From c9d713c15eac352cbf5b5543d79e7ab49dcfae22 Mon Sep 17 00:00:00 2001 From: singjc Date: Sun, 26 Apr 2026 19:52:53 -0400 Subject: [PATCH 1/3] Add tests for OSW export score views and improve parquet export sorting - Introduced a new test file `test_osw_export_score_views.py` to validate the export of score views from OSW files. - Implemented helper functions to create test OSW databases and read joined scores using DuckDB. - Added tests to ensure global and experiment-wide scores are correctly handled when run IDs are null. - Enhanced `test_pyprophet_export.py` by adding a sorting function for exported parquet frames to ensure deterministic snapshots. - Updated existing tests to utilize the new sorting function for parquet exports. --- pyprophet/io/export/osw.py | 89 +++++++---- ...test_parquet_export_no_transition_data.out | 22 +-- ..._export.test_parquet_export_scored_osw.out | 22 +-- tests/test_osw_export_score_views.py | 143 ++++++++++++++++++ tests/test_pyprophet_export.py | 21 +++ 5 files changed, 242 insertions(+), 55 deletions(-) create mode 100644 tests/test_osw_export_score_views.py diff --git a/pyprophet/io/export/osw.py b/pyprophet/io/export/osw.py index 435fa8db..484e1c60 100644 --- a/pyprophet/io/export/osw.py +++ b/pyprophet/io/export/osw.py @@ -2556,13 +2556,20 @@ def _get_peptide_protein_score_table(self, level, contexts: list) -> str: view_name = f"{score_table.lower()}_view" - # Build pivot columns for available contexts + # Build pivot columns for non-global contexts. pivot_cols = [] + non_global_col_names = [] for context in contexts: - # Skip 'global' context as it will be handled separately if context != "global": - # Convert context to column-safe format: 'run-specific' -> 'RUN_SPECIFIC' safe_context = context.upper().replace("-", "_") + non_global_col_names.extend( + [ + f"{score_table}_{safe_context}_SCORE", + f"{score_table}_{safe_context}_PVALUE", + f"{score_table}_{safe_context}_QVALUE", + f"{score_table}_{safe_context}_PEP", + ] + ) pivot_cols.extend( [ f"ANY_VALUE(CASE WHEN context = '{context}' THEN SCORE END) as {score_table}_{safe_context}_SCORE", @@ -2574,8 +2581,8 @@ def _get_peptide_protein_score_table(self, level, contexts: list) -> str: pivot_cols_str = ", ".join(pivot_cols) - # Non-global contexts pivot query - if pivot_cols_str: # Only if there are non-global contexts + # Non-global contexts are keyed by (ID, RUN_ID). + if pivot_cols_str: non_global_query = f""" SELECT {id_col}, RUN_ID, {pivot_cols_str} FROM sqlite_scan('{self.config.infile}', '{score_table}') @@ -2583,47 +2590,61 @@ def _get_peptide_protein_score_table(self, level, contexts: list) -> str: GROUP BY {id_col}, RUN_ID """ else: - # If no non-global contexts, create empty result with same structure - non_global_query = f""" - SELECT {id_col}, RUN_ID - FROM sqlite_scan('{self.config.infile}', '{score_table}') - WHERE 1=0 - """ + non_global_query = None global_exists = "global" in contexts - # Global data query (only if global context exists) + global_col_names = [ + f"{score_table}_GLOBAL_SCORE", + f"{score_table}_GLOBAL_PVALUE", + f"{score_table}_GLOBAL_QVALUE", + f"{score_table}_GLOBAL_PEP", + ] + # Global scores are keyed only by the entity ID. Some files store RUN_ID as NULL. if global_exists: glob_query = f""" SELECT {id_col}, - RUN_ID, - SCORE as {score_table}_GLOBAL_SCORE, - PVALUE as {score_table}_GLOBAL_PVALUE, - QVALUE as {score_table}_GLOBAL_QVALUE, - PEP as {score_table}_GLOBAL_PEP + ANY_VALUE(SCORE) as {score_table}_GLOBAL_SCORE, + ANY_VALUE(PVALUE) as {score_table}_GLOBAL_PVALUE, + ANY_VALUE(QVALUE) as {score_table}_GLOBAL_QVALUE, + ANY_VALUE(PEP) as {score_table}_GLOBAL_PEP FROM sqlite_scan('{self.config.infile}', '{score_table}') WHERE context = 'global' + GROUP BY {id_col} """ + else: + glob_query = None # Build final merged query based on what exists - if pivot_cols_str and global_exists: - # Both non-global and global contexts exist + if non_global_query and glob_query: + non_global_select_cols = ",\n ".join( + f"ng.{col}" for col in non_global_col_names + ) + global_select_cols = ",\n ".join( + f"g.{col}" for col in global_col_names + ) merged_query = f""" - SELECT ng.*, - g.{score_table}_GLOBAL_SCORE, - g.{score_table}_GLOBAL_PVALUE, - g.{score_table}_GLOBAL_QVALUE, - g.{score_table}_GLOBAL_PEP + SELECT + COALESCE(ng.{id_col}, g.{id_col}) AS {id_col}, + ng.RUN_ID, + {non_global_select_cols}, + {global_select_cols} FROM ({non_global_query}) ng - LEFT JOIN ({glob_query}) g ON ng.{id_col} = g.{id_col} AND ng.RUN_ID = g.RUN_ID + FULL OUTER JOIN ({glob_query}) g ON ng.{id_col} = g.{id_col} """ - elif pivot_cols_str and not global_exists: - # Only non-global contexts exist + elif non_global_query: merged_query = non_global_query - elif not pivot_cols_str and global_exists: - # Only global context exists - merged_query = glob_query + elif glob_query: + global_select_cols = ",\n ".join( + f"g.{col}" for col in global_col_names + ) + merged_query = f""" + SELECT + g.{id_col}, + NULL AS RUN_ID, + {global_select_cols} + FROM ({glob_query}) g + """ else: - # No contexts exist - return empty result with ID columns merged_query = f""" SELECT {id_col}, RUN_ID FROM sqlite_scan('{self.config.infile}', '{score_table}') @@ -2683,7 +2704,8 @@ def _build_score_column_selection_and_joins( ) # Add JOIN for peptide score view score_tables_to_join.append( - "LEFT JOIN score_peptide_view ON PEPTIDE.ID = score_peptide_view.PEPTIDE_ID AND FEATURE.RUN_ID = score_peptide_view.RUN_ID" + "LEFT JOIN score_peptide_view ON PEPTIDE.ID = score_peptide_view.PEPTIDE_ID " + "AND (FEATURE.RUN_ID = score_peptide_view.RUN_ID OR score_peptide_view.RUN_ID IS NULL)" ) if column_info["score_protein_exists"]: logger.debug("SCORE_PROTEIN table exists, adding score table view to query") @@ -2694,7 +2716,8 @@ def _build_score_column_selection_and_joins( ) # Add JOIN for protein score view score_tables_to_join.append( - "LEFT JOIN score_protein_view ON PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID = score_protein_view.PROTEIN_ID AND FEATURE.RUN_ID = score_protein_view.RUN_ID" + "LEFT JOIN score_protein_view ON PEPTIDE_PROTEIN_MAPPING.PROTEIN_ID = score_protein_view.PROTEIN_ID " + "AND (FEATURE.RUN_ID = score_protein_view.RUN_ID OR score_protein_view.RUN_ID IS NULL)" ) # Add score columns for peptide and protein contexts diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out index 795ea384..8a62a802 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_no_transition_data.out @@ -1,13 +1,13 @@ Exported 3410 rows with 100 columns (no transition data) Score columns found: ['SCORE_MS2_PEAK_GROUP_RANK', 'SCORE_MS2_PEP', 'SCORE_MS2_P_VALUE', 'SCORE_MS2_Q_VALUE', 'SCORE_MS2_SCORE', 'SCORE_PEPTIDE_GLOBAL_PEP', 'SCORE_PEPTIDE_GLOBAL_P_VALUE', 'SCORE_PEPTIDE_GLOBAL_Q_VALUE', 'SCORE_PEPTIDE_GLOBAL_SCORE', 'SCORE_PROTEIN_GLOBAL_PEP', 'SCORE_PROTEIN_GLOBAL_P_VALUE', 'SCORE_PROTEIN_GLOBAL_Q_VALUE', 'SCORE_PROTEIN_GLOBAL_SCORE'] - ANNOTATION DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FEATURE_TRANSITION_APEX_INTENSITY FEATURE_TRANSITION_AREA_INTENSITY FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_TRANSITION_VAR_LOG_INTENSITY FEATURE_TRANSITION_VAR_LOG_SN_SCORE FEATURE_TRANSITION_VAR_MASSDEV_SCORE FEATURE_TRANSITION_VAR_XCORR_COELUTION FEATURE_TRANSITION_VAR_XCORR_SHAPE FILENAME GENE_DECOY GENE_ID GENE_NAME IM_leftWidth IM_rightWidth IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PRODUCT_MZ PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE TRANSITION_CHARGE TRANSITION_DECOY TRANSITION_DETECTING TRANSITION_ID TRANSITION_LIBRARY_INTENSITY TRANSITION_ORDINAL TRANSITION_TRAML_ID TRANSITION_TYPE UNMODIFIED_SEQUENCE -0 None -85.0733 NaN 1923.17 483971408708572459 192394.8906 935372.0000 0.9919 0.1179 3.1724 0.0000 0.9713 61269.0 321681.0 5.0 0.7829 NaN 0.3415 0.9953 0.0000 0.9944 0.9786 0.2234 0.0893 0.1044 0.2119 3.7524 0.7034 2.8770 1.0938 0.0237 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9660 0.9924 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522 1898.6700 GIGDWSDSK(UniMod:259) 7.0277 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5 1946.4600 -8670811102654834151 1 0.0031 0.0029 0.0033 4.6997 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -1 None -55.2126 NaN 1953.03 6854889104354289238 5696.7271 45882.6016 0.2886 1.6923 20.0342 5.1458 0.5950 7999.0 45147.0 3.0 0.5879 NaN 0.0479 0.6040 0.6485 0.9860 0.9809 0.2040 0.0854 0.1024 0.2154 1.8184 0.8426 7.5457 10.7048 0.0151 NaN NaN NaN NaN NaN NaN 3.4670 1.4506 0.6956 0.8139 3.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522 1946.4600 GIGDWSDSK(UniMod:259) 7.8936 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5 1977.1899 -8670811102654834151 4 1.0000 0.4692 0.4692 -1.7930 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -2 None 9.7944 NaN 2018.03 2696300170322160855 17401.1816 95751.7969 0.9301 0.5084 13.5151 0.7500 0.6966 2243.0 13809.0 4.0 0.5880 NaN 0.0147 -0.0614 0.1439 -0.4161 0.7216 0.6824 0.3240 0.4081 1.2232 0.0221 0.9147 2.4447 2.0283 0.0038 NaN NaN NaN NaN NaN NaN 1.3498 0.4384 0.8111 0.8839 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522 2001.0900 GIGDWSDSK(UniMod:259) 9.7785 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5 2024.9800 -8670811102654834151 2 1.0000 0.4692 0.4692 -0.3786 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -3 None -130.8641 NaN 1877.37 8207933629855485114 6239.5195 48788.5000 -0.5293 1.7491 3.3984 3.2500 0.5946 3336.0 36324.0 3.0 0.4316 NaN 0.0386 0.1794 0.2909 -0.3937 0.8019 0.6135 0.2909 0.3399 1.0151 0.6018 1.1139 5.2642 1.9825 0.0370 NaN NaN NaN NaN NaN NaN 2.2472 0.8549 0.7655 0.8558 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522 1857.7000 GIGDWSDSK(UniMod:259) 5.7000 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5 1898.6700 -8670811102654834151 3 1.0000 0.4692 0.4692 -1.5525 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -4 None -268.6805 NaN 1739.56 745237666153652118 6493.7773 66798.3984 -0.4011 0.7500 16.0151 4.5817 0.6404 7539.0 53232.0 3.0 0.5633 NaN 0.0565 0.3089 0.5266 -0.7130 0.6301 0.8349 0.3552 0.4363 1.3366 1.4128 0.9671 6.3286 10.9637 0.0770 NaN NaN NaN NaN NaN NaN 2.8670 1.1513 0.7267 0.8314 3.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522 1717.7300 GIGDWSDSK(UniMod:259) 1.7038 False 523 2 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5 1762.1100 -8670811102654834151 5 1.0000 0.4692 0.4692 -3.2559 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -5 None -6.0218 NaN 3084.15 1082368609638691369 88839.6328 604041.0000 0.9885 0.1408 0.7967 0.0000 0.9766 37375.0 195175.0 4.0 0.8376 NaN 0.7351 0.9983 0.0000 0.9806 0.9979 0.0536 0.0300 0.0412 0.1268 4.8405 0.6753 2.2770 1.9680 0.0021 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9976 0.9985 8.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385 3066.2200 ESDILAVVK(UniMod:259) 40.6918 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 3110.6101 -8670811102654834151 1 0.0031 0.0029 0.0033 5.5702 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -6 None 228.9700 NaN 3319.15 -1344271892660954750 9115.7090 102078.0000 0.7000 1.0399 16.1263 5.5000 0.4975 4782.0 23890.0 2.0 0.4271 NaN 0.0900 0.9602 1.0000 0.7442 0.9239 0.3826 0.1244 0.1502 0.4641 3.2047 1.1861 14.1720 12.7184 0.0661 NaN NaN NaN NaN NaN NaN 0.7830 0.1486 0.8549 0.8773 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385 3301.7800 ESDILAVVK(UniMod:259) 47.5056 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 3339.3301 -8670811102654834151 5 1.0000 0.4692 0.4692 -1.8443 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -7 None -124.5660 NaN 2965.61 -4515618252120499488 9268.4902 109284.0000 0.6217 1.1110 22.4222 1.5000 0.7138 793.0 6371.0 4.0 0.8481 NaN 0.0240 0.9434 0.0000 0.8820 0.9766 0.2001 0.0990 0.1152 0.3558 1.0582 0.5825 6.0852 4.5232 0.0365 NaN NaN NaN NaN NaN NaN 0.9749 0.0676 0.7227 0.8143 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385 2946.7400 ESDILAVVK(UniMod:259) 37.2545 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 2994.5300 -8670811102654834151 3 1.0000 0.0205 0.0210 1.9398 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -8 None 28.5831 NaN 3118.76 -4044853666210028406 9989.7793 33949.8008 0.2103 0.6817 10.4054 1.0774 0.8894 865.0 2909.0 4.0 0.8179 NaN 0.0110 0.4917 0.0000 0.6890 0.9634 0.2912 0.1309 0.1515 0.4848 1.3179 0.6547 5.8786 5.3254 0.0080 NaN NaN NaN NaN NaN NaN 0.7830 0.3902 0.8943 0.8531 1.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385 3114.0200 ESDILAVVK(UniMod:259) 41.6952 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 3131.0901 -8670811102654834151 2 1.0000 0.0176 0.0180 2.2958 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -9 None -184.3073 NaN 2905.87 7439833196907350500 15059.3516 143080.0000 -0.2753 3.5529 3.1948 3.9578 0.6528 1527.0 8281.0 5.0 0.5666 NaN 0.0312 0.8691 0.0000 -0.3982 0.7375 0.6314 0.2844 0.3777 1.1866 2.5854 0.9876 9.8422 8.8909 0.0538 NaN NaN NaN NaN NaN NaN 3.7575 2.5131 0.6924 0.6775 0.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385 2881.8701 ESDILAVVK(UniMod:259) 35.5222 False 386 2 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8 2929.6699 -8670811102654834151 4 1.0000 0.4692 0.4692 -1.8184 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK + ANNOTATION DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FEATURE_TRANSITION_APEX_INTENSITY FEATURE_TRANSITION_AREA_INTENSITY FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_TRANSITION_VAR_LOG_INTENSITY FEATURE_TRANSITION_VAR_LOG_SN_SCORE FEATURE_TRANSITION_VAR_MASSDEV_SCORE FEATURE_TRANSITION_VAR_XCORR_COELUTION FEATURE_TRANSITION_VAR_XCORR_SHAPE FILENAME GENE_DECOY GENE_ID GENE_NAME IM_leftWidth IM_rightWidth IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PRODUCT_MZ PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE TRANSITION_CHARGE TRANSITION_DECOY TRANSITION_DETECTING TRANSITION_ID TRANSITION_LIBRARY_INTENSITY TRANSITION_ORDINAL TRANSITION_TRAML_ID TRANSITION_TYPE UNMODIFIED_SEQUENCE +0 None 65.9712 NaN 2661.55 -4409520928686189639 117220.7500 8.5464e+05 0.9835 0.1247 1.3707 0.0000 0.9907 30361.0 207283.0 9.0 0.7708 NaN 0.7811 0.9962 0.0000 0.9987 0.9978 0.0659 0.0239 0.0262 0.0725 4.7388 0.7451 0.3398 0.1793 0.0194 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9936 0.9958 11.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32 2640.5100 ADSTGTLVITDPTR(UniMod:267) 28.4379 False 33 2 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0 2705.3701 -8670811102654834151 1 0.0031 0.0029 0.0033 5.7301 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +1 None 10.1667 NaN 2605.74 260819276075322832 8790.7812 1.0401e+05 0.9555 0.2667 5.4202 5.1430 0.6532 990.0 6385.0 2.0 0.7610 NaN 0.0241 0.9216 0.1104 0.8271 0.9764 0.2223 0.0995 0.1102 0.3579 1.3130 0.7675 4.5391 3.5103 0.0032 NaN NaN NaN NaN NaN NaN 7.0474 2.3104 0.7806 0.8341 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32 2575.6399 ADSTGTLVITDPTR(UniMod:267) 26.8198 False 33 2 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0 2623.4399 -8670811102654834151 2 1.0000 0.0674 0.0685 1.2404 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +2 None 237.1922 NaN 2832.77 5163914660633416481 10419.7432 2.4187e+05 0.6123 0.4707 8.9907 4.0083 0.5985 546.0 5180.0 2.0 0.7923 NaN 0.0195 0.8418 0.0911 0.9916 0.9960 0.0958 0.0387 0.0426 0.1243 0.6699 0.6863 4.7328 2.9948 0.0690 NaN NaN NaN NaN NaN NaN 4.3568 2.0950 0.6909 0.6974 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32 2811.2000 ADSTGTLVITDPTR(UniMod:267) 33.4026 False 33 2 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0 2855.5801 -8670811102654834151 5 1.0000 0.4692 0.4692 -0.1013 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +3 None 199.4846 NaN 2795.06 6932937885234622359 4036.5601 2.5862e+04 0.1872 2.4435 1.8505 4.0083 0.6422 497.0 2693.0 4.0 0.7883 NaN 0.0101 0.6804 0.1794 0.4554 0.9481 0.3084 0.1494 0.1882 0.6202 0.6284 0.6986 5.4811 3.8885 0.0581 NaN NaN NaN NaN NaN NaN 1.6487 0.9186 0.7955 0.7971 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32 2790.7200 ADSTGTLVITDPTR(UniMod:267) 32.3092 False 33 2 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0 2811.2000 -8670811102654834151 4 1.0000 0.1994 0.2018 0.6777 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +4 None 112.9550 NaN 2708.53 8534214264242363560 5750.4717 7.3215e+04 -0.3692 0.7498 7.1610 6.7500 0.4827 539.0 3838.0 3.0 0.8181 NaN 0.0145 0.7660 0.1334 0.8344 0.9736 0.2367 0.1055 0.1166 0.3772 0.6034 0.6468 2.5636 1.1471 0.0330 NaN NaN NaN NaN NaN NaN 3.4656 0.9347 0.6790 0.7379 5.