bool(args.header)

    #Get ref file to build dictionary
    csv.field_size_limit(sys.maxsize) # to handle big files
    with open(args.ref_file, "r") as csv_file :
        tab = csv.reader(csv_file, delimiter='\t')

    #Get file and/or ids from input 
    if args.input_type == "list" :
        ids = get_input_ids_from_string(args.input)
    elif args.input_type == "file" :
        input_file, ids = get_input_ids_from_file(args.input,args.column_number,args.header)

    #Mapping ids
    result_dict = map_to_dictionary(ids,ids_dictionary,args.id_type,target_ids)

    #creating output file 

17:1e45ea50f145

    ids_list=[]

    for line in input_file :
        if line != [] and set(line) != {''}: 
            line[nb_col] = re.sub(r"\s+","",line[nb_col])
            if line[nb_col] == "" : line[nb_col]='NA'
            if ";" in line[nb_col] :
                ids = line[nb_col].split(";")
                for id in ids :
                    new_file.append(line[:nb_col]+[id]+line[nb_col+1:])
                    ids_list.append(id)

    header=False
    if args.id_type in target_ids : target_ids.remove(args.id_type)
    if args.input_type=="file" :
        args.column_number = nb_col_to_int(args.column_number)
        header = str2bool(args.header)
    

    #Get ref file to build dictionary
    csv.field_size_limit(sys.maxsize) # to handle big files
    with open(args.ref_file, "r") as csv_file :
        tab = csv.reader(csv_file, delimiter='\t')

    #Get file and/or ids from input 
    if args.input_type == "list" :
        ids = get_input_ids_from_string(args.input)
    elif args.input_type == "file" :
        input_file, ids = get_input_ids_from_file(args.input,args.column_number,header)

    #Mapping ids
    result_dict = map_to_dictionary(ids,ids_dictionary,args.id_type,target_ids)

    #creating output file