diff --git a/pyprophet/io/export/osw.py b/pyprophet/io/export/osw.py index 4dc2256..57ce93a 100644 --- a/pyprophet/io/export/osw.py +++ b/pyprophet/io/export/osw.py @@ -1,25 +1,24 @@ import os -import pickle -from shutil import copyfile -import sqlite3 -from typing import Literal, Tuple import re +import sqlite3 +from typing import Tuple + +import click import duckdb -import pandas as pd import numpy as np -import click +import pandas as pd from loguru import logger + +from ..._config import ExportIOConfig +from .._base import BaseOSWReader, BaseOSWWriter from ..util import ( check_sqlite_table, - check_duckdb_table, - unimod_to_codename, - write_scores_sql_command, - load_sqlite_scanner, get_table_columns, get_table_columns_with_types, + load_sqlite_scanner, + unimod_to_codename, + write_scores_sql_command, ) -from .._base import BaseOSWReader, BaseOSWWriter -from ..._config import ExportIOConfig class OSWReader(BaseOSWReader): @@ -167,10 +166,67 @@ def _check_alignment_presence(self, con): con, "SCORE_ALIGNMENT" ) + def _has_im_boundaries(self, con) -> bool: + """Return True if the FEATURE table contains IM boundary columns. + + Older OSW files may not have these columns; this helper centralises the + PRAGMA check so callers don't duplicate the logic. + """ + try: + cols = [ + r[1] for r in con.execute("PRAGMA table_info('FEATURE')").fetchall() + ] + except Exception: + return False + return "EXP_IM_LEFTWIDTH" in cols and "EXP_IM_RIGHTWIDTH" in cols + + def _has_im(self, con) -> bool: + """Return True if the FEATURE table contains the EXP_IM column. + + Older OSW files may not have this column; centralise the PRAGMA + check so callers don't duplicate the logic. + """ + try: + cols = [ + r[1] for r in con.execute("PRAGMA table_info('FEATURE')").fetchall() + ] + except Exception: + return False + return "EXP_IM" in cols + def _read_unscored_data(self, con): """Read data from unscored files.""" score_sql = self._build_score_sql(con) + # IM columns may or may not be present; centralised checks + has_im_boundaries = self._has_im_boundaries(con) + has_im = self._has_im(con) + + # Compose EXP_IM (or NULL) plus IM boundary columns (or NULLs) + im_cols_sql = ( + ( + """FEATURE.EXP_IM AS EXP_IM, + FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth""" + ) + if has_im and has_im_boundaries + else ( + """FEATURE.EXP_IM AS EXP_IM, + NULL AS IM_leftWidth, + NULL AS IM_rightWidth""" + ) + if has_im and not has_im_boundaries + else ( + """NULL AS EXP_IM, + FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth""" + ) + if (not has_im) and has_im_boundaries + else """NULL AS EXP_IM, + NULL AS IM_leftWidth, + NULL AS IM_rightWidth""" + ) + query = f""" SELECT RUN.ID AS id_run, @@ -191,7 +247,8 @@ def _read_unscored_data(self, con): FEATURE_MS1.AREA_INTENSITY AS aggr_prec_Peak_Area, FEATURE_MS1.APEX_INTENSITY AS aggr_prec_Peak_Apex, FEATURE.LEFT_WIDTH AS leftWidth, - FEATURE.RIGHT_WIDTH AS rightWidth + FEATURE.RIGHT_WIDTH AS rightWidth, + {im_cols_sql} {score_sql} FROM PRECURSOR INNER JOIN PRECURSOR_PEPTIDE_MAPPING ON PRECURSOR.ID = PRECURSOR_PEPTIDE_MAPPING.PRECURSOR_ID @@ -224,6 +281,34 @@ def _read_peptidoform_data(self, con, cfg): """Read data with peptidoform IPF information.""" score_ms1_pep, link_ms1 = self._get_ms1_score_info(con) + # IM columns may or may not be present; centralised checks + has_im_boundaries = self._has_im_boundaries(con) + has_im = self._has_im(con) + + im_cols_sql = ( + ( + """FEATURE.EXP_IM AS EXP_IM, + FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth,""" + ) + if has_im and has_im_boundaries + else ( + """FEATURE.EXP_IM AS EXP_IM, + NULL AS IM_leftWidth, + NULL AS IM_rightWidth,""" + ) + if has_im and not has_im_boundaries + else ( + """NULL AS EXP_IM, + FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth,""" + ) + if (not has_im) and has_im_boundaries + else """NULL AS EXP_IM, + NULL AS IM_leftWidth, + NULL AS IM_rightWidth,""" + ) + query = f""" SELECT RUN.ID AS id_run, PEPTIDE.ID AS id_peptide, @@ -247,6 +332,7 @@ def _read_peptidoform_data(self, con, cfg): FEATURE_MS1.APEX_INTENSITY AS aggr_prec_Peak_Apex, FEATURE.LEFT_WIDTH AS leftWidth, FEATURE.RIGHT_WIDTH AS rightWidth, + {im_cols_sql} {score_ms1_pep} AS ms1_pep, SCORE_MS2.PEP AS ms2_pep, SCORE_IPF.PRECURSOR_PEAKGROUP_PEP AS precursor_pep, @@ -275,6 +361,34 @@ def _read_augmented_data(self, con, cfg): """Read standard data augmented with IPF information.""" score_ms1_pep, link_ms1 = self._get_ms1_score_info(con) + # IM columns may or may not be present; centralised checks + has_im_boundaries = self._has_im_boundaries(con) + has_im = self._has_im(con) + + im_cols_sql = ( + ( + """FEATURE.EXP_IM AS EXP_IM, + FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth,""" + ) + if has_im and has_im_boundaries + else ( + """FEATURE.EXP_IM AS EXP_IM, + NULL AS IM_leftWidth, + NULL AS IM_rightWidth,""" + ) + if has_im and not has_im_boundaries + else ( + """NULL AS EXP_IM, + FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth,""" + ) + if (not