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32 2705.3701 ADSTGTLVITDPTR(UniMod:267) 29.8002 False 33 2 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0 2736.0901 -8670811102654834151 3 1.0000 0.1994 0.2018 0.8151 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +5 None -33.8921 NaN 2915.46 -7771919224870429764 184097.5000 1.3502e+06 0.9791 0.1077 0.4784 0.0000 0.9955 48041.0 356015.0 11.0 0.7672 NaN 0.7753 0.9926 0.0000 0.8733 0.9890 0.1414 0.0968 0.1030 0.2900 4.6343 0.7586 1.1505 1.3231 0.0100 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9987 0.9985 9.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79 2892.9299 ALGYEDATQALGR(UniMod:267) 35.8003 False 80 2 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0 2947.5500 -8670811102654834151 1 0.0031 0.0029 0.0033 5.6547 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +6 None 116.0990 NaN 3065.45 -1618439206596772741 2301.7830 1.0445e+05 -0.2527 3.0023 27.2973 6.2440 0.6421 1677.0 14023.0 8.0 0.7684 NaN 0.0305 0.4049 0.0000 0.9857 0.9992 0.0354 0.0206 0.0227 0.0631 1.2430 0.7016 4.4870 5.4277 0.0335 NaN NaN NaN NaN NaN NaN 0.5749 0.1143 0.7704 0.7332 5.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79 3043.1399 ALGYEDATQALGR(UniMod:267) 40.1495 False 80 2 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0 3087.5200 -8670811102654834151 2 1.0000 0.0674 0.0685 1.5182 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +7 None 159.3408 NaN 3108.69 -1528523763856537095 3486.5154 5.5320e+04 -0.4336 3.6979 7.6742 6.7217 0.6224 908.0 7875.0 4.0 0.5768 NaN 0.0171 0.6492 0.3228 0.7616 0.9878 0.1379 0.0796 0.0899 0.2518 0.7011 0.9173 6.5049 6.5553 0.0460 NaN NaN NaN NaN NaN NaN 5.2085 3.1141 0.8087 0.7578 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79 3087.5200 ALGYEDATQALGR(UniMod:267) 41.4033 False 80 2 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0 3125.0701 -8670811102654834151 5 1.0000 0.4692 0.4692 -1.2624 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +8 None -63.4234 NaN 2885.93 4932359594612728841 8025.5601 7.0488e+04 0.5051 1.5720 3.6487 4.9107 0.4855 1921.0 6866.0 5.0 0.3595 NaN 0.0150 0.4893 0.8436 -0.6868 0.8659 0.4973 0.3252 0.3576 0.9445 1.5314 1.1339 4.0154 5.9697 0.0186 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.8911 0.8734 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79 2869.0300 ALGYEDATQALGR(UniMod:267) 34.9440 False 80 2 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0 2889.5100 -8670811102654834151 4 1.0000 0.4692 0.4692 -1.1134 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +9 None 288.8942 NaN 3238.25 9173417844487548347 3238.0957 6.5173e+04 -0.7411 2.1667 10.3701 9.0000 0.5089 1051.0 9306.0 6.0 0.7827 NaN 0.0203 0.5781 0.3886 0.8789 0.9890 0.1243 0.0848 0.0992 0.2789 0.8313 0.6932 2.6921 1.8259 0.0836 NaN NaN NaN NaN NaN NaN 4.2487 2.0195 0.7744 0.7170 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79 3207.0100 ALGYEDATQALGR(UniMod:267) 45.1599 False 80 2 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0 3247.9700 -8670811102654834151 3 1.0000 0.4692 0.4692 -0.5351 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out index 67a02880..b80556ba 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_scored_osw.out @@ -1,13 +1,13 @@ Exported 97964 rows with 100 columns Score columns found: ['SCORE_MS2_PEAK_GROUP_RANK', 'SCORE_MS2_PEP', 'SCORE_MS2_P_VALUE', 'SCORE_MS2_Q_VALUE', 'SCORE_MS2_SCORE', 'SCORE_PEPTIDE_GLOBAL_PEP', 'SCORE_PEPTIDE_GLOBAL_P_VALUE', 'SCORE_PEPTIDE_GLOBAL_Q_VALUE', 'SCORE_PEPTIDE_GLOBAL_SCORE', 'SCORE_PROTEIN_GLOBAL_PEP', 'SCORE_PROTEIN_GLOBAL_P_VALUE', 'SCORE_PROTEIN_GLOBAL_Q_VALUE', 'SCORE_PROTEIN_GLOBAL_SCORE'] - ANNOTATION DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FEATURE_TRANSITION_APEX_INTENSITY FEATURE_TRANSITION_AREA_INTENSITY FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_TRANSITION_VAR_LOG_INTENSITY FEATURE_TRANSITION_VAR_LOG_SN_SCORE FEATURE_TRANSITION_VAR_MASSDEV_SCORE FEATURE_TRANSITION_VAR_XCORR_COELUTION FEATURE_TRANSITION_VAR_XCORR_SHAPE FILENAME GENE_DECOY GENE_ID GENE_NAME IM_leftWidth IM_rightWidth IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PRODUCT_MZ PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE TRANSITION_CHARGE TRANSITION_DECOY TRANSITION_DETECTING TRANSITION_ID TRANSITION_LIBRARY_INTENSITY TRANSITION_ORDINAL TRANSITION_TRAML_ID TRANSITION_TYPE UNMODIFIED_SEQUENCE -0 None -85.0733 NaN 1923.17 4.8397e+17 192394.8906 935372.0000 0.9919 0.1179 3.1724 0.0000 0.9713 61269.0 321681.0 5.0 0.7829 NaN 0.3415 0.9953 0.0000 0.9944 0.9786 0.2234 0.0893 0.1044 0.2119 3.7524 0.7034 2.8770 1.0938 0.0237 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9660 0.9924 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522.0 1898.6700 GIGDWSDSK(UniMod:259) 7.0277 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1946.4600 -8.6708e+18 1.0 0.0031 0.0029 0.0033 4.6997 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -1 None -55.2126 NaN 1953.03 6.8549e+18 5696.7271 45882.6016 0.2886 1.6923 20.0342 5.1458 0.5950 7999.0 45147.0 3.0 0.5879 NaN 0.0479 0.6040 0.6485 0.9860 0.9809 0.2040 0.0854 0.1024 0.2154 1.8184 0.8426 7.5457 10.7048 0.0151 NaN NaN NaN NaN NaN NaN 3.4670 1.4506 0.6956 0.8139 3.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522.0 1946.4600 GIGDWSDSK(UniMod:259) 7.8936 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1977.1899 -8.6708e+18 4.0 1.0000 0.4692 0.4692 -1.7930 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -2 None 9.7944 NaN 2018.03 2.6963e+18 17401.1816 95751.7969 0.9301 0.5084 13.5151 0.7500 0.6966 2243.0 13809.0 4.0 0.5880 NaN 0.0147 -0.0614 0.1439 -0.4161 0.7216 0.6824 0.3240 0.4081 1.2232 0.0221 0.9147 2.4447 2.0283 0.0038 NaN NaN NaN NaN NaN NaN 1.3498 0.4384 0.8111 0.8839 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522.0 2001.0900 GIGDWSDSK(UniMod:259) 9.7785 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 2024.9800 -8.6708e+18 2.0 1.0000 0.4692 0.4692 -0.3786 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -3 None -130.8641 NaN 1877.37 8.2079e+18 6239.5195 48788.5000 -0.5293 1.7491 3.3984 3.2500 0.5946 3336.0 36324.0 3.0 0.4316 NaN 0.0386 0.1794 0.2909 -0.3937 0.8019 0.6135 0.2909 0.3399 1.0151 0.6018 1.1139 5.2642 1.9825 0.0370 NaN NaN NaN NaN NaN NaN 2.2472 0.8549 0.7655 0.8558 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522.0 1857.7000 GIGDWSDSK(UniMod:259) 5.7000 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1898.6700 -8.6708e+18 3.0 1.0000 0.4692 0.4692 -1.5525 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -4 None -268.6805 NaN 1739.56 7.4524e+17 6493.7773 66798.3984 -0.4011 0.7500 16.0151 4.5817 0.6404 7539.0 53232.0 3.0 0.5633 NaN 0.0565 0.3089 0.5266 -0.7130 0.6301 0.8349 0.3552 0.4363 1.3366 1.4128 0.9671 6.3286 10.9637 0.0770 NaN NaN NaN NaN NaN NaN 2.8670 1.1513 0.7267 0.8314 3.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 522.0 1717.7300 GIGDWSDSK(UniMod:259) 1.7038 False 523.0 2.0 False AQUA4SWATH_HMLangeF_GIGDWSDSK(UniMod:259)/2 119 NaN NaN 9.4 486.7293 AQUA4SWATH_HMLangeF_GIGDWSDSK(Label:13C(6)15N(... NaN AQUA4SWATH_HMLangeF None 5.0 1762.1100 -8.6708e+18 5.0 1.0000 0.4692 0.4692 -3.2559 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None GIGDWSDSK -5 None -6.0218 NaN 3084.15 1.0824e+18 88839.6328 604041.0000 0.9885 0.1408 0.7967 0.0000 0.9766 37375.0 195175.0 4.0 0.8376 NaN 0.7351 0.9983 0.0000 0.9806 0.9979 0.0536 0.0300 0.0412 0.1268 4.8405 0.6753 2.2770 1.9680 0.0021 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9976 0.9985 8.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385.0 3066.2200 ESDILAVVK(UniMod:259) 40.6918 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 3110.6101 -8.6708e+18 1.0 0.0031 0.0029 0.0033 5.5702 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -6 None 228.9700 NaN 3319.15 -1.3443e+18 9115.7090 102078.0000 0.7000 1.0399 16.1263 5.5000 0.4975 4782.0 23890.0 2.0 0.4271 NaN 0.0900 0.9602 1.0000 0.7442 0.9239 0.3826 0.1244 0.1502 0.4641 3.2047 1.1861 14.1720 12.7184 0.0661 NaN NaN NaN NaN NaN NaN 0.7830 0.1486 0.8549 0.8773 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385.0 3301.7800 ESDILAVVK(UniMod:259) 47.5056 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 3339.3301 -8.6708e+18 5.0 1.0000 0.4692 0.4692 -1.8443 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -7 None -124.5660 NaN 2965.61 -4.5156e+18 9268.4902 109284.0000 0.6217 1.1110 22.4222 1.5000 0.7138 793.0 6371.0 4.0 0.8481 NaN 0.0240 0.9434 0.0000 0.8820 0.9766 0.2001 0.0990 0.1152 0.3558 1.0582 0.5825 6.0852 4.5232 0.0365 NaN NaN NaN NaN NaN NaN 0.9749 0.0676 0.7227 0.8143 2.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385.0 2946.7400 ESDILAVVK(UniMod:259) 37.2545 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 2994.5300 -8.6708e+18 3.0 1.0000 0.0205 0.0210 1.9398 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -8 None 28.5831 NaN 3118.76 -4.0449e+18 9989.7793 33949.8008 0.2103 0.6817 10.4054 1.0774 0.8894 865.0 2909.0 4.0 0.8179 NaN 0.0110 0.4917 0.0000 0.6890 0.9634 0.2912 0.1309 0.1515 0.4848 1.3179 0.6547 5.8786 5.3254 0.0080 NaN NaN NaN NaN NaN NaN 0.7830 0.3902 0.8943 0.8531 1.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385.0 3114.0200 ESDILAVVK(UniMod:259) 41.6952 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 3131.0901 -8.6708e+18 2.0 1.0000 0.0176 0.0180 2.2958 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK -9 None -184.3073 NaN 2905.87 7.4398e+18 15059.3516 143080.0000 -0.2753 3.5529 3.1948 3.9578 0.6528 1527.0 8281.0 5.0 0.5666 NaN 0.0312 0.8691 0.0000 -0.3982 0.7375 0.6314 0.2844 0.3777 1.1866 2.5854 0.9876 9.8422 8.8909 0.0538 NaN NaN NaN NaN NaN NaN 3.7575 2.5131 0.6924 0.6775 0.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 385.0 2881.8701 ESDILAVVK(UniMod:259) 35.5222 False 386.0 2.0 False AQUA4SWATH_Lepto_ESDILAVVK(UniMod:259)/2 166 NaN NaN 40.9 491.2890 AQUA4SWATH_Lepto_ESDILAVVK(Label:13C(6)15N(2))... NaN AQUA4SWATH_Lepto None 8.0 2929.6699 -8.6708e+18 4.0 1.0000 0.4692 0.4692 -1.8184 NaN NaN NaN NaN NaN NaN NaN NaN NaN None None NaN NaN NaN None None ESDILAVVK + ANNOTATION DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FEATURE_TRANSITION_APEX_INTENSITY FEATURE_TRANSITION_AREA_INTENSITY FEATURE_TRANSITION_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_TRANSITION_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_TRANSITION_VAR_LOG_INTENSITY FEATURE_TRANSITION_VAR_LOG_SN_SCORE FEATURE_TRANSITION_VAR_MASSDEV_SCORE FEATURE_TRANSITION_VAR_XCORR_COELUTION FEATURE_TRANSITION_VAR_XCORR_SHAPE FILENAME GENE_DECOY GENE_ID GENE_NAME IM_leftWidth IM_rightWidth IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PRODUCT_MZ PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE TRANSITION_CHARGE TRANSITION_DECOY TRANSITION_DETECTING TRANSITION_ID TRANSITION_LIBRARY_INTENSITY TRANSITION_ORDINAL TRANSITION_TRAML_ID TRANSITION_TYPE UNMODIFIED_SEQUENCE +0 None 65.9712 NaN 2661.55 -4.4095e+18 117220.7500 8.5464e+05 0.9835 0.1247 1.3707 0.0000 0.9907 30361.0 207283.0 9.0 0.7708 NaN 0.7811 0.9962 0.0000 0.9987 0.9978 0.0659 0.0239 0.0262 0.0725 4.7388 0.7451 0.3398 0.1793 0.0194 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9936 0.9958 11.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32.0 2640.5100 ADSTGTLVITDPTR(UniMod:267) 28.4379 False 33.0 2.0 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0.0 2705.3701 -8.6708e+18 1.0 0.0031 0.0029 0.0033 5.7301 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +1 None 10.1667 NaN 2605.74 2.6082e+17 8790.7812 1.0401e+05 0.9555 0.2667 5.4202 5.1430 0.6532 990.0 6385.0 2.0 0.7610 NaN 0.0241 0.9216 0.1104 0.8271 0.9764 0.2223 0.0995 0.1102 0.3579 1.3130 0.7675 4.5391 3.5103 0.0032 NaN NaN NaN NaN NaN NaN 7.0474 2.3104 0.7806 0.8341 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32.0 2575.6399 ADSTGTLVITDPTR(UniMod:267) 26.8198 False 33.0 2.0 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0.0 2623.4399 -8.6708e+18 2.0 1.0000 0.0674 0.0685 1.2404 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +2 None 237.1922 NaN 2832.77 5.1639e+18 10419.7432 2.4187e+05 0.6123 0.4707 8.9907 4.0083 0.5985 546.0 5180.0 2.0 0.7923 NaN 0.0195 0.8418 0.0911 0.9916 0.9960 0.0958 0.0387 0.0426 0.1243 0.6699 0.6863 4.7328 2.9948 0.0690 NaN NaN NaN NaN NaN NaN 4.3568 2.0950 0.6909 0.6974 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32.0 2811.2000 ADSTGTLVITDPTR(UniMod:267) 33.4026 False 33.0 2.0 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0.0 2855.5801 -8.6708e+18 5.0 1.0000 0.4692 0.4692 -0.1013 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +3 None 199.4846 NaN 2795.06 6.9329e+18 4036.5601 2.5862e+04 0.1872 2.4435 1.8505 4.0083 0.6422 497.0 2693.0 4.0 0.7883 NaN 0.0101 0.6804 0.1794 0.4554 0.9481 0.3084 0.1494 0.1882 0.6202 0.6284 0.6986 5.4811 3.8885 0.0581 NaN NaN NaN NaN NaN NaN 1.6487 0.9186 0.7955 0.7971 6.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32.0 2790.7200 ADSTGTLVITDPTR(UniMod:267) 32.3092 False 33.0 2.0 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0.0 2811.2000 -8.6708e+18 4.0 1.0000 0.1994 0.2018 0.6777 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +4 None 112.9550 NaN 2708.53 8.5342e+18 5750.4717 7.3215e+04 -0.3692 0.7498 7.1610 6.7500 0.4827 539.0 3838.0 3.0 0.8181 NaN 0.0145 0.7660 0.1334 0.8344 0.9736 0.2367 0.1055 0.1166 0.3772 0.6034 0.6468 2.5636 1.1471 0.0330 NaN NaN NaN NaN NaN NaN 3.4656 0.9347 0.6790 0.7379 5.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 32.0 2705.3701 ADSTGTLVITDPTR(UniMod:267) 29.8002 False 33.0 2.0 False NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... NaN AQUA4SWATH_HMLangeA None 0.0 2736.0901 -8.6708e+18 3.0 1.0000 0.1994 0.2018 0.8151 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ADSTGTLVITDPTR +5 None -33.8921 NaN 2915.46 -7.7719e+18 184097.5000 1.3502e+06 0.9791 0.1077 0.4784 0.0000 0.9955 48041.0 356015.0 11.0 0.7672 NaN 0.7753 0.9926 0.0000 0.8733 0.9890 0.1414 0.0968 0.1030 0.2900 4.6343 0.7586 1.1505 1.3231 0.0100 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9987 0.9985 9.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79.0 2892.9299 ALGYEDATQALGR(UniMod:267) 35.8003 False 80.0 2.0 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0.0 2947.5500 -8.6708e+18 1.0 0.0031 0.0029 0.0033 5.6547 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +6 None 116.0990 NaN 3065.45 -1.6184e+18 2301.7830 1.0445e+05 -0.2527 3.0023 27.2973 6.2440 0.6421 1677.0 14023.0 8.0 0.7684 NaN 0.0305 0.4049 0.0000 0.9857 0.9992 0.0354 0.0206 0.0227 0.0631 1.2430 0.7016 4.4870 5.4277 0.0335 NaN NaN NaN NaN NaN NaN 0.5749 0.1143 0.7704 0.7332 5.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79.0 3043.1399 ALGYEDATQALGR(UniMod:267) 40.1495 False 80.0 2.0 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0.0 3087.5200 -8.6708e+18 2.0 1.0000 0.0674 0.0685 1.5182 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +7 None 159.3408 NaN 3108.69 -1.5285e+18 3486.5154 5.5320e+04 -0.4336 3.6979 7.6742 6.7217 0.6224 908.0 7875.0 4.0 0.5768 NaN 0.0171 0.6492 0.3228 0.7616 0.9878 0.1379 0.0796 0.0899 0.2518 0.7011 0.9173 6.5049 6.5553 0.0460 NaN NaN NaN NaN NaN NaN 5.2085 3.1141 0.8087 0.7578 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79.0 3087.5200 ALGYEDATQALGR(UniMod:267) 41.4033 False 80.0 2.0 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0.0 3125.0701 -8.6708e+18 5.0 1.0000 0.4692 0.4692 -1.2624 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +8 None -63.4234 NaN 2885.93 4.9324e+18 8025.5601 7.0488e+04 0.5051 1.5720 3.6487 4.9107 0.4855 1921.0 6866.0 5.0 0.3595 NaN 0.0150 0.4893 0.8436 -0.6868 0.8659 0.4973 0.3252 0.3576 0.9445 1.5314 1.1339 4.0154 5.9697 0.0186 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.8911 0.8734 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79.0 2869.0300 ALGYEDATQALGR(UniMod:267) 34.9440 False 80.0 2.0 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0.0 2889.5100 -8.6708e+18 4.0 1.0000 0.4692 0.4692 -1.1134 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR +9 None 288.8942 NaN 3238.25 9.1734e+18 3238.0957 6.5173e+04 -0.7411 2.1667 10.3701 9.0000 0.5089 1051.0 9306.0 6.0 0.7827 NaN 0.0203 0.5781 0.3886 0.8789 0.9890 0.1243 0.0848 0.0992 0.2789 0.8313 0.6932 2.6921 1.8259 0.0836 NaN NaN NaN NaN NaN NaN 4.2487 2.0195 0.7744 0.7170 4.