diff --git a/main_GUI.py b/main_GUI.py
deleted file mode 100644
index 0abd4fe..0000000
--- a/main_GUI.py
+++ /dev/null
@@ -1,116 +0,0 @@
-# !/usr/bin/env python3
-
-import argparse
-import configparser
-import sys
-import glob
-import os
-from time import time
-import platform
-import multiprocessing.dummy as mult_proc
-from functools import partial
-
-
-# modules
-from PCprophet import io_ as io
-from PCprophet import collapse as collapse
-from PCprophet import generate_features as generate_features
-from PCprophet import hypothesis as hypothesis
-from PCprophet import map_to_database as map_to_database
-from PCprophet import merge as merge
-from PCprophet import differential as differential
-from PCprophet import predict as predict
-from PCprophet import plots as plots
-
-from PCprophet import exceptions as exceptions
-from PCprophet import validate_input as validate
-
-
-class ParserHelper(argparse.ArgumentParser):
-    def error(self, message):
-        sys.stderr.write('error: %s\n' % message)
-        self.print_help()
-        sys.exit(2)
-
-
-# TODO check os
-def get_os():
-    return platform.system()
-
-
-def create_config():
-    '''
-    parse command line and create .ini file for configuration
-    '''
-    # create config file
-    config = configparser.ConfigParser()
-    config.read('ProphetConfig.conf')
-    return config
-
-
-def preprocessing(infile, config):
-
-    validate.InputTester(infile, 'in').test_file()
-    map_to_database.runner(
-    infile=infile,
-    db=config['GLOBAL']['db'],
-    is_ppi=config['PREPROCESS']['is_ppi'],
-    use_fr=config['PREPROCESS']['all_fract'],
-    )
-    hypothesis.runner(
-    infile=infile,
-    hypothesis=config['PREPROCESS']['merge'],
-    use_fr=config['PREPROCESS']['all_fract'],
-    )
-    # sample specific folder
-    tmp_folder = io.file2folder(infile, prefix=config['GLOBAL']['temp'])
-    merge.runner(base=tmp_folder, mergemode=config['PREPROCESS']['merge'])
-    generate_features.runner(
-    tmp_folder, config['GLOBAL']['go_obo'], config['GLOBAL']['sp_go']
-    )
-    predict.runner(tmp_folder)
-    return True
-
-
-def main():
-    config = create_config()
-    validate.InputTester(config['GLOBAL']['db'], 'db').test_file()
-    validate.InputTester(config['GLOBAL']['sid'], 'ids').test_file()
-    files = io.read_sample_ids(config['GLOBAL']['sid'])
-    files = [os.path.abspath(x) for x in files.keys()]
-    if config['GLOBAL']['mult'] == 'True':
-        p = mult_proc.Pool(len(files))
-        preproc_conf=partial(preprocessing, config=config)
-        p.map(preproc_conf, files)
-        p.close()
-        p.join()
-    else:
-        [preprocessing(infile, config) for infile in files]
-    collapse.runner(
-        config['GLOBAL']['temp'],
-        config['GLOBAL']['sid'],
-        config['GLOBAL']['cal'],
-        config['GLOBAL']['mw'],
-        config['POSTPROCESS']['fdr'],
-        config['POSTPROCESS']['collapse_mode'],
-    )
-    combined_file = os.path.join(config['GLOBAL']['temp'], 'combined.txt')
-    differential.runner(
-        combined_file,
-        config['GLOBAL']['sid'],
-        config['GLOBAL']['output'],
-        config['GLOBAL']['temp']
-    )
-    plots.runner(
-        config['GLOBAL']['temp'],
-        config['GLOBAL']['output'],
-        config['POSTPROCESS']['fdr'],
-        config['GLOBAL']['sid'],
-    )
-
-
-if __name__ == '__main__':
-    try:
-        main()
-    except KeyboardInterrupt:
-        pass