has_im) and has_im_boundaries + else """NULL AS EXP_IM, + NULL AS IM_leftWidth, + NULL AS IM_rightWidth,""" + ) + query = f""" SELECT RUN.ID AS id_run, PEPTIDE.ID AS id_peptide, @@ -298,6 +412,7 @@ def _read_augmented_data(self, con, cfg): FEATURE_MS1.APEX_INTENSITY AS aggr_prec_Peak_Apex, FEATURE.LEFT_WIDTH AS leftWidth, FEATURE.RIGHT_WIDTH AS rightWidth, + {im_cols_sql} SCORE_MS2.RANK AS peak_group_rank, SCORE_MS2.SCORE AS d_score, SCORE_MS2.QVALUE AS m_score, @@ -326,6 +441,17 @@ def _read_standard_data(self, con, cfg): # Check if we should attempt alignment integration use_alignment = cfg.use_alignment and self._check_alignment_presence(con) + # IM boundary columns may or may not be present; centralised check + has_im_boundaries = self._has_im_boundaries(con) + + im_cols_sql = ( + """FEATURE.EXP_IM_LEFTWIDTH AS IM_leftWidth, + FEATURE.EXP_IM_RIGHTWIDTH AS IM_rightWidth,""" + if has_im_boundaries + else """NULL AS IM_leftWidth, + NULL AS IM_rightWidth,""" + ) + # First, get features that pass MS2 QVALUE threshold query = f""" SELECT RUN.ID AS id_run, @@ -350,6 +476,7 @@ def _read_standard_data(self, con, cfg): FEATURE_MS1.APEX_INTENSITY AS aggr_prec_Peak_Apex, FEATURE.LEFT_WIDTH AS leftWidth, FEATURE.RIGHT_WIDTH AS rightWidth, + {im_cols_sql} SCORE_MS2.RANK AS peak_group_rank, SCORE_MS2.SCORE AS d_score, SCORE_MS2.QVALUE AS m_score, diff --git a/pyprophet/io/export/parquet.py b/pyprophet/io/export/parquet.py index 23d9751..1b0087f 100644 --- a/pyprophet/io/export/parquet.py +++ b/pyprophet/io/export/parquet.py @@ -95,6 +95,26 @@ def _read_unscored_data(self, con) -> pd.DataFrame: """ feature_vars_sql = self._build_feature_vars_sql() + # IM columns may or may not be present in the parquet file + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "EXP_IM AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + query = f""" SELECT RUN_ID AS id_run, @@ -115,7 +135,8 @@ def _read_unscored_data(self, con) -> pd.DataFrame: FEATURE_MS1_AREA_INTENSITY AS aggr_prec_Peak_Area, FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, LEFT_WIDTH AS leftWidth, - RIGHT_WIDTH AS rightWidth + RIGHT_WIDTH AS rightWidth, + {im_cols_sql} {feature_vars_sql} FROM data WHERE PROTEIN_ID IS NOT NULL -- Filter to precursor rows @@ -129,6 +150,26 @@ def _read_peptidoform_data(self, con) -> pd.DataFrame: """ score_ms1_pep, _link_ms1 = self._get_ms1_score_info() + # IM columns may or may not be present in the parquet file + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "EXP_IM AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + query = f""" SELECT RUN_ID AS id_run, @@ -153,6 +194,7 @@ def _read_peptidoform_data(self, con) -> pd.DataFrame: FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, LEFT_WIDTH AS leftWidth, RIGHT_WIDTH AS rightWidth, + {im_cols_sql} {score_ms1_pep} AS ms1_pep, SCORE_MS2_PEP AS ms2_pep, SCORE_IPF_PRECURSOR_PEAKGROUP_PEP AS precursor_pep, @@ -175,6 +217,26 @@ def _read_augmented_data(self, con) -> pd.DataFrame: """ score_ms1_pep, _link_ms1 = self._get_ms1_score_info() + # IM columns may or may not be present in the parquet file + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "EXP_IM AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + # First get main data query = f""" SELECT @@ -200,6 +262,7 @@ def _read_augmented_data(self, con) -> pd.DataFrame: FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, LEFT_WIDTH AS leftWidth, RIGHT_WIDTH AS rightWidth, + {im_cols_sql} SCORE_MS2_PEAK_GROUP_RANK AS peak_group_rank, SCORE_MS2_SCORE AS d_score, SCORE_MS2_Q_VALUE AS m_score, @@ -262,6 +325,26 @@ def _read_standard_data(self, con) -> pd.DataFrame: use_alignment = self.config.use_alignment and self._has_alignment # First, get features that pass MS2 QVALUE threshold + # IM columns may or may not be present in the parquet file + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "EXP_IM AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth," + ) + if has_im and has_im_boundaries + else ("EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth,") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, IM_leftWidth AS IM_leftWidth, IM_rightWidth AS IM_rightWidth," + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth," + ) + query = f""" SELECT RUN_ID AS id_run, @@ -286,6 +369,7 @@ def _read_standard_data(self, con) -> pd.DataFrame: FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, LEFT_WIDTH AS leftWidth, RIGHT_WIDTH AS rightWidth, + {im_cols_sql} SCORE_MS2_PEAK_GROUP_RANK AS peak_group_rank, SCORE_MS2_SCORE AS d_score, SCORE_MS2_Q_VALUE AS m_score, @@ -334,6 +418,7 @@ def _read_standard_data(self, con) -> pd.DataFrame: aligned_ids_df = pd.DataFrame({"id": new_aligned_ids}) con.register("aligned_ids_temp", aligned_ids_df) + # For recovered aligned features include IM columns the same way aligned_query = f""" SELECT RUN_ID AS id_run, @@ -358,6 +443,7 @@ def _read_standard_data(self, con) -> pd.DataFrame: FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, LEFT_WIDTH AS leftWidth, RIGHT_WIDTH AS