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN napedro_L120420_010_SW.mzXML.gz None NaN None NaN NaN 79.0 3207.0100 ALGYEDATQALGR(UniMod:267) 45.1599 False 80.0 2.0 False AQUA4SWATH_HMLangeA_ALGYEDATQALGR(UniMod:267)/2 1 NaN NaN 36.8 687.8480 AQUA4SWATH_HMLangeA_ALGYEDATQALGR(Label:13C(6)... NaN AQUA4SWATH_HMLangeA None 0.0 3247.9700 -8.6708e+18 3.0 1.0000 0.4692 0.4692 -0.5351 0.0031 0.0029 0.0033 5.6547 0.3674 0.0625 0.0625 5.8401 NaN None None NaN NaN NaN None None ALGYEDATQALGR diff --git a/tests/test_osw_export_score_views.py b/tests/test_osw_export_score_views.py new file mode 100644 index 00000000..2c9550cf --- /dev/null +++ b/tests/test_osw_export_score_views.py @@ -0,0 +1,143 @@ +import sqlite3 + +import duckdb + +from pyprophet._config import ExportIOConfig +from pyprophet.io.export.osw import OSWWriter +from pyprophet.io.util import load_sqlite_scanner + + +def _create_score_test_osw(path, include_experiment_wide: bool) -> None: + with sqlite3.connect(path) as con: + con.executescript( + """ + CREATE TABLE PEPTIDE (ID INTEGER PRIMARY KEY); + CREATE TABLE PROTEIN (ID INTEGER PRIMARY KEY); + CREATE TABLE PEPTIDE_PROTEIN_MAPPING (PEPTIDE_ID INTEGER, PROTEIN_ID INTEGER); + CREATE TABLE FEATURE (ID INTEGER PRIMARY KEY, RUN_ID INTEGER); + CREATE TABLE SCORE_PEPTIDE ( + CONTEXT TEXT, + RUN_ID INTEGER, + PEPTIDE_ID INTEGER, + SCORE REAL, + PVALUE REAL, + QVALUE REAL, + PEP REAL + ); + CREATE TABLE SCORE_PROTEIN ( + CONTEXT TEXT, + RUN_ID INTEGER, + PROTEIN_ID INTEGER, + SCORE REAL, + PVALUE REAL, + QVALUE REAL, + PEP REAL + ); + """ + ) + con.execute("INSERT INTO PEPTIDE VALUES (1)") + con.execute("INSERT INTO PROTEIN VALUES (10)") + con.execute("INSERT INTO PEPTIDE_PROTEIN_MAPPING VALUES (1, 10)") + con.executemany( + "INSERT INTO FEATURE VALUES (?, ?)", + [(100, 1), (101, 2)], + ) + + peptide_rows = [("global", None, 1, 5.0, 0.005, 0.0005, 0.0002)] + protein_rows = [("global", None, 10, 7.0, 0.007, 0.0007, 0.0003)] + if include_experiment_wide: + peptide_rows.extend( + [ + ("experiment-wide", 1, 1, 3.0, 0.03, 0.003, 0.001), + ("experiment-wide", 2, 1, 4.0, 0.04, 0.004, 0.002), + ] + ) + protein_rows.extend( + [ + ("experiment-wide", 1, 10, 6.0, 0.06, 0.006, 0.004), + ("experiment-wide", 2, 10, 8.0, 0.08, 0.008, 0.005), + ] + ) + + con.executemany( + "INSERT INTO SCORE_PEPTIDE VALUES (?, ?, ?, ?, ?, ?, ?)", + peptide_rows, + ) + con.executemany( + "INSERT INTO SCORE_PROTEIN VALUES (?, ?, ?, ?, ?, ?, ?)", + protein_rows, + ) + con.commit() + + +def _read_joined_scores(path, peptide_contexts, protein_contexts): + config = ExportIOConfig( + infile=str(path), + outfile=str(path.with_suffix(".parquet")), + subsample_ratio=1.0, + level="osw", + context="export", + export_format="parquet", + ) + writer = OSWWriter(config) + column_info = { + "score_ms1_exists": False, + "score_ms2_exists": False, + "score_ipf_exists": False, + "score_peptide_exists": True, + "score_protein_exists": True, + "score_peptide_contexts": peptide_contexts, + "score_protein_contexts": protein_contexts, + } + + con = duckdb.connect(":memory:") + load_sqlite_scanner(con) + try: + score_cols_select, score_table_joins, score_column_views = ( + writer._build_score_column_selection_and_joins(column_info) + ) + query = f""" + {score_column_views} + SELECT + FEATURE.RUN_ID, + {score_cols_select} + FROM sqlite_scan('{path}', 'FEATURE') AS FEATURE + CROSS JOIN sqlite_scan('{path}', 'PEPTIDE') AS PEPTIDE + INNER JOIN sqlite_scan('{path}', 'PEPTIDE_PROTEIN_MAPPING') AS PEPTIDE_PROTEIN_MAPPING + ON PEPTIDE.ID = PEPTIDE_PROTEIN_MAPPING.PEPTIDE_ID + {score_table_joins} + ORDER BY FEATURE.RUN_ID + """ + return con.execute(query).fetchdf() + finally: + con.close() + + +def test_export_score_views_keep_global_scores_when_run_id_is_null(tmp_path): + osw_path = tmp_path / "mixed_contexts.osw" + _create_score_test_osw(osw_path, include_experiment_wide=True) + + df = _read_joined_scores( + osw_path, + peptide_contexts=["experiment-wide", "global"], + protein_contexts=["experiment-wide", "global"], + ) + + assert df["SCORE_PEPTIDE_GLOBAL_Q_VALUE"].tolist() == [0.0005, 0.0005] + assert df["SCORE_PROTEIN_GLOBAL_Q_VALUE"].tolist() == [0.0007, 0.0007] + assert df["SCORE_PEPTIDE_EXPERIMENT_WIDE_Q_VALUE"].tolist() == [0.003, 0.004] + assert df["SCORE_PROTEIN_EXPERIMENT_WIDE_Q_VALUE"].tolist() == [0.006, 0.008] + + +def test_export_score_views_match_global_only_scores_when_run_id_is_null(tmp_path): + osw_path = tmp_path / "global_only_contexts.osw" + _create_score_test_osw(osw_path, include_experiment_wide=False) + + df = _read_joined_scores( + osw_path, + peptide_contexts=["global"], + protein_contexts=["global"], + ) + + assert df["SCORE_PEPTIDE_GLOBAL_Q_VALUE"].tolist() == [0.0005, 0.0005] + assert df["SCORE_PROTEIN_GLOBAL_Q_VALUE"].tolist() == [0.0007, 0.0007] diff --git a/tests/test_pyprophet_export.py b/tests/test_pyprophet_export.py index cbfff358..7b3ff6a9 100644 --- a/tests/test_pyprophet_export.py +++ b/tests/test_pyprophet_export.py @@ -101,6 +101,25 @@ def run_pyprophet_command(cmd, temp_folder): raise +def sort_parquet_export_frame(df): + """Sort exported parquet rows by stable ID columns for deterministic snapshots.""" + sort_cols = [ + col + for col in [ + "RUN_ID", + "PROTEIN_ID", + "PEPTIDE_ID", + "PRECURSOR_ID", + "FEATURE_ID", + "TRANSITION_ID", + ] + if col in df.columns + ] + return df.sort_values(sort_cols, kind="mergesort", na_position="last").reset_index( + drop=True + ) + + def validate_export_results( regtest, input_path, input_type, output_file="test_data.tsv" ): @@ -303,6 +322,7 @@ def test_parquet_export_scored_osw(test_data_osw, temp_folder, regtest): score_columns = [col for col in df.columns if col.startswith("SCORE_")] assert len(score_columns) > 0, "Exported parquet should contain SCORE_ columns" + df = sort_parquet_export_frame(df) print(f"Exported {len(df)} rows with {len(df.columns)} columns", file=regtest) print(f"Score columns found: {sorted(score_columns)}", file=regtest) print(df.head(10).sort_index(axis=1), file=regtest) @@ -344,6 +364,7 @@ def test_parquet_export_no_transition_data(test_data_osw, temp_folder, regtest): score_columns = [col for col in df.columns if col.startswith("SCORE_")] assert len(score_columns) > 0, "Exported parquet should contain SCORE_ columns" + df = sort_parquet_export_frame(df) print( f"Exported {len(df)} rows with {len(df.columns)} columns (no transition data)", file=regtest, From 185a55ad7b891eb964cb8a89ffd3d7b1f9c00ace Mon Sep 17 00:00:00 2001 From: singjc Date: Sun, 26 Apr 2026 21:15:42 -0400 Subject: [PATCH 2/3] Refactor test for parquet export to ensure precursor DataFrame is sorted before validation --- ...ophet_export.test_parquet_export_split_format.out | 12 ++++++------ tests/test_pyprophet_export.py | 2 ++ 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out index 7515c069..75dfe88a 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_parquet_export_split_format.out @@ -2,9 +2,9 @@ Precursor data: 3410 rows with 81 columns Transition data: 96259 rows with 23 columns Precursor score columns: ['SCORE_MS2_PEAK_GROUP_RANK', 'SCORE_MS2_PEP', 'SCORE_MS2_P_VALUE', 'SCORE_MS2_Q_VALUE', 'SCORE_MS2_SCORE', 'SCORE_PEPTIDE_GLOBAL_PEP', 'SCORE_PEPTIDE_GLOBAL_P_VALUE', 'SCORE_PEPTIDE_GLOBAL_Q_VALUE', 'SCORE_PEPTIDE_GLOBAL_SCORE', 'SCORE_PROTEIN_GLOBAL_PEP', 'SCORE_PROTEIN_GLOBAL_P_VALUE', 'SCORE_PROTEIN_GLOBAL_Q_VALUE', 'SCORE_PROTEIN_GLOBAL_SCORE'] Precursor data sample: - DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FILENAME GENE_DECOY GENE_ID GENE_NAME IM_leftWidth IM_rightWidth IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID 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AQUA4SWATH_HMLangeF NaN 5 1762.1100 -8670811102654834151 5 1.0000 0.4692 0.4692 -3.2559 NaN NaN NaN NaN NaN NaN NaN NaN GIGDWSDSK + DELTA_RT EXP_IM EXP_RT FEATURE_ID FEATURE_MS1_APEX_INTENSITY FEATURE_MS1_AREA_INTENSITY FEATURE_MS1_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS1_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS1_VAR_MASSDEV_SCORE FEATURE_MS1_VAR_XCORR_COELUTION FEATURE_MS1_VAR_XCORR_SHAPE FEATURE_MS2_APEX_INTENSITY FEATURE_MS2_AREA_INTENSITY FEATURE_MS2_VAR_BSERIES_SCORE FEATURE_MS2_VAR_DOTPROD_SCORE FEATURE_MS2_VAR_ELUTION_MODEL_FIT_SCORE FEATURE_MS2_VAR_INTENSITY_SCORE FEATURE_MS2_VAR_ISOTOPE_CORRELATION_SCORE FEATURE_MS2_VAR_ISOTOPE_OVERLAP_SCORE FEATURE_MS2_VAR_LIBRARY_CORR FEATURE_MS2_VAR_LIBRARY_DOTPROD FEATURE_MS2_VAR_LIBRARY_MANHATTAN FEATURE_MS2_VAR_LIBRARY_RMSD FEATURE_MS2_VAR_LIBRARY_ROOTMEANSQUARE FEATURE_MS2_VAR_LIBRARY_SANGLE FEATURE_MS2_VAR_LOG_SN_SCORE FEATURE_MS2_VAR_MANHATTAN_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE FEATURE_MS2_VAR_MASSDEV_SCORE_WEIGHTED FEATURE_MS2_VAR_NORM_RT_SCORE FEATURE_MS2_VAR_SONAR_LAG FEATURE_MS2_VAR_SONAR_LOG_DIFF FEATURE_MS2_VAR_SONAR_LOG_SN FEATURE_MS2_VAR_SONAR_LOG_TREND FEATURE_MS2_VAR_SONAR_RSQ FEATURE_MS2_VAR_SONAR_SHAPE FEATURE_MS2_VAR_XCORR_COELUTION FEATURE_MS2_VAR_XCORR_COELUTION_WEIGHTED FEATURE_MS2_VAR_XCORR_SHAPE FEATURE_MS2_VAR_XCORR_SHAPE_WEIGHTED FEATURE_MS2_VAR_YSERIES_SCORE FILENAME GENE_DECOY GENE_ID GENE_NAME IM_leftWidth IM_rightWidth IPF_PEPTIDE_ID LEFT_WIDTH MODIFIED_SEQUENCE NORM_RT PEPTIDE_DECOY PEPTIDE_ID PRECURSOR_CHARGE PRECURSOR_DECOY PRECURSOR_GROUP_LABEL PRECURSOR_ID PRECURSOR_LIBRARY_DRIFT_TIME PRECURSOR_LIBRARY_INTENSITY PRECURSOR_LIBRARY_RT PRECURSOR_MZ PRECURSOR_TRAML_ID PROTEIN_ACCESSION PROTEIN_DECOY PROTEIN_ID RIGHT_WIDTH RUN_ID SCORE_MS2_PEAK_GROUP_RANK SCORE_MS2_PEP SCORE_MS2_P_VALUE SCORE_MS2_Q_VALUE SCORE_MS2_SCORE SCORE_PEPTIDE_GLOBAL_PEP SCORE_PEPTIDE_GLOBAL_P_VALUE SCORE_PEPTIDE_GLOBAL_Q_VALUE SCORE_PEPTIDE_GLOBAL_SCORE SCORE_PROTEIN_GLOBAL_PEP SCORE_PROTEIN_GLOBAL_P_VALUE SCORE_PROTEIN_GLOBAL_Q_VALUE SCORE_PROTEIN_GLOBAL_SCORE UNMODIFIED_SEQUENCE +0 65.9712 NaN 2661.55 -4409520928686189639 117220.7482 854645.0 0.9835 0.1247 1.3707 0.0000 0.9907 30361.0 207283.0 9.0 0.7708 NaN 0.7811 0.9962 0.0000 0.9987 0.9978 0.0659 0.0239 0.0262 0.0725 4.7388 0.7451 0.3398 0.1793 0.0194 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9936 0.9958 11.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN NaN NaN 32 2640.5100 ADSTGTLVITDPTR(UniMod:267) 28.4379 0 33 2 0 NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... 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AQUA4SWATH_HMLangeA NaN 0 2811.2000 -8670811102654834151 4 1.0000 0.1994 0.2018 0.6777 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 ADSTGTLVITDPTR +4 112.9550 NaN 2708.53 8534214264242363560 5750.4716 73215.2 -0.3692 0.7498 7.1610 6.7500 0.4827 539.0 3838.0 3.0 0.8181 NaN 0.0145 0.7660 0.1334 0.8344 0.9736 0.2367 0.1055 0.1166 0.3772 0.6034 0.6468 2.5636 1.1471 0.0330 NaN NaN NaN NaN NaN NaN 3.4656 0.9347 0.6790 0.7379 5.0 napedro_L120420_010_SW.mzXML.gz NaN NaN NaN NaN NaN 32 2705.3701 ADSTGTLVITDPTR(UniMod:267) 29.8002 0 33 2 0 NA 0 NaN NaN 26.5 728.8795 AQUA4SWATH_HMLangeA_ADSTGTLVITDPTR(Label:13C(6... AQUA4SWATH_HMLangeA NaN 0 2736.0901 -8670811102654834151 3 1.0000 0.1994 0.2018 0.8151 0.0031 0.0029 0.0033 5.7301 0.3674 0.0625 0.0625 5.8401 ADSTGTLVITDPTR diff --git a/tests/test_pyprophet_export.py b/tests/test_pyprophet_export.py index 7b3ff6a9..ff63cc01 100644 --- a/tests/test_pyprophet_export.py +++ b/tests/test_pyprophet_export.py @@ -421,6 +421,8 @@ def test_parquet_export_split_format(test_data_osw, temp_folder, regtest): "Precursor parquet should contain SCORE_ columns" ) + precursor_df = sort_parquet_export_frame(precursor_df) + print( f"Precursor data: {len(precursor_df)} rows with {len(precursor_df.columns)} columns", file=regtest, From f7d51583887a42c4194a32df495bc8cda1fe993f Mon Sep 17 00:00:00 2001 From: singjc Date: Mon, 27 Apr 2026 00:25:01 -0400 Subject: [PATCH 3/3] Refactor floating-point normalization in regtests - Introduced _stabilize_regtest_float function to ensure deterministic float rendering across platforms. - Updated _normalize_regtest_frame to utilize the new stabilization function for better consistency in test outputs. - Adjusted _normalize_peakgroup_regtest_frame to call the generalized normalization function. - Improved handling of tiny floating-point values and ensured zero values are consistently represented. --- ...ophet_score.test_multi_split_parquet_0.out | 2 +- ...ophet_score.test_multi_split_parquet_1.out | 12 +- ...ophet_score.test_multi_split_parquet_2.out | 2 +- ...ophet_score.test_multi_split_parquet_3.out | 2 +- ...ophet_score.test_multi_split_parquet_6.out | 4 +- ...ophet_score.test_multi_split_parquet_7.out | 4 +- ...ophet_score.test_multi_split_parquet_8.out | 4 +- ...ophet_score.test_multi_split_parquet_9.out | 2 +- ...test_multi_split_parquet_apply_weights.out | 20 +-- .../test_pyprophet_score.test_osw_1.out | 8 +- .../test_pyprophet_score.test_osw_10.out | 28 ++-- .../test_pyprophet_score.test_osw_5.out | 6 +- .../test_pyprophet_score.test_osw_6.out | 2 +- .../test_pyprophet_score.test_osw_7.out | 2 +- .../test_pyprophet_score.test_osw_8.out | 62 +++---- .../test_pyprophet_score.test_osw_9.out | 12 +- ...est_pyprophet_score.test_osw_subsample.out | 4 +- ...score.test_osw_subsample_apply_weights.out | 20 +-- .../test_pyprophet_score.test_tsv_0.out | 144 ++++++++-------- .../test_pyprophet_score.test_tsv_1.out | 154 +++++++++--------- .../test_pyprophet_score.test_tsv_2.out | 144 ++++++++-------- .../test_pyprophet_score.test_tsv_3.out | 142 ++++++++-------- ...pyprophet_score.test_tsv_apply_weights.out | 144 ++++++++-------- tests/test_pyprophet_score.py | 47 +++++- 24 files changed, 500 insertions(+), 471 deletions(-) diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_0.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_0.out index bd196f7e..1b0a869c 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_0.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_0.out @@ -1,7 +1,7 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0031 0.0987 -1 -9059007664292712863 1.0000 0.3615 NaN +1 -9059007664292712863 1.0000 0.3614 NaN 2 -9009602369958523731 0.0064 0.0031 0.4405 3 -8990894093332793487 0.0064 0.0031 0.0461 4 -8915955323477460297 0.0064 0.0031 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_1.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_1.out index d293d281..bad9ff9a 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_1.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_1.out @@ -1,13 +1,13 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep -0 -9078977811506172301 0.0005 9.9580e-08 0.1119 -1 -9059007664292712863 1.0000 8.6993e-01 NaN -2 -9009602369958523731 0.0005 8.9400e-07 0.4155 -3 -8990894093332793487 0.0005 2.8350e-07 0.0409 -4 -8915955323477460297 0.0003 1.8930e-07 0.0181 +0 -9078977811506172301 0.0005 9.9580e-08 0.1118 +1 -9059007664292712863 1.0000 8.6990e-01 NaN +2 -9009602369958523731 0.0005 8.9390e-07 0.4155 +3 -8990894093332793487 0.0005 2.8340e-07 0.0409 +4 -8915955323477460297 0.0003 1.8920e-07 0.0181 .. ... ... ... ... 95 -4554654845515399609 0.0003 3.8680e-08 NaN -96 -4539808410625597778 0.0094 1.2626e-06 0.0352 +96 -4539808410625597778 0.0094 1.2620e-06 0.0352 97 -4495976808403190115 0.0002 3.8680e-08 0.0378 98 -4474179539802460946 0.0002 3.8680e-08 0.0157 99 -4409520928686189639 0.0002 3.8680e-08 0.1650 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_2.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_2.out index bd196f7e..1b0a869c 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_2.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_2.out @@ -1,7 +1,7 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0031 0.0987 -1 -9059007664292712863 1.0000 0.3615 NaN +1 -9059007664292712863 1.0000 0.3614 NaN 2 -9009602369958523731 0.0064 0.0031 0.4405 3 -8990894093332793487 0.0064 0.0031 0.0461 4 -8915955323477460297 0.0064 0.0031 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_3.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_3.out index bd196f7e..1b0a869c 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_3.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_3.out @@ -1,7 +1,7 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0031 0.0987 -1 -9059007664292712863 1.0000 0.3615 NaN +1 -9059007664292712863 1.0000 0.3614 NaN 2 -9009602369958523731 0.0064 0.0031 0.4405 3 -8990894093332793487 0.0064 0.0031 0.0461 4 -8915955323477460297 0.0064 0.0031 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_6.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_6.out index ffa3df09..534546ab 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_6.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_6.out @@ -1,13 +1,13 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0034 0.0996 -1 -9009602369958523731 0.0064 0.0034 0.4273 +1 -9009602369958523731 0.0064 0.0034 0.4272 2 -8990894093332793487 0.0064 0.0034 0.0464 3 -8915955323477460297 0.0064 0.0034 0.0089 4 -8858715981476206597 0.0064 0.0034 0.0089 .. ... ... ... ... 