From 586bbdc49d55a68a99b50e60902a424ee87c8aa8 Mon Sep 17 00:00:00 2001 From: Mingxun Wang Date: Tue, 1 Mar 2022 14:47:07 -0800 Subject: [PATCH 1/3] updating extractions --- massql/msql_extract.py | 2 +- tests/test_extraction.py | 16 +++++++++++++++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/massql/msql_extract.py b/massql/msql_extract.py index 0b22b7f..72eda4b 100644 --- a/massql/msql_extract.py +++ b/massql/msql_extract.py @@ -96,7 +96,7 @@ def _extract_mzML_scan(input_filename, spectrum_identifier_list): output_list.append(spectrum_obj) except: - raise + pass return output_list diff --git a/tests/test_extraction.py b/tests/test_extraction.py index fb3541c..c4c08bd 100644 --- a/tests/test_extraction.py +++ b/tests/test_extraction.py @@ -87,12 +87,26 @@ def test_waters_uv_extract(): output_mzML_filename="extracted.mzML", output_summary="extracted.tsv") +def test_waters_uv_extract2(): + query = "QUERY scaninfo(MS2DATA)" + results_df = msql_engine.process_query(query, "tests/data/GT15A.mzML") + + results_df["filename"] = "MMSRG_027.mzML" + results_df = results_df.head() + + merged_summary_df = msql_extract._extract_spectra(results_df, + "tests/data/", + output_mzML_filename="extracted.mzML", + output_json_filename="extracted.json", + output_summary="extracted.tsv") + def main(): #test_extract_mzML() #test_extract_mzXML() #test_extract_MGF() #test_gnps_library_extract() - test_waters_uv_extract() + #test_waters_uv_extract() + test_waters_uv_extract2() if __name__ == "__main__": From 1624d9d072d144ff95606c5d92d656232d355079 Mon Sep 17 00:00:00 2001 From: Mingxun Wang Date: Tue, 1 Mar 2022 14:48:48 -0800 Subject: [PATCH 2/3] moving the level check --- massql/msql_extract.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/massql/msql_extract.py b/massql/msql_extract.py index 72eda4b..f6ab052 100644 --- a/massql/msql_extract.py +++ b/massql/msql_extract.py @@ -55,6 +55,12 @@ def _extract_mzML_scan(input_filename, spectrum_identifier_list): for spec in run: if str(spec.ID) in spectrum_identifier_set: try: + try: + spectrum_obj["mslevel"] = int(spec.ms_level) + except: + # This is likely a UV spectrum + continue + peaks = spec.peaks("raw") # Filtering out zero rows @@ -83,11 +89,6 @@ def _extract_mzML_scan(input_filename, spectrum_identifier_list): spectrum_obj = {} spectrum_obj["peaks"] = peaks_list - try: - spectrum_obj["mslevel"] = int(spec.ms_level) - except: - # This is likely a UV spectrum - continue spectrum_obj["scan"] = str(spec.ID) if spec.ms_level > 1: From 6302de8de10f7c21c320134f301eb6d5087d6ec9 Mon Sep 17 00:00:00 2001 From: Mingxun Wang Date: Tue, 1 Mar 2022 14:57:14 -0800 Subject: [PATCH 3/3] fix --- massql/msql_extract.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/massql/msql_extract.py b/massql/msql_extract.py index f6ab052..42629b1 100644 --- a/massql/msql_extract.py +++ b/massql/msql_extract.py @@ -56,7 +56,7 @@ def _extract_mzML_scan(input_filename, spectrum_identifier_list): if str(spec.ID) in spectrum_identifier_set: try: try: - spectrum_obj["mslevel"] = int(spec.ms_level) + int(spec.ms_level) except: # This is likely a UV spectrum continue @@ -90,6 +90,7 @@ def _extract_mzML_scan(input_filename, spectrum_identifier_list): spectrum_obj = {} spectrum_obj["peaks"] = peaks_list spectrum_obj["scan"] = str(spec.ID) + spectrum_obj["mslevel"] = int(spec.ms_level) if spec.ms_level > 1: msn_mz = spec.selected_precursors[0]["mz"]