def main(): if len(argv) < 3: print_usage() experiments_folder = input('Enter folder name with experimental data: ') results_folder = input('Enter folder name for results: ') else: experiments_folder = argv[1] results_folder = argv[2] print('Experimental data will be loaded from \'{0}\''.format(experiments_folder)) print('Results will be saved to \'{0}\''.format(results_folder)) stdout.flush() if not exists(results_folder): makedirs(results_folder) experiments_files = [f for f in listdir(experiments_folder) if isfile(join( experiments_folder, f))] for experiment_file in experiments_files: experiment_file_name = join(experiments_folder, experiment_file) main_data = correlation.load_main_data_from_csv(experiment_file_name) proteins = correlation.construct_proteins(main_data) protein_records = correlation.construct_protein_records(proteins, main_data) correlation.fill_peptide_parameters(protein_records) received, missed = statistics.fill_parameter_lists(protein_records) peptides_file_name = join(results_folder, experiment_file[:-4] + '.peptides.csv') statistics.save_peptide_parameter_lists_to_csv(received, peptides_file_name) stats = statistics.calculate_simple_statistics(received) statistics_file_name = join(results_folder, experiment_file[:-4] + '.statistics.csv') statistics.save_simple_statistics_to_csv(stats, statistics_file_name)
correlation.fill_protein_sequences(proteins) user_choice = input('Do you want to save your proteins into a new file [Yes/No]? ') if user_choice.upper() == 'YES': protein_file_name = input('Please, enter new file name: ') correlation.save_proteins_to_csv(proteins, protein_file_name + '.csv') else: proteins = correlation.load_proteins_from_csv(input('Please, enter proteins file name: ')) protein_records = correlation.construct_protein_records(proteins, main_data) correlation.fill_missed_peptide_records(protein_records) correlation.fill_peptide_parameters(protein_records) received_parameters, missed_parameters = statistics.fill_parameter_lists(protein_records) received_per_peptide_correlations, missed_per_peptide_correlations = statistics.fill_per_peptide_correlations(protein_records) received_statistics = statistics.calculate_simple_statistics(received_parameters, received_per_peptide_correlations) missed_statistics = statistics.calculate_simple_statistics(missed_parameters, missed_per_peptide_correlations) user_choice = input('Do you want to save statistics for received peptides [Yes/No]? ') if user_choice.upper() == 'YES': file_name = input('Please, enter new file name: ') statistics.save_simple_statistics_to_csv(received_statistics, file_name) user_choice = input('Do you want to save statistics for missed peptides [Yes/No]? ') if user_choice.upper() == 'YES': file_name = input('Please, enter new file name: ') statistics.save_simple_statistics_to_csv(missed_statistics, file_name) user_choice = input('Do you want to save your protein records [Yes/No]? ') if user_choice.upper() == 'YES': folder_name = input('Please, enter folder name: ')