95 -4213710682827324837 0.0064 0.0034 0.0089 -96 -4209714083879967850 0.5256 0.0218 NaN +96 -4209714083879967850 0.5255 0.0218 NaN 97 -4195322252177179725 0.0064 0.0034 0.0227 98 -4146541955602089926 0.0064 0.0034 0.0464 99 -4109405113780929799 0.0064 0.0034 0.0050 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_7.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_7.out index ffa3df09..534546ab 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_7.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_7.out @@ -1,13 +1,13 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0034 0.0996 -1 -9009602369958523731 0.0064 0.0034 0.4273 +1 -9009602369958523731 0.0064 0.0034 0.4272 2 -8990894093332793487 0.0064 0.0034 0.0464 3 -8915955323477460297 0.0064 0.0034 0.0089 4 -8858715981476206597 0.0064 0.0034 0.0089 .. ... ... ... ... 95 -4213710682827324837 0.0064 0.0034 0.0089 -96 -4209714083879967850 0.5256 0.0218 NaN +96 -4209714083879967850 0.5255 0.0218 NaN 97 -4195322252177179725 0.0064 0.0034 0.0227 98 -4146541955602089926 0.0064 0.0034 0.0464 99 -4109405113780929799 0.0064 0.0034 0.0050 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_8.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_8.out index 726e560f..59ddf8d2 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_8.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_8.out @@ -1,7 +1,7 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0031 0.0987 -1 -9059007664292712863 1.0000 0.3615 NaN +1 -9059007664292712863 1.0000 0.3614 NaN 2 -9009602369958523731 0.0064 0.0031 0.4405 3 -8990894093332793487 0.0064 0.0031 0.0461 4 -8915955323477460297 0.0064 0.0031 0.0089 @@ -16,7 +16,7 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0031 0.0987 -1 -9059007664292712863 1.0000 0.3615 NaN +1 -9059007664292712863 1.0000 0.3614 NaN 2 -9009602369958523731 0.0064 0.0031 0.4405 3 -8990894093332793487 0.0064 0.0031 0.0461 4 -8915955323477460297 0.0064 0.0031 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_9.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_9.out index bd196f7e..1b0a869c 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_9.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_9.out @@ -1,7 +1,7 @@ 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0031 0.0987 -1 -9059007664292712863 1.0000 0.3615 NaN +1 -9059007664292712863 1.0000 0.3614 NaN 2 -9009602369958523731 0.0064 0.0031 0.4405 3 -8990894093332793487 0.0064 0.0031 0.0461 4 -8915955323477460297 0.0064 0.0031 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_apply_weights.out b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_apply_weights.out index 95a73386..af2ce282 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_apply_weights.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_multi_split_parquet_apply_weights.out @@ -1,16 +1,16 @@ 3410 96259 feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep -0 -9211032279639747263 1.5282e-01 -1 -9202066408251325127 6.6976e-02 -2 -9194114845888269381 1.5282e-01 -3 -9157656806856886367 1.5282e-01 -4 -9154199948799956056 1.5282e-01 +0 -9211032279639747263 1.5280e-01 +1 -9202066408251325127 6.6970e-02 +2 -9194114845888269381 1.5280e-01 +3 -9157656806856886367 1.5280e-01 +4 -9154199948799956056 1.5280e-01 .. ... ... ... ... -95 -7954403927701730016 1.5358e-05 -96 -7945183889919201418 1.5282e-01 -97 -7921043005244251597 5.9199e-02 -98 -7915076791408573751 1.5282e-01 -99 -7898872943061400987 1.1083e-02 +95 -7954403927701730016 1.5350e-05 +96 -7945183889919201418 1.5280e-01 +97 -7921043005244251597 5.9190e-02 +98 -7915076791408573751 1.5280e-01 +99 -7898872943061400987 1.1080e-02 [100 rows x 4 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_1.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_1.out index 1d1edfac..0a41d06b 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_1.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_1.out @@ -1,8 +1,8 @@ feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep -0 -9078977811506172301 0.0005 9.9580e-08 0.1119 -1 -9009602369958523731 0.0005 8.9400e-07 0.4155 -2 -8990894093332793487 0.0005 2.8350e-07 0.0409 -3 -8915955323477460297 0.0003 1.8930e-07 0.0181 +0 -9078977811506172301 0.0005 9.9580e-08 0.1118 +1 -9009602369958523731 0.0005 8.9390e-07 0.4155 +2 -8990894093332793487 0.0005 2.8340e-07 0.0409 +3 -8915955323477460297 0.0003 1.8920e-07 0.0181 4 -8858715981476206597 0.0002 3.8680e-08 0.0144 .. ... ... ... ... 95 -3220457216356394124 0.0002 4.4890e-08 0.0274 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_10.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_10.out index fd0361e2..008c1a6b 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_10.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_10.out @@ -1,17 +1,17 @@ level score weight -0 ms1 main_var_xcorr_shape 3.6907e+00 +0 ms1 main_var_xcorr_shape 3.6906e+00 1 ms1ms2 main_var_xcorr_shape 1.6380e+00 -2 ms1ms2 var_intensity_score 2.8489e+00 -3 ms1 var_isotope_correlation_score 2.8452e-02 -4 ms1ms2 var_isotope_correlation_score 9.0028e-01 -5 ms1 var_isotope_overlap_score -5.8129e-02 -6 ms1ms2 var_isotope_overlap_score -3.5869e-01 -7 ms1ms2 var_library_corr 9.1134e-01 -8 ms1 var_massdev_score 2.1145e-02 -9 ms1ms2 var_massdev_score -3.1249e-02 -10 ms1ms2 var_ms1_isotope_correlation_score 3.8243e-02 -11 ms1ms2 var_ms1_isotope_overlap_score 5.8031e-02 -12 ms1ms2 var_ms1_massdev_score -5.9398e-05 -13 ms1ms2 var_ms1_xcorr_coelution -9.5609e-02 +2 ms1ms2 var_intensity_score 2.8488e+00 +3 ms1 var_isotope_correlation_score 2.8450e-02 +4 ms1ms2 var_isotope_correlation_score 9.0020e-01 +5 ms1 var_isotope_overlap_score -5.8120e-02 +6 ms1ms2 var_isotope_overlap_score -3.5860e-01 +7 ms1ms2 var_library_corr 9.1130e-01 +8 ms1 var_massdev_score 2.1140e-02 +9 ms1ms2 var_massdev_score -3.1240e-02 +10 ms1ms2 var_ms1_isotope_correlation_score 3.8240e-02 +11 ms1ms2 var_ms1_isotope_overlap_score 5.8030e-02 +12 ms1ms2 var_ms1_massdev_score -5.9390e-05 +13 ms1ms2 var_ms1_xcorr_coelution -9.5600e-02 14 ms1ms2 var_norm_rt_score -3.7204e+01 -15 ms1 var_xcorr_coelution -5.1548e-02 +15 ms1 var_xcorr_coelution -5.1540e-02 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_5.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_5.out index ef9b8f89..6c2fb83c 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_5.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_5.out @@ -1,11 +1,11 @@ feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0176 0.0048 0.5738 -1 -9009602369958523731 0.0176 0.0048 0.1118 +1 -9009602369958523731 0.0176 0.0048 0.1117 2 -8990894093332793487 0.0176 0.0048 0.3435 -3 -8915955323477460297 0.0176 0.0048 0.1118 +3 -8915955323477460297 0.0176 0.0048 0.1117 4 -8858715981476206597 0.0176 0.0048 0.5738 .. ... ... ... ... -95 -3212703409469281429 0.0176 0.0048 0.1118 +95 -3212703409469281429 0.0176 0.0048 0.1117 96 -3196707605593292319 0.0176 0.0048 0.5738 97 -3129995828656718688 0.0176 0.0048 0.5738 98 -3096050638984928024 0.0176 0.0048 0.5738 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_6.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_6.out index 6e76f370..39d48b4f 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_6.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_6.out @@ -1,6 +1,6 @@ feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0034 0.0996 -1 -9009602369958523731 0.0064 0.0034 0.4273 +1 -9009602369958523731 0.0064 0.0034 0.4272 2 -8990894093332793487 0.0064 0.0034 0.0464 3 -8915955323477460297 0.0064 0.0034 0.0089 4 -8858715981476206597 0.0064 0.0034 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_7.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_7.out index 6e76f370..39d48b4f 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_7.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_7.out @@ -1,6 +1,6 @@ feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.0064 0.0034 0.0996 -1 -9009602369958523731 0.0064 0.0034 0.4273 +1 -9009602369958523731 0.0064 0.0034 0.4272 2 -8990894093332793487 0.0064 0.0034 0.0464 3 -8915955323477460297 0.0064 0.0034 0.0089 4 -8858715981476206597 0.0064 0.0034 0.0089 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_8.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_8.out index 0cd6337f..5666ea5b 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_8.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_8.out @@ -1,31 +1,31 @@ - level score weight -0 ms1 main_var_xcorr_shape 9.5599e-01 -1 ms2 main_var_xcorr_shape -2.5707e+00 -2 ms2 var_bseries_score 2.9010e-15 -3 ms2 var_dotprod_score 4.8268e+00 -4 ms2 var_intensity_score 1.8417e+00 -5 ms1 var_isotope_correlation_score 9.9777e-02 -6 ms2 var_isotope_correlation_score 3.4469e-01 -7 ms1 var_isotope_overlap_score -8.4481e-02 -8 ms2 var_isotope_overlap_score 1.5073e-01 -9 ms2 var_library_corr 5.6312e-01 -10 ms2 var_library_dotprod -7.0580e+00 -11 ms2 var_library_manhattan -2.2549e+00 -12 ms2 var_library_rmsd -6.9756e+00 -13 ms2 var_library_rootmeansquare -1.0792e+01 -14 ms2 var_library_sangle 6.1293e+00 -15 ms2 var_log_sn_score 4.2718e-01 -16 ms2 var_manhattan_score 7.6499e-01 -17 ms1 var_massdev_score -1.8875e-03 -18 ms2 var_massdev_score -1.7858e-02 -19 ms2 var_massdev_score_weighted -1.4218e-02 -20 ms2 var_norm_rt_score -6.1086e+01 -21 ms1 var_xcorr_coelution -4.6643e-02 -22 ms2 var_xcorr_coelution -6.4718e-02 -23 ms1 var_xcorr_coelution_combined 1.2248e+00 -24 ms1 var_xcorr_coelution_contrast -1.2179e+00 -25 ms2 var_xcorr_coelution_weighted 1.3923e-01 -26 ms1 var_xcorr_shape_combined -2.5555e+01 -27 ms1 var_xcorr_shape_contrast 2.9255e+01 -28 ms2 var_xcorr_shape_weighted 6.7453e-01 -29 ms2 var_yseries_score 0.0000e+00 + level score weight +0 ms1 main_var_xcorr_shape 0.9559 +1 ms2 main_var_xcorr_shape -2.5706 +2 ms2 var_bseries_score 0.0000 +3 ms2 var_dotprod_score 4.8268 +4 ms2 var_intensity_score 1.8416 +5 ms1 var_isotope_correlation_score 0.0998 +6 ms2 var_isotope_correlation_score 0.3446 +7 ms1 var_isotope_overlap_score -0.0845 +8 ms2 var_isotope_overlap_score 0.1507 +9 ms2 var_library_corr 0.5631 +10 ms2 var_library_dotprod -7.0580 +11 ms2 var_library_manhattan -2.2548 +12 ms2 var_library_rmsd -6.9756 +13 ms2 var_library_rootmeansquare -10.7921 +14 ms2 var_library_sangle 6.1293 +15 ms2 var_log_sn_score 0.4271 +16 ms2 var_manhattan_score 0.7649 +17 ms1 var_massdev_score -0.0019 +18 ms2 var_massdev_score -0.0179 +19 ms2 var_massdev_score_weighted -0.0142 +20 ms2 var_norm_rt_score -61.0859 +21 ms1 var_xcorr_coelution -0.0466 +22 ms2 var_xcorr_coelution -0.0647 +23 ms1 var_xcorr_coelution_combined 1.2248 +24 ms1 var_xcorr_coelution_contrast -1.2179 +25 ms2 var_xcorr_coelution_weighted 0.1392 +26 ms1 var_xcorr_shape_combined -25.5552 +27 ms1 var_xcorr_shape_contrast 29.2545 +28 ms2 var_xcorr_shape_weighted 0.6745 +29 ms2 var_yseries_score 0.0000 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_9.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_9.out index 17a83c0b..52165d16 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_9.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_9.out @@ -1,13 +1,13 @@ level score weight -0 ms1 main_var_xcorr_shape 3.6907 +0 ms1 main_var_xcorr_shape 3.6906 1 ms2 main_var_xcorr_shape 1.8019 2 ms2 var_intensity_score 2.9725 -3 ms1 var_isotope_correlation_score 0.0285 -4 ms2 var_isotope_correlation_score 0.7824 +3 ms1 var_isotope_correlation_score 0.0284 +4 ms2 var_isotope_correlation_score 0.7823 5 ms1 var_isotope_overlap_score -0.0581 -6 ms2 var_isotope_overlap_score -0.3541 -7 ms2 var_library_corr 0.9053 +6 ms2 var_isotope_overlap_score -0.3540 +7 ms2 var_library_corr 0.9052 8 ms1 var_massdev_score 0.0211 9 ms2 var_massdev_score -0.0305 -10 ms2 var_norm_rt_score -60.9504 +10 ms2 var_norm_rt_score -60.9503 11 ms1 var_xcorr_coelution -0.0515 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample.out index a1f4ff86..d7910c8c 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample.out @@ -1,11 +1,11 @@ feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep 0 -9078977811506172301 0.007 0.0036 0.0981 -1 -9009602369958523731 0.007 0.0036 0.4161 +1 -9009602369958523731 0.007 0.0036 0.4160 2 -8990894093332793487 0.007 0.0036 0.0621 3 -8915955323477460297 0.007 0.0036 0.0288 4 -8858715981476206597 0.007 0.0036 0.0046 .. ... ... ... ... -95 -3220457216356394124 0.007 0.0036 0.0101 +95 -3220457216356394124 0.007 0.0036 0.0100 96 -3212703409469281429 0.007 0.0036 0.0046 97 -3196707605593292319 0.007 0.0036 0.0674 98 -3129995828656718688 0.007 0.0036 0.0621 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample_apply_weights.out b/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample_apply_weights.out index b7da8a5c..11b6e4af 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample_apply_weights.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_osw_subsample_apply_weights.out @@ -1,14 +1,14 @@ feature_id ms1_precursor_pep ms2_peakgroup_pep ms2_precursor_pep -0 -9211032279639747263 1.5282e-01 -1 -9202066408251325127 6.6976e-02 -2 -9194114845888269381 1.5282e-01 -3 -9157656806856886367 1.5282e-01 -4 -9154199948799956056 1.5282e-01 +0 -9211032279639747263 1.5280e-01 +1 -9202066408251325127 6.6970e-02 +2 -9194114845888269381 1.5280e-01 +3 -9157656806856886367 1.5280e-01 +4 -9154199948799956056 1.5280e-01 .. ... ... ... ... -95 -7954403927701730016 1.5358e-05 -96 -7945183889919201418 1.5282e-01 -97 -7921043005244251597 5.9199e-02 -98 -7915076791408573751 1.5282e-01 -99 -7898872943061400987 1.1083e-02 +95 -7954403927701730016 1.5350e-05 +96 -7945183889919201418 1.5280e-01 +97 -7921043005244251597 5.9190e-02 +98 -7915076791408573751 1.5280e-01 +99 -7898872943061400987 1.1080e-02 [100 rows x 4 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_0.out b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_0.out index bc51dc69..3dacaba9 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_0.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_0.out @@ -1,92 +1,92 @@ cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 3.0866 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.00 0.9212 25.5215 332.9339 -1 1.0884 0.0086 -3.4139 0.0000 3.1737 0.1240 0.3590 0.1240 0.01 1.0000 22.4139 364.8263 -2 0.6049 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.02 1.0000 19.7692 367.1816 -3 -0.6061 0.0507 -1.2151 0.0000 19.3725 0.7571 1.0000 0.7571 0.05 1.0000 6.2151 362.6275 -4 -2.4409 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.10 1.0000 0.1984 361.6107 +0 3.0866 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.00 0.9212 25.5214 332.9338 +1 1.0883 0.0086 -3.4139 0.0000 3.1736 0.1240 0.3589 0.1240 0.01 1.0000 22.4139 364.8263 +2 0.6048 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.02 1.0000 19.7692 367.1816 +3 -0.6061 0.0507 -1.2150 0.0000 19.3725 0.7571 1.0000 0.7571 0.05 1.0000 6.2150 362.6274 +4 -2.4408 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.10 1.0000 0.1983 361.6107 5 NaN NaN NaN NaN NaN NaN NaN NaN 0.20 NaN NaN NaN 6 NaN NaN NaN NaN NaN NaN NaN NaN 0.30 NaN NaN NaN 7 NaN NaN NaN NaN NaN NaN NaN NaN 0.40 NaN NaN NaN 8 NaN NaN NaN NaN NaN NaN NaN NaN 0.50 NaN NaN NaN cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 -2.9318 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -1 -2.7158 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -2 -2.4998 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -3 -2.2838 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -4 -2.0678 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -5 -1.8518 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -6 -1.6358 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -7 -1.4198 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -8 -1.2038 0.0611 -0.0497 0.0000 23.5380 0.9199 1.0000 0.9199 0.0611 1.0000 2.0497 361.4620 -9 -0.9878 0.0587 -0.0414 0.0000 22.5462 0.8811 1.0000 0.8811 0.0587 1.0000 3.0414 361.4538 -10 -0.7718 0.0575 0.4296 0.1074 22.0172 0.8605 1.0000 0.8605 0.0575 1.0000 3.5704 360.9828 -11 -0.5558 0.0507 -1.2151 0.0000 19.3725 0.7571 1.0000 0.7571 0.0507 1.0000 6.2151 362.6275 -12 -0.3398 0.0448 0.3386 0.0376 16.9262 0.6615 1.0000 0.6615 0.0448 1.0000 8.6614 361.0738 -13 -0.1238 0.0352 -1.3640 0.0000 13.2236 0.5168 1.0000 0.5168 0.0352 1.0000 12.3640 362.7764 -14 0.0923 0.0331 -0.2236 0.0000 12.3640 0.4832 1.0000 0.4832 0.0331 1.0000 13.2236 361.6360 -15 0.3083 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.0156 1.0000 19.7692 367.1816 -16 0.5243 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.0156 