rightWidth, + {im_cols_sql} SCORE_MS2_PEAK_GROUP_RANK AS peak_group_rank, SCORE_MS2_SCORE AS d_score, SCORE_MS2_Q_VALUE AS m_score diff --git a/pyprophet/io/export/split_parquet.py b/pyprophet/io/export/split_parquet.py index 0aebef6..309cf4f 100644 --- a/pyprophet/io/export/split_parquet.py +++ b/pyprophet/io/export/split_parquet.py @@ -150,6 +150,26 @@ def _read_unscored_data(self, con) -> pd.DataFrame: """ feature_vars_sql = self._build_feature_vars_sql() + # IM columns may or may not be present in the parquet files + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "p.EXP_IM AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("p.EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + query = f""" SELECT p.RUN_ID AS id_run, @@ -170,7 +190,8 @@ def _read_unscored_data(self, con) -> pd.DataFrame: p.FEATURE_MS1_AREA_INTENSITY AS aggr_prec_Peak_Area, p.FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, p.LEFT_WIDTH AS leftWidth, - p.RIGHT_WIDTH AS rightWidth + p.RIGHT_WIDTH AS rightWidth, + {im_cols_sql} {feature_vars_sql} FROM precursors p WHERE p.PROTEIN_ID IS NOT NULL -- Filter to precursor rows @@ -184,6 +205,26 @@ def _read_peptidoform_data(self, con) -> pd.DataFrame: """ score_ms1_pep, _link_ms1 = self._get_ms1_score_info() + # IM columns may or may not be present in the parquet files + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "p.EXP_IM AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("p.EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + query = f""" SELECT p.RUN_ID AS id_run, @@ -208,6 +249,7 @@ def _read_peptidoform_data(self, con) -> pd.DataFrame: p.FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, p.LEFT_WIDTH AS leftWidth, p.RIGHT_WIDTH AS rightWidth, + {im_cols_sql}, {score_ms1_pep} AS ms1_pep, p.SCORE_MS2_PEP AS ms2_pep, p.SCORE_IPF_PRECURSOR_PEAKGROUP_PEP AS precursor_pep, @@ -230,6 +272,26 @@ def _read_augmented_data(self, con) -> pd.DataFrame: """ score_ms1_pep, _link_ms1 = self._get_ms1_score_info() + # IM columns may or may not be present in the parquet files + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "p.EXP_IM AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("p.EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + # First get main data query = f""" SELECT @@ -255,6 +317,7 @@ def _read_augmented_data(self, con) -> pd.DataFrame: p.FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, p.LEFT_WIDTH AS leftWidth, p.RIGHT_WIDTH AS rightWidth, + {im_cols_sql}, p.SCORE_MS2_PEAK_GROUP_RANK AS peak_group_rank, p.SCORE_MS2_SCORE AS d_score, p.SCORE_MS2_Q_VALUE AS m_score, @@ -379,6 +442,26 @@ def _read_standard_data(self, con) -> pd.DataFrame: use_alignment = self.config.use_alignment and self._has_alignment # First, get features that pass MS2 QVALUE threshold + # IM columns may or may not be present in the parquet files + has_im = "EXP_IM" in self._columns + has_im_boundaries = ( + "IM_leftWidth" in self._columns and "IM_rightWidth" in self._columns + ) + + im_cols_sql = ( + ( + "p.EXP_IM AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if has_im and has_im_boundaries + else ("p.EXP_IM AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth") + if has_im and not has_im_boundaries + else ( + "NULL AS EXP_IM, p.IM_leftWidth AS IM_leftWidth, p.IM_rightWidth AS IM_rightWidth" + ) + if (not has_im) and has_im_boundaries + else "NULL AS EXP_IM, NULL AS IM_leftWidth, NULL AS IM_rightWidth" + ) + query = f""" SELECT p.RUN_ID AS id_run, @@ -403,6 +486,7 @@ def _read_standard_data(self, con) -> pd.DataFrame: p.FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, p.LEFT_WIDTH AS leftWidth, p.RIGHT_WIDTH AS rightWidth, + {im_cols_sql}, p.SCORE_MS2_PEAK_GROUP_RANK AS peak_group_rank, p.SCORE_MS2_SCORE AS d_score, p.SCORE_MS2_Q_VALUE AS m_score, @@ -451,6 +535,7 @@ def _read_standard_data(self, con) -> pd.DataFrame: aligned_ids_df = pd.DataFrame({"id": new_aligned_ids}) con.register("aligned_ids_temp", aligned_ids_df) + # For recovered aligned features include IM columns the same way aligned_query = f""" SELECT p.RUN_ID AS id_run, @@ -475,6 +560,7 @@ def _read_standard_data(self, con) -> pd.DataFrame: p.FEATURE_MS1_APEX_INTENSITY AS aggr_prec_Peak_Apex, p.LEFT_WIDTH AS leftWidth, p.RIGHT_WIDTH AS rightWidth, + {im_cols_sql} p.SCORE_MS2_PEAK_GROUP_RANK AS peak_group_rank, p.SCORE_MS2_SCORE AS d_score, p.SCORE_MS2_Q_VALUE AS m_score diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-augmented].out b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-augmented].out index eb64c5e..4b61ae2 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-augmented].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-augmented].