diff --git a/massql/msql_extract.py b/massql/msql_extract.py index 155806b..8385df6 100644 --- a/massql/msql_extract.py +++ b/massql/msql_extract.py @@ -36,7 +36,8 @@ def main(): output_summary=args.extracted_result) except Exception as e: print("FAILURE ON EXTRACTION") - pass + #pass + raise def _extract_mzML_scan(input_filename, spectrum_identifier_list): MS_precisions = { @@ -197,7 +198,8 @@ def _extract_spectra(results_df, input_spectra_folder, output_mgf_filename=None, output_mzML_filename=None, output_json_filename=None, - output_summary=None): + output_summary=None, + max_extracted_scans=10000): spectrum_list = [] result_df_list = [] @@ -251,7 +253,7 @@ def _extract_spectra(results_df, input_spectra_folder, if output_summary is not None: merged_summary_df.to_csv(output_summary, sep='\t', index=False) - if len(spectrum_list) > arg.max_extracted_scans: + if len(spectrum_list) > max_extracted_scans: print("Not Extracting, too many spectra") return None