1.0000 19.7692 367.1816 -17 0.7403 0.0135 -5.5626 0.0000 5.0250 0.1964 0.7397 0.1964 0.0135 1.0000 20.5626 366.9750 -18 0.9563 0.0114 -4.3561 0.0000 4.2315 0.1654 0.5455 0.1654 0.0114 1.0000 21.3561 365.7685 -19 1.1723 0.0079 -2.6784 0.0000 2.9092 0.1137 0.3211 0.1137 0.0079 1.0000 22.6784 364.0908 -20 1.3883 0.0054 -1.6041 0.0000 1.9835 0.0775 0.2089 0.0775 0.0054 1.0000 23.6041 363.0165 -21 1.6043 0.0053 1.3298 0.0532 1.9174 0.0749 0.2019 0.0749 0.0053 0.9963 23.6702 360.0826 -22 1.8203 0.0033 5.6025 0.1868 1.1901 0.0465 0.1281 0.0465 0.0033 0.9845 24.3975 355.8099 -23 2.0363 0.0019 7.0736 0.2210 0.6612 0.0258 0.0547 0.0258 0.0019 0.9804 24.9264 354.3388 -24 2.2523 0.0017 9.0075 0.2649 0.5951 0.0233 0.0433 0.0233 0.0017 0.9751 24.9925 352.4049 -25 2.4683 0.0013 10.8752 0.3021 0.4628 0.0181 0.0227 0.0181 0.0013 0.9699 25.1248 350.5372 -26 2.6843 0.0008 15.6769 0.3824 0.2645 0.0103 0.0049 0.0103 0.0008 0.9566 25.3231 345.7355 -27 2.9003 0.0004 16.5446 0.3939 0.1322 0.0052 0.0011 0.0052 0.0004 0.9542 25.4554 344.8678 -28 3.1163 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -29 3.3323 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -30 3.5483 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -31 3.7643 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -32 3.9803 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -33 4.1964 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -34 4.4124 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -35 4.6284 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -36 4.8444 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -37 5.0604 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -38 5.2764 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -39 5.4924 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -40 5.7084 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -41 5.9244 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -42 6.1404 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -43 6.3564 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -44 6.5724 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -45 6.7884 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -46 7.0044 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -47 7.2204 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -48 7.4364 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -49 7.6524 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -50 7.8684 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 +0 -2.9318 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +1 -2.7158 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +2 -2.4998 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +3 -2.2838 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +4 -2.0677 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +5 -1.8517 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +6 -1.6357 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +7 -1.4197 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +8 -1.2037 0.0611 -0.0496 0.0000 23.5379 0.9198 1.0000 0.9198 0.0611 1.0000 2.0496 361.4620 +9 -0.9877 0.0587 -0.0414 0.0000 22.5461 0.8811 1.0000 0.8811 0.0587 1.0000 3.0414 361.4538 +10 -0.7717 0.0575 0.4296 0.1074 22.0172 0.8604 1.0000 0.8604 0.0575 1.0000 3.5703 360.9827 +11 -0.5557 0.0507 -1.2150 0.0000 19.3725 0.7571 1.0000 0.7571 0.0507 1.0000 6.2150 362.6274 +12 -0.3397 0.0448 0.3385 0.0376 16.9261 0.6614 1.0000 0.6614 0.0448 1.0000 8.6614 361.0738 +13 -0.1237 0.0352 -1.3640 0.0000 13.2235 0.5167 1.0000 0.5167 0.0352 1.0000 12.3640 362.7764 +14 0.0922 0.0331 -0.2235 0.0000 12.3640 0.4832 1.0000 0.4832 0.0331 1.0000 13.2235 361.6359 +15 0.3082 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.0156 1.0000 19.7692 367.1816 +16 0.5242 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.0156 1.0000 19.7692 367.1816 +17 0.7402 0.0135 -5.5626 0.0000 5.0249 0.1963 0.7396 0.1963 0.0135 1.0000 20.5626 366.9750 +18 0.9562 0.0114 -4.3560 0.0000 4.2315 0.1653 0.5454 0.1653 0.0114 1.0000 21.3560 365.7684 +19 1.1722 0.0079 -2.6784 0.0000 2.9091 0.1136 0.3210 0.1136 0.0079 1.0000 22.6784 364.0908 +20 1.3882 0.0054 -1.6040 0.0000 1.9835 0.0775 0.2088 0.0775 0.0054 1.0000 23.6040 363.0164 +21 1.6042 0.0053 1.3298 0.0532 1.9174 0.0749 0.2018 0.0749 0.0053 0.9963 23.6701 360.0825 +22 1.8202 0.0033 5.6025 0.1867 1.1901 0.0465 0.1281 0.0465 0.0033 0.9844 24.3974 355.8098 +23 2.0363 0.0019 7.0735 0.2210 0.6611 0.0258 0.0547 0.0258 0.0019 0.9804 24.9264 354.3388 +24 2.2523 0.0017 9.0074 0.2649 0.5950 0.0232 0.0433 0.0232 0.0017 0.9750 24.9925 352.4049 +25 2.4683 0.0013 10.8752 0.3020 0.4628 0.0181 0.0226 0.0181 0.0013 0.9699 25.1247 350.5371 +26 2.6843 0.0008 15.6768 0.3823 0.2644 0.0103 0.0049 0.0103 0.0008 0.9566 25.3231 345.7355 +27 2.9003 0.0004 16.5446 0.3939 0.1322 0.0052 0.0011 0.0052 0.0004 0.9542 25.4553 344.8677 +28 3.1163 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +29 3.3323 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +30 3.5483 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +31 3.7643 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +32 3.9803 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +33 4.1963 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +34 4.4123 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +35 4.6283 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +36 4.8443 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +37 5.0603 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +38 5.2763 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +39 5.4923 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +40 5.7083 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +41 5.9243 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +42 6.1404 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +43 6.3564 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +44 6.5724 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +45 6.7884 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +46 7.0044 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +47 7.2204 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +48 7.4364 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +49 7.6524 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +50 7.8684 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 d_score decoy group_id main_var_xx_swath_prelim_score p_value peak_group_rank pep q_value r_score run_id var_bseries_score var_elution_model_fit_score var_intensity_score var_isotope_correlation_score var_isotope_overlap_score var_library_corr var_library_rmsd var_log_sn_score var_massdev_score var_massdev_score_weighted var_norm_rt_score var_xcorr_coelution var_xcorr_coelution_weighted var_xcorr_shape var_xcorr_shape_weighted var_yseries_score -0 5.1547 0 459_run0 5.2789 0.0026 1 0.0005 0.0002 6.0024 0 5 0.9931 0.9305 0.9987 0.0000 0.9124 0.0399 5.0166 8.8392 3.8845 0.0023 0.0000 0.0000 0.9604 0.9710 6 -1 -1.3725 0 459_run0 -0.1397 0.9354 2 1.0000 0.0620 0.5231 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7888 27.0803 21.2037 0.0107 1.3967 0.8592 0.7892 0.7164 0 -2 -4.3197 0 459_run0 -0.7750 0.9922 7 1.0000 0.0656 -1.9510 0 0 0.6667 0.0004 0.6579 0.0000 0.3765 0.1117 0.5299 8.7979 8.3272 0.0601 2.3868 1.9700 0.1190 0.0150 0 -3 -2.4375 0 459_run0 -1.0545 0.9922 4 1.0000 0.0656 -0.3709 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5683 15.3263 17.4562 0.0200 4.3932 2.7893 0.3292 0.3308 0 -4 -1.6028 0 459_run0 -1.2462 0.9354 3 1.0000 0.0620 0.3297 0 0 -1.0000 0.0004 0.5638 0.0455 0.4459 0.1497 0.5420 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 +0 5.1546 0 459_run0 5.2789 0.0026 1 0.0005 0.0002 6.0024 0 5 0.9930 0.9304 0.9987 0.0000 0.9124 0.0399 5.0165 8.8391 3.8845 0.0023 0.0000 0.0000 0.9603 0.9709 6 +1 -1.3724 0 459_run0 -0.1397 0.9354 2 1.0000 0.0620 0.5231 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7887 27.0802 21.2036 0.0107 1.3966 0.8591 0.7891 0.7163 0 +2 -4.3197 0 459_run0 -0.7750 0.9922 7 1.0000 0.0656 -1.9510 0 0 0.6666 0.0004 0.6579 0.0000 0.3764 0.1117 0.5298 8.7978 8.3272 0.0601 2.3867 1.9700 0.1190 0.0150 0 +3 -2.4374 0 459_run0 -1.0545 0.9922 4 1.0000 0.0656 -0.3709 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5682 15.3263 17.4562 0.0200 4.3932 2.7893 0.3291 0.3308 0 +4 -1.6028 0 459_run0 -1.2461 0.9354 3 1.0000 0.0620 0.3297 0 0 -1.0000 0.0004 0.5638 0.0454 0.4459 0.1497 0.5419 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 .. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 -3.0650 0 168_run0 -1.0780 0.9922 4 1.0000 0.0656 -0.8978 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6926 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5829 0.1919 0.1538 0 -96 -3.5587 0 168_run0 -1.0963 0.9922 7 1.0000 0.0656 -1.3122 0 0 1.0000 0.0012 0.8673 0.0000 -0.6748 0.2056 0.0000 10.1516 12.0983 0.0327 2.2331 1.6284 0.3333 0.1858 0 -97 -2.7735 0 168_run0 -1.4446 0.9922 2 1.0000 0.0656 -0.6530 0 0 0.9411 0.0012 0.0797 0.0000 -0.4017 0.1385 0.0000 14.8865 13.4708 0.0586 2.0539 0.9411 0.7334 0.6821 0 -98 -3.0728 0 168_run0 -1.4526 0.9922 5 1.0000 0.0656 -0.9043 0 1 0.1498 0.0164 0.9644 0.0000 -0.7028 0.3422 0.2301 1.3878 0.8742 0.0664 7.7597 5.5046 0.3111 0.1785 0 -99 -2.8249 0 168_run0 -1.4706 0.9922 3 1.0000 0.0656 -0.6962 0 1 0.1509 0.0053 0.6996 0.0000 0.0856 0.2511 0.0000 10.4594 9.8099 0.0235 4.5054 2.9492 0.3262 0.2549 0 +95 -3.0650 0 168_run0 -1.0780 0.9922 4 1.0000 0.0656 -0.8977 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6925 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5828 0.1919 0.1538 0 +96 -3.5587 0 168_run0 -1.0962 0.9922 7 1.0000 0.0656 -1.3121 0 0 0.9999 0.0012 0.8672 0.0000 -0.6748 0.2055 0.0000 10.1515 12.0982 0.0327 2.2330 1.6284 0.3333 0.1857 0 +97 -2.7734 0 168_run0 -1.4445 0.9922 2 1.0000 0.0656 -0.6530 0 0 0.9411 0.0012 0.0797 0.0000 -0.4016 0.1384 0.0000 14.8864 13.4707 0.0586 2.0539 0.9410 0.7334 0.6820 0 +98 -3.0728 0 168_run0 -1.4525 0.9922 5 1.0000 0.0656 -0.9043 0 1 0.1498 0.0164 0.9643 0.0000 -0.7027 0.3421 0.2301 1.3877 0.8742 0.0664 7.7597 5.5046 0.3111 0.1784 0 +99 -2.8249 0 168_run0 -1.4706 0.9922 3 1.0000 0.0656 -0.6962 0 1 0.1509 0.0053 0.6995 0.0000 0.0856 0.2510 0.0000 10.4594 9.8098 0.0235 4.5054 2.9491 0.3262 0.2549 0 [100 rows x 26 columns] level score weight 0 ms2 main_var_xx_swath_prelim_score 0.1554 -1 ms2 var_bseries_score -0.1381 -2 ms2 var_elution_model_fit_score -2.3916 +1 ms2 var_bseries_score -0.1380 +2 ms2 var_elution_model_fit_score -2.3915 3 ms2 var_intensity_score 0.8477 4 ms2 var_isotope_correlation_score 2.8853 -5 ms2 var_isotope_overlap_score -1.3842 +5 ms2 var_isotope_overlap_score -1.3841 6 ms2 var_library_corr -0.7260 -7 ms2 var_library_rmsd -13.8757 -8 ms2 var_log_sn_score -0.1271 +7 ms2 var_library_rmsd -13.8756 +8 ms2 var_log_sn_score -0.1270 9 ms2 var_massdev_score 0.0054 10 ms2 var_massdev_score_weighted -0.0283 -11 ms2 var_norm_rt_score -11.5622 +11 ms2 var_norm_rt_score -11.5621 12 ms2 var_xcorr_coelution 0.1361 13 ms2 var_xcorr_coelution_weighted -0.0913 14 ms2 var_xcorr_shape 3.9496 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_1.out b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_1.out index d5448bf2..aff9bed2 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_1.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_1.out @@ -1,94 +1,94 @@ - cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 7.2603 2.3214e-12 360.9667 0.9376 4.6427e-12 1.9318e-13 7.5526e-09 1.9318e-13 0.00 0.0055 24.0333 2.0000 -1 0.9932 1.0469e-02 -1.1808 0.0000 3.8525e+00 1.6030e-01 6.4070e-01 1.6030e-01 0.01 1.0000 20.1808 364.1475 -2 0.4446 2.1154e-02 -2.1428 0.0000 7.8905e+00 3.2832e-01 1.0000e+00 3.2832e-01 0.02 1.0000 16.1428 365.1095 -3 -0.9442 5.1924e-02 -0.1463 0.0000 1.9887e+01 8.2748e-01 1.0000e+00 8.2748e-01 0.05 1.0000 4.1463 363.1130 -4 -2.3458 6.1512e-02 -0.2281 0.0000 2.3805e+01 9.9051e-01 1.0000e+00 9.9051e-01 0.10 1.0000 0.2281 363.1948 -5 NaN NaN NaN NaN NaN NaN NaN NaN 0.20 NaN NaN NaN -6 NaN NaN NaN NaN NaN NaN NaN NaN 0.30 NaN NaN NaN -7 NaN NaN NaN NaN NaN NaN NaN NaN 0.40 NaN NaN NaN -8 NaN NaN NaN NaN NaN NaN NaN NaN 0.50 NaN NaN NaN + cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp +0 7.2602 2.3210e-12 360.9666 0.9375 4.6420e-12 0.0000 7.5520e-09 0.0000 0.00 0.0055 24.0333 1.9999 +1 0.9932 1.0460e-02 -1.1807 0.0000 3.8525e+00 0.1602 6.4070e-01 0.1602 0.01 1.0000 20.1807 364.1474 +2 0.4445 2.1150e-02 -2.1427 0.0000 7.8905e+00 0.3283 1.0000e+00 0.3283 0.02 1.0000 16.1427 365.1094 +3 -0.9442 5.1920e-02 -0.1463 0.0000 1.9887e+01 0.8274 1.0000e+00 0.8274 0.05 1.0000 4.1463 363.1130 +4 -2.3458 6.1510e-02 -0.2281 0.0000 2.3805e+01 0.9905 1.0000e+00 0.9905 0.10 1.0000 0.2281 363.1948 +5 NaN NaN NaN NaN NaN NaN NaN NaN 0.20 NaN NaN NaN +6 NaN NaN NaN NaN NaN NaN NaN NaN 0.30 NaN NaN NaN +7 NaN NaN NaN NaN NaN NaN NaN NaN 0.40 NaN NaN NaN +8 NaN NaN NaN NaN NaN NaN NaN NaN 0.50 NaN NaN NaN cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 -2.8288 6.1512e-02 -0.2281 0.0000 2.3805e+01 9.9051e-01 1.0000e+00 9.9051e-01 6.1512e-02 1.0000 0.2281 363.1948 -1 -2.6163 6.1512e-02 -0.2281 0.0000 2.3805e+01 9.9051e-01 1.0000e+00 9.9051e-01 6.1512e-02 1.0000 0.2281 363.1948 -2 -2.4038 6.1512e-02 -0.2281 0.0000 2.3805e+01 9.9051e-01 1.0000e+00 9.9051e-01 6.1512e-02 1.0000 0.2281 363.1948 -3 -2.1913 6.1512e-02 -0.2281 0.0000 2.3805e+01 9.9051e-01 1.0000e+00 9.9051e-01 6.1512e-02 1.0000 0.2281 363.1948 -4 -1.9788 6.1512e-02 -0.2281 0.0000 2.3805e+01 9.9051e-01 1.0000e+00 9.9051e-01 6.1512e-02 1.0000 0.2281 363.1948 -5 -1.7662 5.7662e-02 -0.7759 0.0000 2.2257e+01 9.2611e-01 1.0000e+00 9.2611e-01 5.7662e-02 1.0000 1.7759 363.7426 -6 -1.5537 5.7662e-02 -0.7759 0.0000 2.2257e+01 9.2611e-01 1.0000e+00 9.2611e-01 5.7662e-02 1.0000 1.7759 363.7426 -7 -1.3412 5.7662e-02 -0.7759 0.0000 2.2257e+01 9.2611e-01 1.0000e+00 9.2611e-01 5.7662e-02 1.0000 1.7759 363.7426 -8 -1.1287 5.5410e-02 -0.7005 0.0000 2.1333e+01 8.8764e-01 1.0000e+00 8.8764e-01 5.5410e-02 1.0000 2.7005 363.6672 -9 -0.9162 5.1924e-02 -0.1463 0.0000 1.9887e+01 8.2748e-01 1.0000e+00 8.2748e-01 5.1924e-02 1.0000 4.1463 363.1130 -10 -0.7036 4.7798e-02 -0.7743 0.0000 1.8259e+01 7.5974e-01 1.0000e+00 7.5974e-01 4.7798e-02 1.0000 5.7743 363.7410 -11 -0.4911 4.1650e-02 -2.1648 0.0000 1.5869e+01 6.6027e-01 1.0000e+00 6.6027e-01 4.1650e-02 1.0000 8.1648 365.1314 -12 -0.2786 4.1017e-02 0.4710 0.0523 1.5504e+01 6.4512e-01 1.0000e+00 6.4512e-01 4.1017e-02 1.0000 8.5290 362.4957 -13 -0.0661 3.4406e-02 0.8688 0.0724 1.2902e+01 5.3684e-01 1.0000e+00 5.3684e-01 3.4406e-02 1.0000 11.1312 362.0979 -14 0.1464 2.7190e-02 -0.8643 0.0000 1.0169e+01 4.2312e-01 1.0000e+00 4.2312e-01 2.7190e-02 1.0000 13.8643 363.8310 -15 0.3590 2.1154e-02 -2.1428 0.0000 7.8905e+00 3.2832e-01 1.0000e+00 3.2832e-01 2.1154e-02 1.0000 16.1428 365.1095 -16 0.5715 1.8472e-02 -2.1616 0.0000 6.8717e+00 2.8593e-01 1.0000e+00 2.8593e-01 1.8472e-02 1.0000 17.1616 365.1283 -17 0.7840 1.3393e-02 -3.0646 0.0000 4.9687e+00 2.0674e-01 8.2627e-01 2.0674e-01 1.3393e-02 1.0000 19.0646 366.0313 -18 0.9965 1.0469e-02 -0.1911 0.0000 3.8422e+00 1.5987e-01 6.3894e-01 1.5987e-01 1.0469e-02 1.0000 20.1911 363.1578 -19 1.2090 5.4738e-03 -1.0299 0.0000 2.0034e+00 8.3359e-02 3.1806e-01 8.3359e-02 5.4738e-03 1.0000 22.0299 363.9966 -20 1.4216 4.8798e-03 -0.2522 0.0000 1.7811e+00 7.4111e-02 2.8019e-01 7.4111e-02 4.8798e-03 1.0000 22.2522 363.2189 -21 1.6341 3.3101e-03 1.1683 0.0487 1.2016e+00 4.9996e-02 1.8487e-01 4.9996e-02 3.3101e-03 0.9968 22.8317 361.7984 -22 1.8466 2.0696e-03 6.7055 0.2235 7.3886e-01 3.0743e-02 1.1260e-01 3.0743e-02 2.0696e-03 0.9815 23.2945 356.2611 -23 2.0591 1.2942e-03 8.4261 0.2633 4.5945e-01 1.9117e-02 6.9529e-02 1.9117e-02 1.2942e-03 0.9768 23.5739 354.5405 -24 2.2716 8.2920e-04 10.2594 0.3017 2.9271e-01 1.2179e-02 4.3333e-02 1.2179e-02 8.2920e-04 0.9717 23.7406 352.7073 -25 2.4841 4.3067e-04 15.1166 0.3876 1.4987e-01 6.2361e-03 2.0743e-02 6.2361e-03 4.3067e-04 0.9584 23.8834 347.8501 -26 2.6967 2.5332e-04 17.0543 0.4160 8.7649e-02 3.6470e-03 1.1307e-02 3.6470e-03 2.5332e-04 0.9530 23.9457 345.9124 -27 2.9092 1.2364e-04 23.0087 0.4895 4.2038e-02 1.7491e-03 4.9269e-03 1.7491e-03 1.2364e-04 0.9366 23.9913 339.9580 -28 3.1217 6.8274e-05 30.9894 0.5634 2.2667e-02 9.4315e-04 2.4682e-03 9.4315e-04 6.8274e-05 0.9146 24.0106 331.9773 -29 3.3342 2.9535e-05 36.9763 0.6062 9.6284e-03 4.0063e-04 9.5402e-04 4.0063e-04 2.9535e-05 0.8981 24.0237 325.9904 -30 3.5467 1.4724e-05 42.9714 0.6414 4.7117e-03 1.9605e-04 4.3330e-04 1.9605e-04 1.4724e-05 0.8816 24.0286 