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id ipf_FullUniModPeptideName ipf_peptidoform_m_score ipf_peptidoform_pep ipf_precursor_peakgroup_pep leftWidth m_score ms1_pep ms2_pep mz peak_group_rank rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 ADSTGTLVITDPTR(Label:13C(6)15N(4)) 0.0 0.0 6.0486e-09 2640.5100 0.0033 0.0003 0.0031 728.8795 1 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 NaN NaN NaN NaN 2575.6399 0.0685 1.0000 1.0000 728.8795 2 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 NaN NaN NaN NaN 2705.3701 0.2018 1.0000 1.0000 728.8795 3 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 NaN NaN NaN NaN 2790.7200 0.2018 1.0000 1.0000 728.8795 4 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 NaN NaN NaN NaN 2811.2000 0.4692 1.0000 1.0000 728.8795 5 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 VYVYAVDQTR(Label:13C(6)15N(4)) 0.0 0.0 7.2479e-09 2213.2600 0.0033 0.0003 0.0031 612.3184 1 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 NaN NaN NaN NaN 2302.0200 0.2507 1.0000 1.0000 612.3184 2 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 NaN NaN NaN NaN 2100.6001 0.4000 1.0000 1.0000 612.3184 3 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 NaN NaN NaN NaN 2267.8799 0.4692 1.0000 1.0000 612.3184 4 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 NaN NaN NaN NaN 2520.5100 0.4692 1.0000 1.0000 612.3184 5 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id ipf_FullUniModPeptideName ipf_peptidoform_m_score ipf_peptidoform_pep ipf_precursor_peakgroup_pep leftWidth m_score ms1_pep ms2_pep mz peak_group_rank rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 ADSTGTLVITDPTR(Label:13C(6)15N(4)) 0.0 0.0 6.0486e-09 2640.5100 0.0033 0.0003 0.0031 728.8795 1 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 NaN NaN NaN NaN 2575.6399 0.0685 1.0000 1.0000 728.8795 2 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 NaN NaN NaN NaN 2705.3701 0.2018 1.0000 1.0000 728.8795 3 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 NaN NaN NaN NaN 2790.7200 0.2018 1.0000 1.0000 728.8795 4 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 NaN NaN NaN NaN 2811.2000 0.4692 1.0000 1.0000 728.8795 5 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 VYVYAVDQTR(Label:13C(6)15N(4)) 0.0 0.0 7.2479e-09 2213.2600 0.0033 0.0003 0.0031 612.3184 1 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 NaN NaN NaN NaN 2302.0200 0.2507 1.0000 1.0000 612.3184 2 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 NaN NaN NaN NaN 2100.6001 0.4000 1.0000 1.0000 612.3184 3 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 NaN NaN NaN NaN 2267.8799 0.4692 1.0000 1.0000 612.3184 4 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 NaN NaN NaN NaN 2520.5100 0.4692 1.0000 1.0000 612.3184 5 2544.4099 -8670811102654834151 19 -[100 rows x 30 columns] +[100 rows x 33 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-disable].out b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-disable].out index c59ca7c..82a0ad8 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-disable].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-disable].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 25 columns] +[100 rows x 27 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-peptidoform].out b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-peptidoform].out index cad97aa..6496f16 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-peptidoform].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[False-peptidoform].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id ipf_pep leftWidth m_score ms1_pep ms2_m_score ms2_pep mz peak_group_rank precursor_pep rightWidth run_id transition_group_id -0 2 AAEDFTLLVK(Label:13C(6)15N(2)) 189687.0 AQUA4SWATH_HMLangeE 3665.82 AAEDFTLLVK 107855.1703 702922.0 58.9 3708.4232 5.5390 0 -1.3421 -42.6032 napedro_L120420_010_SW.mzXML.gz 57.5579 6227384657721288232 0.0000e+00 3646.8899 0.0000e+00 0.0003 0.0033 0.0031 557.8153 1 9.4008e-09 3698.1001 -8670811102654834151 AAEDFTLLVK(Label:13C(6)15N(2))_87 -1 2 AAGASAQVLGQEGK(Label:13C(6)15N(2)) 265021.0 AQUA4SWATH_Spyo 1521.11 AAGASAQVLGQEGK 231000.0046 1051340.0 -5.3 1503.3343 5.8582 0 0.6697 17.7757 napedro_L120420_010_SW.mzXML.gz -4.6303 -4109405113780929799 0.0000e+00 1503.2700 0.0000e+00 0.0003 0.0033 0.0031 647.8457 1 7.0709e-10 1537.4000 -8670811102654834151 AAGASAQVLGQEGK(Label:13C(6)15N(2))_257 -2 2 AASEIATAELAPTHPIR(Label:13C(6)15N(4)) 63749.0 AQUA4SWATH_PombeSchmidt 2754.99 AASEIATAELAPTHPIR 56607.9433 320548.0 31.5 2767.3108 5.6965 0 -0.3526 -12.3208 napedro_L120420_010_SW.mzXML.gz 31.1474 -4579089096808240748 0.0000e+00 2736.7000 0.0000e+00 0.0003 0.0033 0.0031 879.4746 1 7.0709e-10 2774.2600 -8670811102654834151 AASEIATAELAPTHPIR(Label:13C(6)15N(4))_235 -3 2 AAVPVLVHPAPR(Label:13C(6)15N(4)) 47860.0 AQUA4SWATH_Tuberculosis 2370.16 AAVPVLVHPAPR 30508.2548 135628.0 19.6 2358.5846 5.1771 0 0.3887 11.5754 napedro_L120420_010_SW.mzXML.gz 19.9887 1080224756928033227 0.0000e+00 2349.8101 0.0000e+00 0.0003 0.0033 0.0031 618.8762 1 1.5978e-09 2390.7800 -8670811102654834151 AAVPVLVHPAPR(Label:13C(6)15N(4))_279 -4 2 ADDYTYEHLR(Label:13C(6)15N(4)) 97468.0 AQUA4SWATH_HMLangeG 1743.79 ADDYTYEHLR 89956.6100 330373.0 4.8 1850.2388 5.3371 0 -2.9734 -106.4488 napedro_L120420_010_SW.mzXML.gz 1.8266 -6595106422864423511 0.0000e+00 1728.5800 0.0000e+00 0.0003 0.0033 0.0031 