319.9953 -31 3.7593 7.2480e-06 54.9689 0.6958 2.2324e-03 9.2887e-05 1.9065e-04 9.2887e-05 7.2480e-06 0.8486 24.0311 307.9978 -32 3.9718 2.7076e-06 63.9675 0.7269 8.0957e-04 3.3685e-05 6.2623e-05 3.3685e-05 2.7076e-06 0.8238 24.0325 298.9992 -33 4.1843 1.2012e-06 74.9670 0.7572 3.4595e-04 1.4394e-05 2.4351e-05 1.4394e-05 1.2012e-06 0.7935 24.0330 287.9997 -34 4.3968 5.0882e-07 88.9668 0.7873 1.3942e-04 5.8010e-06 8.6323e-06 5.8010e-06 5.0882e-07 0.7549 24.0332 273.9999 -35 4.6093 1.8281e-07 103.9667 0.8122 4.7347e-05 1.9700e-06 2.4108e-06 1.9700e-06 1.8281e-07 0.7136 24.0333 259.0000 -36 4.8219 6.8916e-08 120.9667 0.8343 1.6678e-05 6.9394e-07 6.8750e-07 6.9394e-07 6.8916e-08 0.6667 24.0333 242.0000 -37 5.0344 2.5977e-08 141.9667 0.8552 5.7408e-06 2.3887e-07 1.9504e-07 2.3887e-07 2.5977e-08 0.6089 24.0333 221.0000 -38 5.2469 9.7491e-09 175.9667 0.8798 1.8231e-06 7.5856e-08 5.4245e-08 7.5856e-08 9.7491e-09 0.5152 24.0333 187.0000 -39 5.4594 3.6786e-09 204.9667 0.8951 5.8121e-07 2.4184e-08 1.6964e-08 2.4184e-08 3.6786e-09 0.4353 24.0333 158.0000 -40 5.6719 1.4372e-09 246.9667 0.9113 1.6672e-07 6.9370e-09 7.5526e-09 6.9370e-09 1.4372e-09 0.3196 24.0333 116.0000 -41 5.8845 5.1396e-10 270.9667 0.9185 4.7284e-08 1.9674e-09 7.5526e-09 1.9674e-09 5.1396e-10 0.2535 24.0333 92.0000 -42 6.0970 2.1540e-10 301.9667 0.9263 1.3139e-08 5.4672e-10 7.5526e-09 5.4672e-10 2.1086e-10 0.1681 24.0333 61.0000 -43 6.3095 1.0090e-10 329.9667 0.9321 3.3296e-09 1.3854e-10 7.5526e-09 1.3854e-10 1.0090e-10 0.0909 24.0333 33.0000 -44 6.5220 4.5677e-11 341.9667 0.9343 9.5922e-10 3.9912e-11 7.5526e-09 3.9912e-11 4.5677e-11 0.0579 24.0333 21.0000 -45 6.7345 1.5795e-11 350.9667 0.9359 1.8954e-10 7.8864e-12 7.5526e-09 7.8864e-12 1.5795e-11 0.0331 24.0333 12.0000 -46 6.9471 5.4440e-12 355.9667 0.9368 3.8108e-11 1.5856e-12 7.5526e-09 1.5856e-12 5.4440e-12 0.0193 24.0333 7.0000 -47 7.1596 2.7690e-12 358.9667 0.9372 1.1076e-11 4.6085e-13 7.5526e-09 4.6085e-13 2.7690e-12 0.0110 24.0333 4.0000 -48 7.3721 3.1112e-12 361.9667 0.9377 3.1112e-12 1.2945e-13 7.5526e-09 1.2945e-13 2.3214e-12 0.0028 24.0333 1.0000 -49 7.5846 3.1112e-12 361.9667 0.9377 3.1112e-12 1.2945e-13 7.5526e-09 1.2945e-13 2.3214e-12 0.0028 24.0333 1.0000 -50 7.7971 3.1112e-12 361.9667 0.9377 3.1112e-12 1.2945e-13 7.5526e-09 1.2945e-13 2.3214e-12 0.0028 24.0333 1.0000 +0 -2.8288 6.1510e-02 -0.2281 0.0000 2.3805e+01 9.9050e-01 1.0000e+00 9.9050e-01 6.1510e-02 1.0000 0.2281 363.1948 +1 -2.6163 6.1510e-02 -0.2281 0.0000 2.3805e+01 9.9050e-01 1.0000e+00 9.9050e-01 6.1510e-02 1.0000 0.2281 363.1948 +2 -2.4037 6.1510e-02 -0.2281 0.0000 2.3805e+01 9.9050e-01 1.0000e+00 9.9050e-01 6.1510e-02 1.0000 0.2281 363.1948 +3 -2.1912 6.1510e-02 -0.2281 0.0000 2.3805e+01 9.9050e-01 1.0000e+00 9.9050e-01 6.1510e-02 1.0000 0.2281 363.1948 +4 -1.9787 6.1510e-02 -0.2281 0.0000 2.3805e+01 9.9050e-01 1.0000e+00 9.9050e-01 6.1510e-02 1.0000 0.2281 363.1948 +5 -1.7662 5.7660e-02 -0.7759 0.0000 2.2257e+01 9.2610e-01 1.0000e+00 9.2610e-01 5.7660e-02 1.0000 1.7759 363.7426 +6 -1.5537 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307.9977 +32 3.9717 2.7070e-06 63.9675 0.7269 8.0950e-04 3.3680e-05 6.2620e-05 3.3680e-05 2.7070e-06 0.8237 24.0324 298.9991 +33 4.1843 1.2010e-06 74.9670 0.7572 3.4590e-04 1.4390e-05 2.4350e-05 1.4390e-05 1.2010e-06 0.7934 24.0329 287.9996 +34 4.3968 5.0880e-07 88.9668 0.7873 1.3940e-04 5.8000e-06 8.6320e-06 5.8000e-06 5.0880e-07 0.7548 24.0331 273.9998 +35 4.6093 1.8280e-07 103.9667 0.8122 4.7340e-05 1.9700e-06 2.4100e-06 1.9700e-06 1.8280e-07 0.7135 24.0332 258.9999 +36 4.8218 6.8910e-08 120.9667 0.8342 1.6670e-05 6.9390e-07 6.8740e-07 6.9390e-07 6.8910e-08 0.6667 24.0332 241.9999 +37 5.0343 2.5970e-08 141.9666 0.8552 5.7400e-06 2.3880e-07 1.9500e-07 2.3880e-07 2.5970e-08 0.6088 24.0333 220.9999 +38 5.2468 9.7490e-09 175.9666 0.8798 1.8230e-06 7.5850e-08 5.4240e-08 7.5850e-08 9.7490e-09 0.5151 24.0333 186.9999 +39 5.4594 3.6780e-09 204.9666 0.8950 5.8120e-07 2.4180e-08 1.6960e-08 2.4180e-08 3.6780e-09 0.4353 24.0333 157.9999 +40 5.6719 1.4370e-09 246.9666 0.9113 1.6670e-07 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7.5846 3.1110e-12 361.9666 0.9377 3.1110e-12 0.0000e+00 7.5520e-09 0.0000e+00 2.3210e-12 0.0028 24.0333 0.9999 +50 7.7971 3.1110e-12 361.9666 0.9377 3.1110e-12 0.0000e+00 7.5520e-09 0.0000e+00 2.3210e-12 0.0028 24.0333 0.9999 d_score decoy group_id main_var_xx_swath_prelim_score p_value peak_group_rank pep q_value r_score run_id var_bseries_score var_elution_model_fit_score var_intensity_score var_isotope_correlation_score var_isotope_overlap_score var_library_corr var_library_rmsd var_log_sn_score var_massdev_score var_massdev_score_weighted var_norm_rt_score var_xcorr_coelution var_xcorr_coelution_weighted var_xcorr_shape var_xcorr_shape_weighted var_yseries_score -0 5.2398 0 459_run0 5.2789 8.0383e-08 1 5.7724e-08 1.0276e-08 6.0809 0 5 0.9931 0.9305 0.9987 0.0000 0.9124 0.0399 5.0166 8.8392 3.8845 0.0023 0.0000 0.0000 0.9604 0.9710 6 -1 -1.3671 0 459_run0 -0.1397 9.2611e-01 2 1.0000e+00 5.7662e-02 0.4673 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7888 27.0803 21.2037 0.0107 1.3967 0.8592 0.7892 0.7164 0 -2 -4.4541 0 459_run0 -0.7750 9.9051e-01 7 1.0000e+00 6.1512e-02 -2.1556 0 0 0.6667 0.0004 0.6579 0.0000 0.3765 0.1117 0.5299 8.7979 8.3272 0.0601 2.3868 1.9700 0.1190 0.0150 0 -3 -2.6194 0 459_run0 -1.0545 9.9051e-01 4 1.0000e+00 6.1512e-02 -0.5968 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5683 15.3263 17.4562 0.0200 4.3932 2.7893 0.3292 0.3308 0 -4 -1.5273 0 459_run0 -1.2462 9.2611e-01 3 1.0000e+00 5.7662e-02 0.3311 0 0 -1.0000 0.0004 0.5638 0.0455 0.4459 0.1497 0.5420 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 +0 5.2397 0 459_run0 5.2789 8.0380e-08 1 5.7720e-08 1.0270e-08 6.0808 0 5 0.9930 0.9304 0.9987 0.0000 0.9124 0.0399 5.0165 8.8391 3.8845 0.0023 0.0000 0.0000 0.9603 0.9709 6 +1 -1.3670 0 459_run0 -0.1397 9.2610e-01 2 1.0000e+00 5.7660e-02 0.4672 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7887 27.0802 21.2036 0.0107 1.3966 0.8591 0.7891 0.7163 0 +2 -4.4540 0 459_run0 -0.7750 9.9050e-01 7 1.0000e+00 6.1510e-02 -2.1556 0 0 0.6666 0.0004 0.6579 0.0000 0.3764 0.1117 0.5298 8.7978 8.3272 0.0601 2.3867 1.9700 0.1190 0.0150 0 +3 -2.6193 0 459_run0 -1.0545 9.9050e-01 4 1.0000e+00 6.1510e-02 -0.5967 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5682 15.3263 17.4562 0.0200 4.3932 2.7893 0.3291 0.3308 0 +4 -1.5273 0 459_run0 -1.2461 9.2610e-01 3 1.0000e+00 5.7660e-02 0.3311 0 0 -1.0000 0.0004 0.5638 0.0454 0.4459 0.1497 0.5419 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 .. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 -3.2021 0 168_run0 -1.0780 9.9051e-01 4 1.0000e+00 6.1512e-02 -1.0918 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6926 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5829 0.1919 0.1538 0 -96 -3.9021 0 168_run0 -1.0963 9.9051e-01 8 1.0000e+00 6.1512e-02 -1.6867 0 0 1.0000 0.0012 0.8673 0.0000 -0.6748 0.2056 0.0000 10.1516 12.0983 0.0327 2.2331 1.6284 0.3333 0.1858 0 -97 -2.7778 0 168_run0 -1.4446 9.9051e-01 2 1.0000e+00 6.1512e-02 -0.7314 0 0 0.9411 0.0012 0.0797 0.0000 -0.4017 0.1385 0.0000 14.8865 13.4708 0.0586 2.0539 0.9411 0.7334 0.6821 0 -98 -3.2729 0 168_run0 -1.4526 9.9051e-01 5 1.0000e+00 6.1512e-02 -1.1520 0 1 0.1498 0.0164 0.9644 0.0000 -0.7028 0.3422 0.2301 1.3878 0.8742 0.0664 7.7597 5.5046 0.3111 0.1785 0 -99 -2.9289 0 168_run0 -1.4706 9.9051e-01 3 1.0000e+00 6.1512e-02 -0.8598 0 1 0.1509 0.0053 0.6996 0.0000 0.0856 0.2511 0.0000 10.4594 9.8099 0.0235 4.5054 2.9492 0.3262 0.2549 0 +95 -3.2020 0 168_run0 -1.0780 9.9050e-01 4 1.0000e+00 6.1510e-02 -1.0918 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6925 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5828 0.1919 0.1538 0 +96 -3.9021 0 168_run0 -1.0962 9.9050e-01 8 1.0000e+00 6.1510e-02 -1.6866 0 0 0.9999 0.0012 0.8672 0.0000 -0.6748 0.2055 0.0000 10.1515 12.0982 0.0327 2.2330 1.6284 0.3333 0.1857 0 +97 -2.7778 0 168_run0 -1.4445 9.9050e-01 2 1.0000e+00 6.1510e-02 -0.7314 0 0 0.9411 0.0012 0.0797 0.0000 -0.4016 0.1384 0.0000 14.8864 13.4707 0.0586 2.0539 0.9410 0.7334 0.6820 0 +98 -3.2728 0 168_run0 -1.4525 9.9050e-01 5 1.0000e+00 6.1510e-02 -1.1519 0 1 0.1498 0.0164 0.9643 0.0000 -0.7027 0.3421 0.2301 1.3877 0.8742 0.0664 7.7597 5.5046 0.3111 0.1784 0 +99 -2.9289 0 168_run0 -1.4706 9.9050e-01 3 1.0000e+00 6.1510e-02 -0.8597 0 1 0.1509 0.0053 0.6995 0.0000 0.0856 0.2510 0.0000 10.4594 9.8098 0.0235 4.5054 2.9491 0.3262 0.2549 0 [100 rows x 26 columns] level score weight -0 ms2 main_var_xx_swath_prelim_score 0.1506 +0 ms2 main_var_xx_swath_prelim_score 0.1505 1 ms2 var_bseries_score -0.1351 2 ms2 var_elution_model_fit_score -2.5085 3 ms2 var_intensity_score 0.8575 -4 ms2 var_isotope_correlation_score 2.6838 -5 ms2 var_isotope_overlap_score -1.4558 +4 ms2 var_isotope_correlation_score 2.6837 +5 ms2 var_isotope_overlap_score -1.4557 6 ms2 var_library_corr -0.6974 -7 ms2 var_library_rmsd -13.9710 +7 ms2 var_library_rmsd -13.9709 8 ms2 var_log_sn_score -0.0745 9 ms2 var_massdev_score 0.0124 10 ms2 var_massdev_score_weighted -0.0362 -11 ms2 var_norm_rt_score -11.2724 +11 ms2 var_norm_rt_score -11.2723 12 ms2 var_xcorr_coelution 0.1530 -13 ms2 var_xcorr_coelution_weighted -0.1148 +13 ms2 var_xcorr_coelution_weighted -0.1147 14 ms2 var_xcorr_shape 3.6203 15 ms2 var_xcorr_shape_weighted 2.0371 16 ms2 var_yseries_score 0.1906 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_2.out b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_2.out index a46fda88..8356fa07 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_2.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_2.out @@ -1,92 +1,92 @@ cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 3.0866 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.00 0.9212 25.5215 332.9339 -1 1.0884 0.0086 -3.4139 0.0000 3.1737 0.1240 0.3590 0.1240 0.01 1.0000 22.4139 364.8263 -2 0.6049 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.02 1.0000 19.7692 367.1816 -3 -0.6061 0.0507 -1.2151 0.0000 19.3725 0.7571 1.0000 0.7571 0.05 1.0000 6.2151 362.6275 -4 -2.4409 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.10 1.0000 0.1984 361.6107 +0 3.0866 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.00 0.9212 25.5214 332.9338 +1 1.0883 0.0086 -3.4139 0.0000 3.1736 0.1240 0.3589 0.1240 0.01 1.0000 22.4139 364.8263 +2 0.6048 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.02 1.0000 19.7692 367.1816 +3 -0.6061 0.0507 -1.2150 0.0000 19.3725 0.7571 1.0000 0.7571 0.05 1.0000 6.2150 362.6274 +4 -2.4408 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.10 1.0000 0.1983 361.6107 5 NaN NaN NaN NaN NaN NaN NaN NaN 0.20 NaN NaN NaN 6 NaN NaN NaN NaN NaN NaN NaN NaN 0.30 NaN NaN NaN 7 NaN NaN NaN NaN NaN NaN NaN NaN 0.40 NaN NaN NaN 8 NaN NaN NaN NaN NaN NaN NaN NaN 0.50 NaN NaN NaN cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 -2.9318 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -1 -2.7158 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -2 -2.4998 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -3 -2.2838 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -4 -2.0678 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -5 -1.8518 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -6 -1.6358 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -7 -1.4198 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -8 -1.2038 0.0611 -0.0497 0.0000 23.5380 0.9199 1.0000 0.9199 0.0611 1.0000 2.0497 361.4620 -9 -0.9878 0.0587 -0.0414 0.0000 22.5462 0.8811 1.0000 0.8811 0.0587 1.0000 3.0414 361.4538 -10 -0.7718 0.0575 0.4296 0.1074 22.0172 0.8605 1.0000 0.8605 0.0575 1.0000 3.5704 360.9828 -11 -0.5558 0.0507 -1.2151 0.0000 19.3725 0.7571 1.0000 0.7571 0.0507 1.0000 6.2151 362.6275 -12 -0.3398 0.0448 0.3386 0.0376 16.9262 0.6615 1.0000 0.6615 0.0448 1.0000 8.6614 361.0738 -13 -0.1238 0.0352 -1.3640 0.0000 13.2236 0.5168 1.0000 0.5168 0.0352 1.0000 12.3640 362.7764 -14 0.0923 0.0331 -0.2236 0.0000 12.3640 0.4832 1.0000 0.4832 0.0331 1.0000 13.2236 361.6360 -15 0.3083 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.0156 1.0000 19.7692 367.1816 -16 0.5243 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.0156 1.0000 19.7692 367.1816 -17 0.7403 0.0135 -5.5626 0.0000 5.0250 0.1964 0.7397 0.1964 0.0135 1.0000 20.5626 366.9750 -18 0.9563 0.0114 -4.3561 0.0000 4.2315 0.1654 0.5455 0.1654 0.0114 1.0000 21.3561 365.7685 -19 1.1723 0.0079 -2.6784 0.0000 2.9092 0.1137 0.3211 0.1137 0.0079 1.0000 22.6784 364.0908 -20 1.3883 0.0054 -1.6041 0.0000 1.9835 0.0775 0.2089 0.0775 0.0054 1.0000 23.6041 363.0165 -21 1.6043 0.0053 1.3298 0.0532 1.9174 0.0749 0.2019 0.0749 0.0053 0.9963 23.6702 360.0826 -22 1.8203 0.0033 5.6025 0.1868 1.1901 0.0465 0.1281 0.0465 0.0033 0.9845 24.3975 355.8099 -23 2.0363 0.0019 7.0736 0.2210 0.6612 0.0258 0.0547 0.0258 0.0019 0.9804 24.9264 354.3388 -24 2.2523 0.0017 9.0075 0.2649 0.5951 0.0233 0.0433 0.0233 0.0017 0.9751 24.9925 352.4049 -25 2.4683 0.0013 10.8752 0.3021 0.4628 0.0181 0.0227 0.0181 0.0013 0.9699 25.1248 350.5372 -26 2.6843 0.0008 15.6769 0.3824 0.2645 0.0103 0.0049 0.0103 0.0008 0.9566 25.3231 345.7355 -27 2.9003 0.0004 16.5446 0.3939 0.1322 0.0052 0.0011 0.0052 0.0004 0.9542 25.4554 344.8678 -28 3.1163 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -29 3.3323 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -30 3.5483 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -31 3.7643 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -32 3.9803 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -33 4.1964 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -34 4.4124 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -35 4.6284 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -36 4.8444 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -37 5.0604 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -38 5.2764 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -39 5.4924 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -40 5.7084 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -41 5.9244 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -42 6.1404 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -43 6.3564 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -44 6.5724 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -45 6.7884 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -46 7.0044 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -47 7.2204 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -48 7.4364 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -49 7.6524 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 -50 7.8684 0.0003 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5215 332.9339 +0 -2.9318 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +1 -2.7158 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +2 -2.4998 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +3 -2.2838 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +4 -2.0677 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +5 -1.8517 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +6 -1.6357 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +7 -1.4197 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +8 -1.2037 0.0611 -0.0496 0.0000 23.5379 0.9198 1.0000 0.9198 0.0611 1.0000 2.0496 361.4620 +9 -0.9877 0.0587 -0.0414 0.0000 22.5461 0.8811 1.0000 0.8811 0.0587 1.0000 3.0414 361.4538 +10 -0.7717 0.0575 0.4296 0.1074 22.0172 0.8604 1.0000 0.8604 0.0575 1.0000 3.5703 360.9827 +11 -0.5557 0.0507 -1.2150 0.0000 19.3725 0.7571 1.0000 0.7571 0.0507 1.0000 6.2150 362.6274 +12 -0.3397 0.0448 0.3385 0.0376 16.9261 0.6614 1.0000 0.6614 0.0448 1.0000 8.6614 361.0738 +13 -0.1237 0.0352 -1.3640 0.0000 13.2235 0.5167 1.0000 0.5167 0.0352 1.0000 12.3640 362.7764 +14 0.0922 0.0331 -0.2235 0.0000 12.3640 0.4832 1.0000 0.4832 0.0331 1.0000 13.2235 361.6359 +15 0.3082 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.0156 1.0000 19.7692 367.1816 +16 0.5242 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.0156 1.0000 19.7692 367.1816 +17 0.7402 0.0135 -5.5626 0.0000 5.0249 0.1963 0.7396 0.1963 0.0135 1.0000 20.5626 366.9750 +18 0.9562 0.0114 -4.3560 0.0000 4.2315 0.1653 0.5454 0.1653 0.0114 1.0000 21.3560 365.7684 +19 1.1722 0.0079 -2.6784 0.0000 2.9091 0.1136 0.3210 0.1136 0.0079 1.0000 22.6784 364.0908 +20 1.3882 0.0054 -1.6040 0.0000 1.9835 0.0775 0.2088 0.0775 0.0054 1.0000 23.6040 363.0164 +21 1.6042 0.0053 1.3298 0.0532 1.9174 0.0749 0.2018 0.0749 0.0053 0.9963 23.6701 360.0825 +22 1.8202 0.0033 5.6025 0.1867 1.1901 0.0465 0.1281 0.0465 0.0033 0.9844 24.3974 355.8098 +23 2.0363 0.0019 7.0735 0.2210 0.6611 0.0258 0.0547 0.0258 0.0019 0.9804 24.9264 354.3388 +24 2.2523 0.0017 9.0074 0.2649 0.5950 0.0232 0.0433 0.0232 0.0017 0.9750 24.9925 352.4049 +25 2.4683 0.0013 10.8752 0.3020 0.4628 0.0181 0.0226 0.0181 0.0013 0.9699 25.1247 350.5371 +26 2.6843 0.0008 15.6768 0.3823 0.2644 0.0103 0.0049 0.0103 0.0008 0.9566 25.3231 345.7355 +27 2.9003 0.0004 16.5446 0.3939 0.1322 0.0052 0.0011 0.0052 0.0004 0.9542 25.4553 344.8677 +28 3.1163 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +29 3.3323 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +30 3.5483 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +31 3.7643 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +32 3.9803 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +33 4.1963 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +34 4.4123 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +35 4.6283 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +36 4.8443 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +37 5.0603 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +38 5.2763 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +39 5.4923 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +40 5.7083 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +41 5.9243 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +42 6.1404 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +43 6.3564 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +44 6.5724 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +45 6.7884 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +46 7.0044 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +47 7.2204 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +48 7.4364 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +49 7.6524 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 +50 7.8684 0.0003 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0003 0.9212 25.5214 332.9338 d_score decoy group_id main_var_xx_swath_prelim_score p_value peak_group_rank pep q_value r_score run_id var_bseries_score var_elution_model_fit_score var_intensity_score var_isotope_correlation_score var_isotope_overlap_score var_library_corr var_library_rmsd var_log_sn_score var_massdev_score var_massdev_score_weighted var_norm_rt_score var_xcorr_coelution var_xcorr_coelution_weighted var_xcorr_shape var_xcorr_shape_weighted var_yseries_score -0 5.1547 0 459_run0 5.2789 0.0026 1 0.0005 0.0003 6.0024 0 5 0.9931 0.9305 0.9987 0.0000 0.9124 0.0399 5.0166 8.8392 3.8845 0.0023 0.0000 0.0000 0.9604 0.9710 6 -1 -1.3725 0 459_run0 -0.1397 0.9354 2 1.0000 0.0620 0.5231 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7888 27.0803 21.2037 0.0107 1.3967 0.8592 0.7892 0.7164 0 -2 -4.3197 0 459_run0 -0.7750 0.9922 7 1.0000 0.0656 -1.9510 0 0 0.6667 0.0004 0.6579 0.0000 0.3765 0.1117 0.5299 8.7979 8.3272 0.0601 2.3868 1.9700 0.1190 0.0150 0 -3 -2.4375 0 459_run0 -1.0545 0.9922 4 1.0000 0.0656 -0.3709 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5683 15.3263 17.4562 0.0200 4.3932 2.7893 0.3292 0.3308 0 -4 -1.6028 0 459_run0 -1.2462 0.9354 3 1.0000 0.0620 0.3297 0 0 -1.0000 0.0004 0.5638 0.0455 0.4459 0.1497 0.5420 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 +0 5.1546 0 459_run0 5.2789 0.0026 1 0.0005 0.0003 6.0024 0 5 0.9930 0.9304 0.9987 0.0000 0.9124 0.0399 5.0165 8.8391 3.8845 0.0023 0.0000 0.0000 0.9603 0.9709 6 +1 -1.3724 0 459_run0 -0.1397 0.9354 2 1.0000 0.0620 0.5231 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7887 27.0802 21.2036 0.0107 1.3966 0.8591 0.7891 0.7163 0 +2 -4.3197 0 459_run0 -0.7750 0.9922 7 1.0000 0.0656 -1.9510 0 0 0.6666 0.0004 0.6579 0.0000 0.3764 0.1117 0.5298 8.7978 8.3272 0.0601 2.3867 1.9700 0.1190 0.0150 0 +3 -2.4374 0 459_run0 -1.0545 0.9922 4 1.0000 0.0656 -0.3709 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5682 15.3263 17.4562 0.0200 4.3932 2.7893 0.3291 0.3308 0 +4 -1.6028 0 459_run0 -1.2461 0.9354 3 1.0000 0.0620 0.3297 0 0 -1.0000 0.0004 0.5638 0.0454 0.4459 0.1497 0.5419 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 .. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 -3.0650 0 168_run0 -1.0780 0.9922 4 1.0000 0.0656 -0.8978 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6926 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5829 0.1919 0.1538 0 -96 -3.5587 0 168_run0 -1.0963 0.9922 7 1.0000 0.0656 -1.3122 0 0 1.0000 0.0012 0.8673 0.0000 -0.6748 0.2056 0.0000 10.1516 12.0983 0.0327 2.2331 1.6284 0.3333 0.1858 0 -97 -2.7735 0 168_run0 -1.4446 0.9922 2 1.0000 0.0656 -0.6530 0 0 0.9411 0.0012 0.0797 0.0000 -0.4017 0.1385 0.0000 14.8865 13.4708 0.0586 2.0539 0.9411 0.7334 0.6821 0 -98 -3.0728 0 168_run0 -1.4526 0.9922 5 1.0000 0.0656 -0.9043 0 1 0.1498 0.0164 0.9644 0.0000 -0.7028 0.3422 0.2301 1.3878 0.8742 0.0664 7.7597 5.5046 0.3111 0.1785 0 -99 -2.8249 0 168_run0 -1.4706 0.9922 3 1.0000 0.0656 -0.6962 0 1 0.1509 0.0053 0.6996 0.0000 0.0856 0.2511 0.0000 10.4594 9.8099 0.0235 4.5054 2.9492 0.3262 0.2549 0 +95 -3.0650 0 168_run0 -1.0780 0.9922 4 1.0000 0.0656 -0.8977 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6925 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5828 0.1919 0.1538 0 +96 -3.5587 0 168_run0 -1.0962 0.9922 7 1.0000 0.0656 -1.3121 0 0 0.9999 0.0012 0.8672 0.0000 -0.6748 0.2055 0.0000 10.1515 12.0982 0.0327 2.2330 1.6284 0.3333 0.1857 0 +97 -2.7734 0 168_run0 -1.4445 0.9922 2 1.0000 0.0656 -0.6530 0 0 0.9411 0.0012 0.0797 0.0000 -0.4016 0.1384 0.0000 14.8864 13.4707 0.0586 2.0539 0.9410 0.7334 0.6820 0 +98 -3.0728 0 168_run0 -1.4525 0.9922 5 1.0000 0.0656 -0.9043 0 1 0.1498 0.0164 0.9643 0.0000 -0.7027 0.3421 0.2301 1.3877 0.8742 0.0664 7.7597 5.5046 0.3111 0.1784 0 +99 -2.8249 0 168_run0 -1.4706 0.9922 3 1.0000 0.0656 -0.6962 0 1 0.1509 0.0053 0.6995 0.0000 0.0856 0.2510 0.0000 10.4594 9.8098 0.0235 4.5054 2.9491 0.3262 0.2549 0 [100 rows x 26 columns] level score weight 0 ms2 main_var_xx_swath_prelim_score 0.1554 -1 ms2 var_bseries_score -0.1381 -2 ms2 var_elution_model_fit_score -2.3916 +1 ms2 var_bseries_score -0.1380 +2 ms2 var_elution_model_fit_score -2.3915 3 ms2 var_intensity_score 0.8477 4 ms2 var_isotope_correlation_score 2.8853 -5 ms2 var_isotope_overlap_score -1.3842 +5 ms2 var_isotope_overlap_score -1.3841 6 ms2 var_library_corr -0.7260 -7 ms2 var_library_rmsd -13.8757 -8 ms2 var_log_sn_score -0.1271 +7 ms2 var_library_rmsd -13.8756 +8 ms2 var_log_sn_score -0.1270 9 ms2 var_massdev_score 0.0054 10 ms2 var_massdev_score_weighted -0.0283 -11 ms2 var_norm_rt_score -11.5622 +11 ms2 var_norm_rt_score -11.5621 12 ms2 var_xcorr_coelution 0.1361 13 ms2 var_xcorr_coelution_weighted -0.0913 14 ms2 var_xcorr_shape 3.9496 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_3.out b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_3.out index 7e56e278..10eeb550 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_3.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_3.out @@ -1,93 +1,93 @@ cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 3.0616 0.0002 29.8641 0.553 0.0625 0.0026 0.0004 0.0026 0.00 0.9177 24.1359 332.9375 -1 1.0463 0.0092 -1.8219 0.000 3.3765 0.1395 0.4089 0.1395 0.01 1.0000 20.8219 364.6235 -2 0.5812 0.0151 -4.5709 0.000 5.6275 0.2326 0.8947 0.2326 0.02 1.0000 18.5709 367.3725 -3 -0.6304 0.0491 -0.4400 0.000 18.7585 0.7752 1.0000 0.7752 0.05 1.0000 5.4400 363.2415 -4 -2.4225 0.0622 -0.1251 0.000 24.0734 0.9948 1.0000 0.9948 0.10 1.0000 0.1251 362.9266 +0 3.0616 0.0002 29.8640 0.553 0.0625 0.0026 0.0004 0.0026 0.00 0.9176 24.1359 332.9374 +1 1.0463 0.0092 -1.8219 0.000 3.3765 0.1395 0.4089 0.1395 0.01 1.0000 20.8219 364.6234 +2 0.5811 0.0151 -4.5708 0.000 5.6275 0.2325 0.8946 0.2325 0.02 1.0000 18.5708 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-6 -1.6276 0.0588 -0.5007 0.0000 22.6978 0.9380 1.0000 0.9380 0.0588 1.0000 1.5007 363.3022 -7 -1.4144 0.0588 -0.5007 0.0000 22.6978 0.9380 1.0000 0.9380 0.0588 1.0000 1.5007 363.3022 -8 -1.2011 0.0581 0.1867 0.0933 22.3851 0.9251 1.0000 0.9251 0.0581 1.0000 1.8133 362.6149 -9 -0.9879 0.0550 0.8736 0.2184 21.0720 0.8708 1.0000 0.8708 0.0550 1.0000 3.1264 361.9280 -10 -0.7746 0.0491 -0.4400 0.0000 18.7585 0.7752 1.0000 0.7752 0.0491 1.0000 5.4400 363.2415 -11 -0.5613 0.0461 -0.6280 0.0000 17.5704 0.7261 1.0000 0.7261 0.0461 1.0000 6.6280 363.4296 -12 -0.3481 0.0409 0.2460 0.0273 15.4445 0.6382 1.0000 0.6382 0.0409 1.0000 8.7540 362.5555 -13 -0.1348 0.0334 -0.6303 0.0000 12.5682 0.5194 1.0000 0.5194 0.0334 1.0000 11.6303 363.4318 -14 0.0785 0.0293 -0.2560 0.0000 10.9424 0.4522 1.0000 0.4522 0.0293 1.0000 13.2560 363.0576 -15 0.2917 0.0293 -0.2560 0.0000 10.9424 0.4522 1.0000 0.4522 0.0293 1.0000 13.2560 363.0576 -16 0.5050 0.0151 -4.5709 0.0000 5.6275 0.2326 0.8947 0.2326 0.0151 1.0000 18.5709 367.3725 -17 0.7182 0.0129 -4.3838 0.0000 4.8147 0.1990 0.6706 0.1990 0.0129 1.0000 19.3838 367.1853 -18 0.9315 0.0115 -1.9465 0.0000 4.2519 0.1757 0.5531 0.1757 0.0115 1.0000 19.9465 364.7481 -19 1.1448 0.0070 -0.6348 0.0000 2.5637 0.1059 0.2964 0.1059 0.0070 1.0000 21.6348 363.4363 -20 1.3580 0.0070 -0.6348 0.0000 2.5637 0.1059 0.2964 0.1059 0.0070 1.0000 21.6348 363.4363 -21 1.5713 0.0051 -0.3226 0.0000 1.8758 0.0775 0.2100 0.0775 0.0051 1.0000 22.3226 363.1242 -22 1.7846 0.0038 6.1772 0.2130 1.3756 0.0568 0.1522 0.0568 0.0038 0.9830 22.8228 356.6244 -23 1.9978 0.0025 7.6770 0.2476 0.8754 0.0362 0.0904 0.0362 0.0025 0.9788 23.3230 355.1246 -24 2.2111 0.0016 10.3643 0.3048 0.5628 0.0233 0.0397 0.0233 0.0016 0.9714 23.6357 352.4372 -25 2.4243 0.0012 12.2393 0.3400 0.4377 0.0181 0.0208 0.0181 0.0012 0.9663 23.7607 350.5623 -26 2.6376 0.0009 17.1142 0.4174 0.3126 0.0129 0.0082 0.0129 0.0009 0.9528 23.8858 345.6874 -27 2.8509 0.0004 17.9266 0.4268 0.1251 0.0052 0.0010 0.0052 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+20 1.3580 0.0070 -0.6347 0.0000 2.5636 0.1059 0.2963 0.1059 0.0070 1.0000 21.6347 363.4363 +21 1.5712 0.0051 -0.3225 0.0000 1.8758 0.0775 0.2100 0.0775 0.0051 1.0000 22.3225 363.1241 +22 1.7845 0.0038 6.1771 0.2130 1.3756 0.0568 0.1522 0.0568 0.0038 0.9829 22.8228 356.6243 +23 1.9978 0.0025 7.6769 0.2476 0.8753 0.0362 0.0904 0.0362 0.0025 0.9788 23.3230 355.1246 +24 2.2110 0.0016 10.3643 0.3048 0.5627 0.0232 0.0397 0.0232 0.0016 0.9714 23.6356 352.4372 +25 2.4243 0.0012 12.2392 0.3399 0.4376 0.0181 0.0208 0.0181 0.0012 0.9662 23.7607 350.5623 +26 2.6376 0.0009 17.1141 0.4174 0.3126 0.0129 0.0082 0.0129 0.0009 0.9528 23.8858 345.6873 +27 2.8508 0.0004 17.9266 0.4268 0.1250 0.0052 0.0010 0.0052 0.0004 0.9505 24.0733 344.8749 +28 3.0641 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +29 3.2773 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +30 3.4906 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +31 3.7039 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +32 3.9171 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +33 4.1304 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +34 4.3437 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +35 4.5569 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +36 4.7702 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +37 4.9834 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +38 5.1967 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +39 5.4100 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +40 5.6232 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 0.9176 24.1359 332.9374 +41 5.8365 0.0002 29.8640 0.5530 0.0625 0.0026 0.0004 0.0026 0.0002 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var_elution_model_fit_score var_intensity_score var_isotope_correlation_score var_isotope_overlap_score var_library_corr var_library_rmsd var_log_sn_score var_massdev_score var_massdev_score_weighted var_norm_rt_score var_xcorr_coelution var_xcorr_coelution_weighted var_xcorr_shape var_xcorr_shape_weighted var_yseries_score -0 5.1350 0 459_run0 5.2789 0.0026 1 0.0004 0.0002 5.9840 0 5 0.9931 0.9305 0.9987 0.0000 0.9124 0.0399 5.0166 8.8392 3.8845 0.0023 0.0000 0.0000 0.9604 0.9710 6 -1 -1.3753 0 459_run0 -0.1397 0.9251 2 1.0000 0.0581 0.4918 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7888 27.0803 21.2037 0.0107 1.3967 0.8592 0.7892 0.7164 0 -2 -4.2603 0 459_run0 -0.7750 0.9948 7 1.0000 0.0622 -1.9419 0 0 0.6667 0.0004 0.6579 0.0000 0.3765 0.1117 0.5299 8.7979 8.3272 0.0601 2.3868 1.9700 0.1190 0.0150 0 -3 -2.5293 0 459_run0 -1.0545 0.9948 4 1.0000 0.0622 -0.4816 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5683 15.3263 17.4562 0.0200 4.3932 2.7893 0.3292 0.3308 0 -4 -1.5927 0 459_run0 -1.2462 0.9380 3 1.0000 0.0588 0.3084 0 0 -1.0000 0.0004 0.5638 0.0455 0.4459 0.1497 0.5420 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 +0 5.1350 0 459_run0 5.2789 0.0026 1 0.0004 0.0002 5.9839 0 5 0.9930 0.9304 0.9987 0.0000 0.9124 0.0399 5.0165 8.8391 3.8845 0.0023 0.0000 0.0000 0.9603 0.9709 6 +1 -1.3753 0 459_run0 -0.1397 0.9250 2 1.0000 0.0581 0.4918 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7887 27.0802 21.2036 0.0107 1.3966 0.8591 0.7891 0.7163 0 +2 -4.2602 0 459_run0 -0.7750 0.9948 7 1.0000 0.0622 -1.9418 0 0 0.6666 0.0004 0.6579 0.0000 0.3764 0.1117 0.5298 8.7978 8.3272 0.0601 2.3867 1.9700 0.1190 0.0150 0 +3 -2.5292 0 459_run0 -1.0545 0.9948 4 1.0000 0.0622 -0.4816 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5682 15.3263 17.4562 0.0200 4.3932 2.7893 0.3291 0.3308 0 +4 -1.5927 0 459_run0 -1.2461 0.9379 3 1.0000 0.0588 0.3084 0 0 -1.0000 0.0004 0.5638 0.0454 0.4459 0.1497 0.5419 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 .. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 -3.0560 0 168_run0 -1.0780 0.9948 5 1.0000 0.0622 -0.9259 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6926 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5829 0.1919 0.1538 0 -96 -3.6403 0 168_run0 -1.0963 0.9948 8 1.0000 0.0622 -1.4189 0 0 1.0000 0.0012 0.8673 0.0000 -0.6748 0.2056 0.0000 10.1516 12.0983 0.0327 2.2331 1.6284 0.3333 0.1858 0 -97 -2.6884 0 168_run0 -1.4446 0.9948 2 1.0000 0.0622 -0.6159 0 0 0.9411 0.0012 0.0797 0.0000 -0.4017 0.1385 0.0000 14.8865 13.4708 0.0586 2.0539 0.9411 0.7334 0.6821 0 -98 -3.0479 0 168_run0 -1.4526 0.9948 4 1.0000 0.0622 -0.9191 0 1 0.1498 0.0164 0.9644 0.0000 -0.7028 0.3422 0.2301 1.3878 0.8742 0.0664 7.7597 5.5046 0.3111 0.1785 0 -99 -2.8848 0 168_run0 -1.4706 0.9948 3 1.0000 0.0622 -0.7816 0 1 0.1509 0.0053 0.6996 0.0000 0.0856 0.2511 0.0000 10.4594 9.8099 0.0235 4.5054 2.9492 0.3262 0.2549 0 +95 -3.0559 0 168_run0 -1.0780 0.9948 5 1.0000 0.0622 -0.9259 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6925 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5828 0.1919 0.1538 0 +96 -3.6402 0 168_run0 -1.0962 0.9948 8 1.0000 0.0622 -1.4188 0 0 0.9999 0.0012 0.8672 0.0000 -0.6748 0.2055 0.0000 10.1515 12.0982 0.0327 2.2330 1.6284 0.3333 0.1857 0 +97 -2.6883 0 168_run0 -1.4445 0.9948 2 1.0000 0.0622 -0.6158 0 0 0.9411 0.0012 0.0797 0.0000 -0.4016 0.1384 0.0000 14.8864 13.4707 0.0586 2.0539 0.9410 0.7334 0.6820 0 +98 -3.0478 0 168_run0 -1.4525 0.9948 4 1.0000 0.0622 -0.9191 0 1 0.1498 0.0164 0.9643 0.0000 -0.7027 0.3421 0.2301 1.3877 0.8742 0.0664 7.7597 5.5046 0.3111 0.1784 0 +99 -2.8848 0 168_run0 -1.4706 0.9948 3 1.0000 0.0622 -0.7815 0 1 0.1509 0.0053 0.6995 0.0000 0.0856 0.2510 0.0000 10.4594 9.8098 0.0235 4.5054 2.9491 0.3262 0.2549 0 [100 rows x 26 columns] level score weight 0 ms2 main_var_xx_swath_prelim_score 0.1627 1 ms2 var_bseries_score -0.1323 -2 ms2 var_elution_model_fit_score -2.3538 +2 ms2 var_elution_model_fit_score -2.3537 3 ms2 var_intensity_score 0.8737 4 ms2 var_isotope_correlation_score 2.6704 -5 ms2 var_isotope_overlap_score -1.5062 -6 ms2 var_library_corr -0.7323 -7 ms2 var_library_rmsd -13.6940 +5 ms2 var_isotope_overlap_score -1.5061 +6 ms2 var_library_corr -0.7322 +7 ms2 var_library_rmsd -13.6939 8 ms2 var_log_sn_score -0.0809 9 ms2 var_massdev_score 0.0035 10 ms2 var_massdev_score_weighted -0.0265 11 ms2 var_norm_rt_score -9.9260 -12 ms2 var_xcorr_coelution 0.1339 +12 ms2 var_xcorr_coelution 0.1338 13 ms2 var_xcorr_coelution_weighted -0.0755 14 ms2 var_xcorr_shape 3.6423 15 ms2 var_xcorr_shape_weighted 1.8102 diff --git a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_apply_weights.out b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_apply_weights.out index bc51dc69..3dacaba9 100644 --- a/tests/_regtest_outputs/test_pyprophet_score.test_tsv_apply_weights.out +++ b/tests/_regtest_outputs/test_pyprophet_score.test_tsv_apply_weights.out @@ -1,92 +1,92 @@ cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 3.0866 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.00 0.9212 25.5215 332.9339 -1 1.0884 0.0086 -3.4139 0.0000 3.1737 0.1240 0.3590 0.1240 0.01 1.0000 22.4139 364.8263 -2 0.6049 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.02 1.0000 19.7692 367.1816 -3 -0.6061 0.0507 -1.2151 0.0000 19.3725 0.7571 1.0000 0.7571 0.05 1.0000 6.2151 362.6275 -4 -2.4409 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.10 1.0000 0.1984 361.6107 +0 3.0866 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.00 0.9212 25.5214 332.9338 +1 1.0883 0.0086 -3.4139 0.0000 3.1736 0.1240 0.3589 0.1240 0.01 1.0000 22.4139 364.8263 +2 0.6048 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.02 1.0000 19.7692 367.1816 +3 -0.6061 0.0507 -1.2150 0.0000 19.3725 0.7571 1.0000 0.7571 0.05 1.0000 6.2150 362.6274 +4 -2.4408 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.10 1.0000 0.1983 361.6107 5 NaN NaN NaN NaN NaN NaN NaN NaN 0.20 NaN NaN NaN 6 NaN NaN NaN NaN NaN NaN NaN NaN 0.30 NaN NaN NaN 7 NaN NaN NaN NaN NaN NaN NaN NaN 0.40 NaN NaN NaN 8 NaN NaN NaN NaN NaN NaN NaN NaN 0.50 NaN NaN NaN cutoff fdr fn fnr fp fpr pep pvalue qvalue svalue tn tp -0 -2.9318 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -1 -2.7158 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -2 -2.4998 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -3 -2.2838 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -4 -2.0678 0.0656 -0.1984 0.0000 25.3893 0.9922 1.0000 0.9922 0.0656 1.0000 0.1984 361.6107 -5 -1.8518 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -6 -1.6358 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -7 -1.4198 0.0620 -0.6529 0.0000 23.9347 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 -8 -1.2038 0.0611 -0.0497 0.0000 23.5380 0.9199 1.0000 0.9199 0.0611 1.0000 2.0497 361.4620 -9 -0.9878 0.0587 -0.0414 0.0000 22.5462 0.8811 1.0000 0.8811 0.0587 1.0000 3.0414 361.4538 -10 -0.7718 0.0575 0.4296 0.1074 22.0172 0.8605 1.0000 0.8605 0.0575 1.0000 3.5704 360.9828 -11 -0.5558 0.0507 -1.2151 0.0000 19.3725 0.7571 1.0000 0.7571 0.0507 1.0000 6.2151 362.6275 -12 -0.3398 0.0448 0.3386 0.0376 16.9262 0.6615 1.0000 0.6615 0.0448 1.0000 8.6614 361.0738 -13 -0.1238 0.0352 -1.3640 0.0000 13.2236 0.5168 1.0000 0.5168 0.0352 1.0000 12.3640 362.7764 -14 0.0923 0.0331 -0.2236 0.0000 12.3640 0.4832 1.0000 0.4832 0.0331 1.0000 13.2236 361.6360 -15 0.3083 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.0156 1.0000 19.7692 367.1816 -16 0.5243 0.0156 -5.7692 0.0000 5.8184 0.2274 1.0000 0.2274 0.0156 1.0000 19.7692 367.1816 -17 0.7403 0.0135 -5.5626 0.0000 5.0250 0.1964 0.7397 0.1964 0.0135 1.0000 20.5626 366.9750 -18 0.9563 0.0114 -4.3561 0.0000 4.2315 0.1654 0.5455 0.1654 0.0114 1.0000 21.3561 365.7685 -19 1.1723 0.0079 -2.6784 0.0000 2.9092 0.1137 0.3211 0.1137 0.0079 1.0000 22.6784 364.0908 -20 1.3883 0.0054 -1.6041 0.0000 1.9835 0.0775 0.2089 0.0775 0.0054 1.0000 23.6041 363.0165 -21 1.6043 0.0053 1.3298 0.0532 1.9174 0.0749 0.2019 0.0749 0.0053 0.9963 23.6702 360.0826 -22 1.8203 0.0033 5.6025 0.1868 1.1901 0.0465 0.1281 0.0465 0.0033 0.9845 24.3975 355.8099 -23 2.0363 0.0019 7.0736 0.2210 0.6612 0.0258 0.0547 0.0258 0.0019 0.9804 24.9264 354.3388 -24 2.2523 0.0017 9.0075 0.2649 0.5951 0.0233 0.0433 0.0233 0.0017 0.9751 24.9925 352.4049 -25 2.4683 0.0013 10.8752 0.3021 0.4628 0.0181 0.0227 0.0181 0.0013 0.9699 25.1248 350.5372 -26 2.6843 0.0008 15.6769 0.3824 0.2645 0.0103 0.0049 0.0103 0.0008 0.9566 25.3231 345.7355 -27 2.9003 0.0004 16.5446 0.3939 0.1322 0.0052 0.0011 0.0052 0.0004 0.9542 25.4554 344.8678 -28 3.1163 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -29 3.3323 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -30 3.5483 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -31 3.7643 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -32 3.9803 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -33 4.1964 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -34 4.4124 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -35 4.6284 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -36 4.8444 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -37 5.0604 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -38 5.2764 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -39 5.4924 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -40 5.7084 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -41 5.9244 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -42 6.1404 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -43 6.3564 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -44 6.5724 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -45 6.7884 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -46 7.0044 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -47 7.2204 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -48 7.4364 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -49 7.6524 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 -50 7.8684 0.0002 28.4785 0.5274 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5215 332.9339 +0 -2.9318 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +1 -2.7158 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +2 -2.4998 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +3 -2.2838 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +4 -2.0677 0.0656 -0.1983 0.0000 25.3892 0.9922 1.0000 0.9922 0.0656 1.0000 0.1983 361.6107 +5 -1.8517 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +6 -1.6357 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +7 -1.4197 0.0620 -0.6529 0.0000 23.9346 0.9354 1.0000 0.9354 0.0620 1.0000 1.6529 362.0653 +8 -1.2037 0.0611 -0.0496 0.0000 23.5379 0.9198 1.0000 0.9198 0.0611 1.0000 2.0496 361.4620 +9 -0.9877 0.0587 -0.0414 0.0000 22.5461 0.8811 1.0000 0.8811 0.0587 1.0000 3.0414 361.4538 +10 -0.7717 0.0575 0.4296 0.1074 22.0172 0.8604 1.0000 0.8604 0.0575 1.0000 3.5703 360.9827 +11 -0.5557 0.0507 -1.2150 0.0000 19.3725 0.7571 1.0000 0.7571 0.0507 1.0000 6.2150 362.6274 +12 -0.3397 0.0448 0.3385 0.0376 16.9261 0.6614 1.0000 0.6614 0.0448 1.0000 8.6614 361.0738 +13 -0.1237 0.0352 -1.3640 0.0000 13.2235 0.5167 1.0000 0.5167 0.0352 1.0000 12.3640 362.7764 +14 0.0922 0.0331 -0.2235 0.0000 12.3640 0.4832 1.0000 0.4832 0.0331 1.0000 13.2235 361.6359 +15 0.3082 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.0156 1.0000 19.7692 367.1816 +16 0.5242 0.0156 -5.7692 0.0000 5.8183 0.2273 1.0000 0.2273 0.0156 1.0000 19.7692 367.1816 +17 0.7402 0.0135 -5.5626 0.0000 5.0249 0.1963 0.7396 0.1963 0.0135 1.0000 20.5626 366.9750 +18 0.9562 0.0114 -4.3560 0.0000 4.2315 0.1653 0.5454 0.1653 0.0114 1.0000 21.3560 365.7684 +19 1.1722 0.0079 -2.6784 0.0000 2.9091 0.1136 0.3210 0.1136 0.0079 1.0000 22.6784 364.0908 +20 1.3882 0.0054 -1.6040 0.0000 1.9835 0.0775 0.2088 0.0775 0.0054 1.0000 23.6040 363.0164 +21 1.6042 0.0053 1.3298 0.0532 1.9174 0.0749 0.2018 0.0749 0.0053 0.9963 23.6701 360.0825 +22 1.8202 0.0033 5.6025 0.1867 1.1901 0.0465 0.1281 0.0465 0.0033 0.9844 24.3974 355.8098 +23 2.0363 0.0019 7.0735 0.2210 0.6611 0.0258 0.0547 0.0258 0.0019 0.9804 24.9264 354.3388 +24 2.2523 0.0017 9.0074 0.2649 0.5950 0.0232 0.0433 0.0232 0.0017 0.9750 24.9925 352.4049 +25 2.4683 0.0013 10.8752 0.3020 0.4628 0.0181 0.0226 0.0181 0.0013 0.9699 25.1247 350.5371 +26 2.6843 0.0008 15.6768 0.3823 0.2644 0.0103 0.0049 0.0103 0.0008 0.9566 25.3231 345.7355 +27 2.9003 0.0004 16.5446 0.3939 0.1322 0.0052 0.0011 0.0052 0.0004 0.9542 25.4553 344.8677 +28 3.1163 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +29 3.3323 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +30 3.5483 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +31 3.7643 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +32 3.9803 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +33 4.1963 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +34 4.4123 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +35 4.6283 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +36 4.8443 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +37 5.0603 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +38 5.2763 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +39 5.4923 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +40 5.7083 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +41 5.9243 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +42 6.1404 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +43 6.3564 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +44 6.5724 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +45 6.7884 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +46 7.0044 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +47 7.2204 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +48 7.4364 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +49 7.6524 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 +50 7.8684 0.0002 28.4785 0.5273 0.0661 0.0026 0.0005 0.0026 0.0002 0.9212 25.5214 332.9338 d_score decoy group_id main_var_xx_swath_prelim_score p_value peak_group_rank pep q_value r_score run_id var_bseries_score var_elution_model_fit_score var_intensity_score var_isotope_correlation_score var_isotope_overlap_score var_library_corr var_library_rmsd var_log_sn_score var_massdev_score var_massdev_score_weighted var_norm_rt_score var_xcorr_coelution var_xcorr_coelution_weighted var_xcorr_shape var_xcorr_shape_weighted var_yseries_score -0 5.1547 0 459_run0 5.2789 0.0026 1 0.0005 0.0002 6.0024 0 5 0.9931 0.9305 0.9987 0.0000 0.9124 0.0399 5.0166 8.8392 3.8845 0.0023 0.0000 0.0000 0.9604 0.9710 6 -1 -1.3725 0 459_run0 -0.1397 0.9354 2 1.0000 0.0620 0.5231 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7888 27.0803 21.2037 0.0107 1.3967 0.8592 0.7892 0.7164 0 -2 -4.3197 0 459_run0 -0.7750 0.9922 7 1.0000 0.0656 -1.9510 0 0 0.6667 0.0004 0.6579 0.0000 0.3765 0.1117 0.5299 8.7979 8.3272 0.0601 2.3868 1.9700 0.1190 0.0150 0 -3 -2.4375 0 459_run0 -1.0545 0.9922 4 1.0000 0.0656 -0.3709 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5683 15.3263 17.4562 0.0200 4.3932 2.7893 0.3292 0.3308 0 -4 -1.6028 0 459_run0 -1.2462 0.9354 3 1.0000 0.0620 0.3297 0 0 -1.0000 0.0004 0.5638 0.0455 0.4459 0.1497 0.5420 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 +0 5.1546 0 459_run0 5.2789 0.0026 1 0.0005 0.0002 6.0024 0 5 0.9930 0.9304 0.9987 0.0000 0.9124 0.0399 5.0165 8.8391 3.8845 0.0023 0.0000 0.0000 0.9603 0.9709 6 +1 -1.3724 0 459_run0 -0.1397 0.9354 2 1.0000 0.0620 0.5231 0 0 0.9539 0.0259 0.6325 0.0000 -0.2855 0.1939 2.7887 27.0802 21.2036 0.0107 1.3966 0.8591 0.7891 0.7163 0 +2 -4.3197 0 459_run0 -0.7750 0.9922 7 1.0000 0.0656 -1.9510 0 0 0.6666 0.0004 0.6579 0.0000 0.3764 0.1117 0.5298 8.7978 8.3272 0.0601 2.3867 1.9700 0.1190 0.0150 0 +3 -2.4374 0 459_run0 -1.0545 0.9922 4 1.0000 0.0656 -0.3709 0 0 0.8473 0.0009 0.7984 0.2553 0.5187 0.0881 0.5682 15.3263 17.4562 0.0200 4.3932 2.7893 0.3291 0.3308 0 +4 -1.6028 0 459_run0 -1.2461 0.9354 3 1.0000 0.0620 0.3297 0 0 -1.0000 0.0004 0.5638 0.0454 0.4459 0.1497 0.5419 13.6321 17.1255 0.0515 1.0000 1.0000 0.0000 0.0000 0 .. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 -3.0650 0 168_run0 -1.0780 0.9922 4 1.0000 0.0656 -0.8978 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6926 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5829 0.1919 0.1538 0 -96 -3.5587 0 168_run0 -1.0963 0.9922 7 1.0000 0.0656 -1.3122 0 0 1.0000 0.0012 0.8673 0.0000 -0.6748 0.2056 0.0000 10.1516 12.0983 0.0327 2.2331 1.6284 0.3333 0.1858 0 -97 -2.7735 0 168_run0 -1.4446 0.9922 2 1.0000 0.0656 -0.6530 0 0 0.9411 0.0012 0.0797 0.0000 -0.4017 0.1385 0.0000 14.8865 13.4708 0.0586 2.0539 0.9411 0.7334 0.6821 0 -98 -3.0728 0 168_run0 -1.4526 0.9922 5 1.0000 0.0656 -0.9043 0 1 0.1498 0.0164 0.9644 0.0000 -0.7028 0.3422 0.2301 1.3878 0.8742 0.0664 7.7597 5.5046 0.3111 0.1785 0 -99 -2.8249 0 168_run0 -1.4706 0.9922 3 1.0000 0.0656 -0.6962 0 1 0.1509 0.0053 0.6996 0.0000 0.0856 0.2511 0.0000 10.4594 9.8099 0.0235 4.5054 2.9492 0.3262 0.2549 0 +95 -3.0650 0 168_run0 -1.0780 0.9922 4 1.0000 0.0656 -0.8977 0 1 -0.2038 0.0028 0.9669 0.0000 -0.6925 0.3447 0.0000 0.0604 0.0381 0.0737 3.5921 2.5828 0.1919 0.1538 0 +96 -3.5587 0 168_run0 -1.0962 0.9922 7 1.0000 0.0656 -1.3121 0 0 0.9999 0.0012 0.8672 0.0000 -0.6748 0.2055 0.0000 10.1515 12.0982 0.0327 2.2330 1.6284 0.3333 0.1857 0 +97 -2.7734 0 168_run0 -1.4445 0.9922 2 1.0000 0.0656 -0.6530 0 0 0.9411 0.0012 0.0797 0.0000 -0.4016 0.1384 0.0000 14.8864 13.4707 0.0586 2.0539 0.9410 0.7334 0.6820 0 +98 -3.0728 0 168_run0 -1.4525 0.9922 5 1.0000 0.0656 -0.9043 0 1 0.1498 0.0164 0.9643 0.0000 -0.7027 0.3421 0.2301 1.3877 0.8742 0.0664 7.7597 5.5046 0.3111 0.1784 0 +99 -2.8249 0 168_run0 -1.4706 0.9922 3 1.0000 0.0656 -0.6962 0 1 0.1509 0.0053 0.6995 0.0000 0.0856 0.2510 0.0000 10.4594 9.8098 0.0235 4.5054 2.9491 0.3262 0.2549 0 [100 rows x 26 columns] level score weight 0 ms2 main_var_xx_swath_prelim_score 0.1554 -1 ms2 var_bseries_score -0.1381 -2 ms2 var_elution_model_fit_score -2.3916 +1 ms2 var_bseries_score -0.1380 +2 ms2 var_elution_model_fit_score -2.3915 3 ms2 var_intensity_score 0.8477 4 ms2 var_isotope_correlation_score 2.8853 -5 ms2 var_isotope_overlap_score -1.3842 +5 ms2 var_isotope_overlap_score -1.3841 6 ms2 var_library_corr -0.7260 -7 ms2 var_library_rmsd -13.8757 -8 ms2 var_log_sn_score -0.1271 +7 ms2 var_library_rmsd -13.8756 +8 ms2 var_log_sn_score -0.1270 9 ms2 var_massdev_score 0.0054 10 ms2 var_massdev_score_weighted -0.0283 -11 ms2 var_norm_rt_score -11.5622 +11 ms2 var_norm_rt_score -11.5621 12 ms2 var_xcorr_coelution 0.1361 13 ms2 var_xcorr_coelution_weighted -0.0913 14 ms2 var_xcorr_shape 3.9496 diff --git a/tests/test_pyprophet_score.py b/tests/test_pyprophet_score.py index 9079d479..5ccf9781 100644 --- a/tests/test_pyprophet_score.py +++ b/tests/test_pyprophet_score.py @@ -6,6 +6,7 @@ import sys import sqlite3 import math +from decimal import Decimal, ROUND_DOWN import pandas as pd import pytest @@ -29,23 +30,51 @@ def _round_sig(value, sig_digits=4): return round(value, sig_digits - int(math.floor(math.log10(abs(value)))) - 1) -def _normalize_peakgroup_regtest_frame(df): +def _stabilize_regtest_float(value, sig_digits=4, decimal_places=4, zero_eps=1e-12): """ - Normalize tiny floating-point values so regtest output is stable across - Python/pandas/platform combinations. This only affects the peakgroup - summary tables used by the OSW/parquet score tests. + Make float rendering deterministic across Python/pandas/platform variants. + + For values >= 1 we truncate to a fixed number of decimal places. + For values < 1 we truncate to a fixed number of significant digits. + Tiny near-zero values are snapped to 0. """ - normalized = df.head(100).sort_index(axis=1).copy() + if pd.isna(value): + return value + + value = float(value) + if value == 0 or abs(value) < zero_eps: + return 0.0 + + dec_value = Decimal(str(value)) + if abs(value) >= 1: + quantum = Decimal("1").scaleb(-decimal_places) + return float(dec_value.quantize(quantum, rounding=ROUND_DOWN)) + + digits_after_decimal = sig_digits - int(math.floor(math.log10(abs(value)))) - 1 + quantum = Decimal("1").scaleb(-digits_after_decimal) + return float(dec_value.quantize(quantum, rounding=ROUND_DOWN)) + + +def _normalize_regtest_frame(df, head=100): + """Normalize floating-point output so regtests are stable across environments.""" + normalized = df.head(head).sort_index(axis=1).copy() float_cols = normalized.select_dtypes(include=["floating"]).columns for col in float_cols: - values = normalized[col] - mask = values.notna() & values.ne(0) & values.abs().lt(1e-6) - normalized.loc[mask, col] = values.loc[mask].map(_round_sig) + normalized[col] = normalized[col].map(_stabilize_regtest_float) return normalized +def _normalize_peakgroup_regtest_frame(df): + """ + Normalize tiny floating-point values so regtest output is stable across + Python/pandas/platform combinations. This only affects the peakgroup + summary tables used by the OSW/parquet score tests. + """ + return _normalize_regtest_frame(df, head=100) + + def _print_peakgroup_regtest_frame(df, regtest): print(_normalize_peakgroup_regtest_frame(df), file=regtest) @@ -186,7 +215,7 @@ def verify(self, regtest): df = pd.read_csv( f"test_data_{suffix}", sep="\t" if "tsv" in suffix else "," ) - print(df.head(100).sort_index(axis=1), file=regtest) + print(_normalize_regtest_frame(df), file=regtest) class OSWTestStrategy(TestStrategy):