646.7927 1 7.0709e-10 1759.3101 -8670811102654834151 ADDYTYEHLR(Label:13C(6)15N(4))_132 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 GFDATYHVR(Label:13C(6)15N(4)) 92840.0 AQUA4SWATH_HMLangeE 1750.75 GFDATYHVR 135806.9267 1026610.0 3.9 1819.3275 4.4511 0 -1.8716 -68.5775 napedro_L120420_010_SW.mzXML.gz 2.0284 6575595963013729151 3.9968e-13 1731.5900 1.8148e-15 0.5778 0.0062 0.0225 538.2634 1 8.4452e-03 1769.1400 -8670811102654834151 GFDATYHVR(Label:13C(6)15N(4))_95 -96 2 GFTPDGPAGTEPNIAPGYK(Label:13C(6)15N(2)) 304459.0 AQUA4SWATH_Lepto 3075.75 GFTPDGPAGTEPNIAPGYK 194847.4074 968985.0 39.4 3038.6533 5.9861 0 1.0482 37.0967 napedro_L120420_010_SW.mzXML.gz 40.4482 725624140668631730 0.0000e+00 3057.8201 0.0000e+00 0.0003 0.0033 0.0031 948.9645 1 7.0709e-10 3095.3701 -8670811102654834151 GFTPDGPAGTEPNIAPGYK(Label:13C(6)15N(2))_169 -97 2 GGNFGFGDSR(Label:13C(6)15N(4)) 382433.0 AQUA4SWATH_HumanEbhardt 1984.57 GGNFGFGDSR 158928.4812 843945.0 11.9 2094.1085 5.0378 0 -3.0918 -109.5385 napedro_L120420_010_SW.mzXML.gz 8.8082 -7797929030476974532 0.0000e+00 1963.6300 0.0000e+00 0.0003 0.0033 0.0031 512.2295 1 5.9397e-08 2011.4301 -8670811102654834151 GGNFGFGDSR(Label:13C(6)15N(4))_149 -98 2 GHFYYDISDVR(Label:13C(6)15N(4)) 55289.0 AQUA4SWATH_HMLangeG 2889.39 GHFYYDISDVR 46057.1329 272430.0 39.4 3038.6590 4.9333 0 -4.3557 -149.2690 napedro_L120420_010_SW.mzXML.gz 35.0443 9218597765662578237 0.0000e+00 2869.0300 0.0000e+00 0.0003 0.0033 0.0031 691.3242 1 2.4091e-08 2913.4099 -8670811102654834151 GHFYYDISDVR(Label:13C(6)15N(4))_134 -99 2 GIAASDGVAVAK(Label:13C(6)15N(2)) 319128.0 AQUA4SWATH_Spyo 1715.56 GIAASDGVAVAK 228311.6217 1060010.0 -1.4 1637.2919 5.8413 0 2.4079 78.2681 napedro_L120420_010_SW.mzXML.gz 1.0079 7617756229621228830 0.0000e+00 1697.4500 0.0000e+00 0.0003 0.0033 0.0031 533.8028 1 7.2479e-09 1735.0000 -8670811102654834151 GIAASDGVAVAK(Label:13C(6)15N(2))_263 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id ipf_pep leftWidth m_score ms1_pep ms2_m_score ms2_pep mz peak_group_rank precursor_pep rightWidth run_id transition_group_id +0 2 NaN AAEDFTLLVK(Label:13C(6)15N(2)) NaN NaN 189687.0 AQUA4SWATH_HMLangeE 3665.82 AAEDFTLLVK 107855.1703 702922.0 58.9 3708.4232 5.5390 0 -1.3421 -42.6032 napedro_L120420_010_SW.mzXML.gz 57.5579 6227384657721288232 0.0000e+00 3646.8899 0.0000e+00 0.0003 0.0033 0.0031 557.8153 1 9.4008e-09 3698.1001 -8670811102654834151 AAEDFTLLVK(Label:13C(6)15N(2))_87 +1 2 NaN AAGASAQVLGQEGK(Label:13C(6)15N(2)) NaN NaN 265021.0 AQUA4SWATH_Spyo 1521.11 AAGASAQVLGQEGK 231000.0046 1051340.0 -5.3 1503.3343 5.8582 0 0.6697 17.7757 napedro_L120420_010_SW.mzXML.gz -4.6303 -4109405113780929799 0.0000e+00 1503.2700 0.0000e+00 0.0003 0.0033 0.0031 647.8457 1 7.0709e-10 1537.4000 -8670811102654834151 AAGASAQVLGQEGK(Label:13C(6)15N(2))_257 +2 2 NaN AASEIATAELAPTHPIR(Label:13C(6)15N(4)) NaN NaN 63749.0 AQUA4SWATH_PombeSchmidt 2754.99 AASEIATAELAPTHPIR 56607.9433 320548.0 31.5 2767.3108 5.6965 0 -0.3526 -12.3208 napedro_L120420_010_SW.mzXML.gz 31.1474 -4579089096808240748 0.0000e+00 2736.7000 0.0000e+00 0.0003 0.0033 0.0031 879.4746 1 7.0709e-10 2774.2600 -8670811102654834151 AASEIATAELAPTHPIR(Label:13C(6)15N(4))_235 +3 2 NaN AAVPVLVHPAPR(Label:13C(6)15N(4)) NaN NaN 47860.0 AQUA4SWATH_Tuberculosis 2370.16 AAVPVLVHPAPR 30508.2548 135628.0 19.6 2358.5846 5.1771 0 0.3887 11.5754 napedro_L120420_010_SW.mzXML.gz 19.9887 1080224756928033227 0.0000e+00 2349.8101 0.0000e+00 0.0003 0.0033 0.0031 618.8762 1 1.5978e-09 2390.7800 -8670811102654834151 AAVPVLVHPAPR(Label:13C(6)15N(4))_279 +4 2 NaN ADDYTYEHLR(Label:13C(6)15N(4)) NaN NaN 97468.0 AQUA4SWATH_HMLangeG 1743.79 ADDYTYEHLR 89956.6100 330373.0 4.8 1850.2388 5.3371 0 -2.9734 -106.4488 napedro_L120420_010_SW.mzXML.gz 1.8266 -6595106422864423511 0.0000e+00 1728.5800 0.0000e+00 0.0003 0.0033 0.0031 646.7927 1 7.0709e-10 1759.3101 -8670811102654834151 ADDYTYEHLR(Label:13C(6)15N(4))_132 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN GFDATYHVR(Label:13C(6)15N(4)) NaN NaN 92840.0 AQUA4SWATH_HMLangeE 1750.75 GFDATYHVR 135806.9267 1026610.0 3.9 1819.3275 4.4511 0 -1.8716 -68.5775 napedro_L120420_010_SW.mzXML.gz 2.0284 6575595963013729151 3.9968e-13 1731.5900 1.8148e-15 0.5778 0.0062 0.0225 538.2634 1 8.4452e-03 1769.1400 -8670811102654834151 GFDATYHVR(Label:13C(6)15N(4))_95 +96 2 NaN GFTPDGPAGTEPNIAPGYK(Label:13C(6)15N(2)) NaN NaN 304459.0 AQUA4SWATH_Lepto 3075.75 GFTPDGPAGTEPNIAPGYK 194847.4074 968985.0 39.4 3038.6533 5.9861 0 1.0482 37.0967 napedro_L120420_010_SW.mzXML.gz 40.4482 725624140668631730 0.0000e+00 3057.8201 0.0000e+00 0.0003 0.0033 0.0031 948.9645 1 7.0709e-10 3095.3701 -8670811102654834151 GFTPDGPAGTEPNIAPGYK(Label:13C(6)15N(2))_169 +97 2 NaN GGNFGFGDSR(Label:13C(6)15N(4)) NaN NaN 382433.0 AQUA4SWATH_HumanEbhardt 1984.57 GGNFGFGDSR 158928.4812 843945.0 11.9 2094.1085 5.0378 0 -3.0918 -109.5385 napedro_L120420_010_SW.mzXML.gz 8.8082 -7797929030476974532 0.0000e+00 1963.6300 0.0000e+00 0.0003 0.0033 0.0031 512.2295 1 5.9397e-08 2011.4301 -8670811102654834151 GGNFGFGDSR(Label:13C(6)15N(4))_149 +98 2 NaN GHFYYDISDVR(Label:13C(6)15N(4)) NaN NaN 55289.0 AQUA4SWATH_HMLangeG 2889.39 GHFYYDISDVR 46057.1329 272430.0 39.4 3038.6590 4.9333 0 -4.3557 -149.2690 napedro_L120420_010_SW.mzXML.gz 35.0443 9218597765662578237 0.0000e+00 2869.0300 0.0000e+00 0.0003 0.0033 0.0031 691.3242 1 2.4091e-08 2913.4099 -8670811102654834151 GHFYYDISDVR(Label:13C(6)15N(4))_134 +99 2 NaN GIAASDGVAVAK(Label:13C(6)15N(2)) NaN NaN 319128.0 AQUA4SWATH_Spyo 1715.56 GIAASDGVAVAK 228311.6217 1060010.0 -1.4 1637.2919 5.8413 0 2.4079 78.2681 napedro_L120420_010_SW.mzXML.gz 1.0079 7617756229621228830 0.0000e+00 1697.4500 0.0000e+00 0.0003 0.0033 0.0031 533.8028 1 7.2479e-09 1735.0000 -8670811102654834151 GIAASDGVAVAK(Label:13C(6)15N(2))_263 -[100 rows x 29 columns] +[100 rows x 32 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[True-disable].out b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[True-disable].out index 8f4829a..fcb9c15 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[True-disable].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_ipf_analysis[True-disable].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 1343_b4_1;1359_y3_1;1344_b5_1;1360_y4_1;1345_b... 969.0;36907.0;1426.0;6131.0;2071.0;11984.0;559... 10322.0;251772.0;9915.0;43365.0;15040.0;80527.... 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR NaN NaN NaN 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR NaN NaN NaN 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR NaN NaN NaN 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR NaN NaN NaN 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 1803_b3_1;1813_y3_1;1821_y8_2;1804_b4_1;1814_y... 20367.0;19321.0;4323.0;3974.0;17424.0;5191.0;1... 89094.0;85016.0;20487.0;17689.0;74968.0;25322.... 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR NaN NaN NaN 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR NaN NaN NaN 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR NaN NaN NaN 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR NaN NaN NaN 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 1343_b4_1;1359_y3_1;1344_b5_1;1360_y4_1;1345_b... 969.0;36907.0;1426.0;6131.0;2071.0;11984.0;559... 10322.0;251772.0;9915.0;43365.0;15040.0;80527.... 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR NaN NaN NaN 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR NaN NaN NaN 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR NaN NaN NaN 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR NaN NaN NaN 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 1803_b3_1;1813_y3_1;1821_y8_2;1804_b4_1;1814_y... 20367.0;19321.0;4323.0;3974.0;17424.0;5191.0;1... 89094.0;85016.0;20487.0;17689.0;74968.0;25322.... 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR NaN NaN NaN 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR NaN NaN NaN 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR NaN NaN NaN 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR NaN NaN NaN 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 28 columns] +[100 rows x 30 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-False].out index c59ca7c..82a0ad8 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 25 columns] +[100 rows x 27 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-True].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-True].out index 9d5ced6..1df5aa7 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-True].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-False-True].out @@ -1,3 +1,3 @@ Empty DataFrame -Columns: [Charge, FullPeptideName, Intensity, ProteinName, RT, Sequence, aggr_prec_Peak_Apex, aggr_prec_Peak_Area, assay_iRT, assay_rt, d_score, decoy, delta_iRT, delta_rt, filename, iRT, id, leftWidth, m_score, m_score_protein_experiment_wide, m_score_protein_global, m_score_protein_run_specific, mz, peak_group_rank, pep, rightWidth, run_id, transition_group_id] +Columns: [Charge, FullPeptideName, IM_leftWidth, IM_rightWidth, Intensity, ProteinName, RT, Sequence, aggr_prec_Peak_Apex, aggr_prec_Peak_Area, assay_iRT, assay_rt, d_score, decoy, delta_iRT, delta_rt, filename, iRT, id, leftWidth, m_score, m_score_protein_experiment_wide, m_score_protein_global, m_score_protein_run_specific, mz, peak_group_rank, pep, rightWidth, run_id, transition_group_id] Index: [] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-True-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-True-False].out index b3014b4..11b6527 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-True-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-False-True-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_peptide_experiment_wide m_score_peptide_global m_score_peptide_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.00 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0033 0.0033 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.00 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0033 0.0033 0.0033 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.20 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0033 0.0033 0.0033 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.30 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0033 0.0033 0.0033 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.00 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0033 0.0033 0.0033 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 YTSDPDVTSVGPSK(UniMod:259) 230755.0 AQUA4SWATH_HMLangeA 1802.63 YTSDPDVTSVGPSK 194786.2681 924585.00 1.5 1736.8945 5.6930 0 2.0327 65.7355 napedro_L120420_010_SW.mzXML.gz 3.5327 6243564357659176748 1787.0300 0.0033 0.0033 0.0033 0.0033 730.8534 1 0.0031 1821.1700 -8670811102654834151 20 -96 2 YTSDPDVTSVGPSK(UniMod:259) 4683.0 AQUA4SWATH_HMLangeA 1727.20 YTSDPDVTSVGPSK 2721.4443 21561.90 1.5 1736.8978 3.6145 0 -0.1546 -9.6978 napedro_L120420_010_SW.mzXML.gz 1.3454 8621961886436053858 1711.9200 0.0091 0.0033 0.0033 0.0033 730.8534 2 0.1143 1749.4700 -8670811102654834151 20 -97 2 YTSDPDVTSVGPSK(UniMod:259) 2042.0 AQUA4SWATH_HMLangeA 1846.77 YTSDPDVTSVGPSK 670.7683 6339.12 1.5 1736.8956 0.4186 0 3.3126 109.8744 napedro_L120420_010_SW.mzXML.gz 4.8126 -5596989166542619604 1834.8199 0.2507 0.0033 0.0033 0.0033 730.8534 3 1.0000 1858.7200 -8670811102654834151 20 -98 2 YTSDPDVTSVGPSK(UniMod:259) 1801.0 AQUA4SWATH_HMLangeA 1657.80 YTSDPDVTSVGPSK 1076.2317 4819.60 1.5 1736.8914 0.2832 0 -2.1667 -79.0914 napedro_L120420_010_SW.mzXML.gz -0.6667 -2650714328790198942 1653.8800 0.4000 0.0033 0.0033 0.0033 730.8534 4 1.0000 1681.2000 -8670811102654834151 20 -99 2 YTSDPDVTSVGPSK(UniMod:259) 32774.0 AQUA4SWATH_HMLangeA 1930.69 YTSDPDVTSVGPSK 76935.7696 571655.00 1.5 1736.8936 -5.7742 0 5.7460 193.7964 napedro_L120420_010_SW.mzXML.gz 7.2460 9040480247797844482 1906.5100 0.4692 0.0033 0.0033 0.0033 730.8534 5 1.0000 1971.3800 -8670811102654834151 20 + Charge FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_peptide_experiment_wide m_score_peptide_global m_score_peptide_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 117220.7482 854645.00 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0033 0.0033 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 8790.7812 104006.00 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0033 0.0033 0.0033 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 5750.4716 73215.20 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0033 0.0033 0.0033 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 4036.5600 25862.30 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0033 0.0033 0.0033 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 10419.7435 241873.00 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0033 0.0033 0.0033 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 YTSDPDVTSVGPSK(UniMod:259) NaN NaN 230755.0 AQUA4SWATH_HMLangeA 1802.63 YTSDPDVTSVGPSK 194786.2681 924585.00 1.5 1736.8945 5.6930 0 2.0327 65.7355 napedro_L120420_010_SW.mzXML.gz 3.5327 6243564357659176748 1787.0300 0.0033 0.0033 0.0033 0.0033 730.8534 1 0.0031 1821.1700 -8670811102654834151 20 +96 2 YTSDPDVTSVGPSK(UniMod:259) NaN NaN 4683.0 AQUA4SWATH_HMLangeA 1727.20 YTSDPDVTSVGPSK 2721.4443 21561.90 1.5 1736.8978 3.6145 0 -0.1546 -9.6978 napedro_L120420_010_SW.mzXML.gz 1.3454 8621961886436053858 1711.9200 0.0091 0.0033 0.0033 0.0033 730.8534 2 0.1143 1749.4700 -8670811102654834151 20 +97 2 YTSDPDVTSVGPSK(UniMod:259) NaN NaN 2042.0 AQUA4SWATH_HMLangeA 1846.77 YTSDPDVTSVGPSK 670.7683 6339.12 1.5 1736.8956 0.4186 0 3.3126 109.8744 napedro_L120420_010_SW.mzXML.gz 4.8126 -5596989166542619604 1834.8199 0.2507 0.0033 0.0033 0.0033 730.8534 3 1.0000 1858.7200 -8670811102654834151 20 +98 2 YTSDPDVTSVGPSK(UniMod:259) NaN NaN 1801.0 AQUA4SWATH_HMLangeA 1657.80 YTSDPDVTSVGPSK 1076.2317 4819.60 1.5 1736.8914 0.2832 0 -2.1667 -79.0914 napedro_L120420_010_SW.mzXML.gz -0.6667 -2650714328790198942 1653.8800 0.4000 0.0033 0.0033 0.0033 730.8534 4 1.0000 1681.2000 -8670811102654834151 20 +99 2 YTSDPDVTSVGPSK(UniMod:259) NaN NaN 32774.0 AQUA4SWATH_HMLangeA 1930.69 YTSDPDVTSVGPSK 76935.7696 571655.00 1.5 1736.8936 -5.7742 0 5.7460 193.7964 napedro_L120420_010_SW.mzXML.gz 7.2460 9040480247797844482 1906.5100 0.4692 0.0033 0.0033 0.0033 730.8534 5 1.0000 1971.3800 -8670811102654834151 20 -[100 rows x 28 columns] +[100 rows x 30 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-True-False-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-True-False-False].out index fa31d5c..471e5b9 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-True-False-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[osw-True-False-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 41.0;787.0;969.0;36907.0;479.0;60.0;1426.0;30.... 223.0;12510.0;10322.0;251772.0;5557.0;500.0;99... 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;520.0;181.0;1338.0;294.0;20.0;232.0;10.0;1... 150.0;13418.0;3123.0;9325.0;2329.0;100.0;4328.... 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;541.0;294.0;1060.0;90.0;0.0;190.0;30.0;429... 50.0;5415.0;1984.0;6992.0;1344.0;60.0;1748.0;1... 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;702.0;334.0;386.0;241.0;10.0;212.0;20.0;29... 10.0;4454.0;1675.0;2411.0;1323.0;60.0;1121.0;1... 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;592.0;397.0;743.0;427.0;20.0;222.0;0.0;348... 30.0;10869.0;5111.0;8116.0;33319.0;271.0;6193.... 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 439.0;20367.0;40.0;19321.0;968.0;120.0;4323.0;... 3589.0;89094.0;571.0;85016.0;4040.0;965.0;2048... 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 224.0;847.0;10.0;582.0;30.0;50.0;295.0;531.0;5... 2071.0;5859.0;141.0;4805.0;321.0;503.0;2775.0;... 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 283.0;913.0;50.0;1597.0;60.0;50.0;643.0;937.0;... 4611.0;12157.0;330.0;11363.0;594.0;1098.0;5460... 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 397.0;263.0;50.0;520.0;162.0;80.0;441.0;296.0;... 4032.0;2661.0;580.0;6989.0;1362.0;732.0;6854.0... 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 306.0;233.0;30.0;510.0;40.0;213.0;406.0;562.0;... 1334.0;1410.0;140.0;2288.0;140.0;1194.0;1952.0... 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA 2661.55 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 41.0;787.0;969.0;36907.0;479.0;60.0;1426.0;30.... 223.0;12510.0;10322.0;251772.0;5557.0;500.0;99... 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA 2605.74 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;520.0;181.0;1338.0;294.0;20.0;232.0;10.0;1... 150.0;13418.0;3123.0;9325.0;2329.0;100.0;4328.... 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA 2708.53 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;541.0;294.0;1060.0;90.0;0.0;190.0;30.0;429... 50.0;5415.0;1984.0;6992.0;1344.0;60.0;1748.0;1... 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA 2795.06 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;702.0;334.0;386.0;241.0;10.0;212.0;20.0;29... 10.0;4454.0;1675.0;2411.0;1323.0;60.0;1121.0;1... 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA 2832.77 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;592.0;397.0;743.0;427.0;20.0;222.0;0.0;348... 30.0;10869.0;5111.0;8116.0;33319.0;271.0;6193.... 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA 2230.18 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 439.0;20367.0;40.0;19321.0;968.0;120.0;4323.0;... 3589.0;89094.0;571.0;85016.0;4040.0;965.0;2048... 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA 2317.38 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 224.0;847.0;10.0;582.0;30.0;50.0;295.0;531.0;5... 2071.0;5859.0;141.0;4805.0;321.0;503.0;2775.0;... 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA 2120.97 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 283.0;913.0;50.0;1597.0;60.0;50.0;643.0;937.0;... 4611.0;12157.0;330.0;11363.0;594.0;1098.0;5460... 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA 2291.53 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 397.0;263.0;50.0;520.0;162.0;80.0;441.0;296.0;... 4032.0;2661.0;580.0;6989.0;1362.0;732.0;6854.0... 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA 2538.15 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 306.0;233.0;30.0;510.0;40.0;213.0;406.0;562.0;... 1334.0;1410.0;140.0;2288.0;140.0;1194.0;1952.0... 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 28 columns] +[100 rows x 30 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-False].out index f117c36..e74c7ed 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 25 columns] +[100 rows x 28 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-True].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-True].out index 2520c48..6d221df 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-True].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-False-True].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_protein_experiment_wide m_score_protein_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0625 0.0625 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0625 0.0625 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0625 0.0625 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0625 0.0625 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0625 0.0625 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0625 0.0625 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0625 0.0625 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0625 0.0625 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0625 0.0625 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0625 0.0625 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_protein_experiment_wide m_score_protein_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0625 0.0625 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0625 0.0625 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0625 0.0625 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0625 0.0625 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0625 0.0625 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0625 0.0625 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0625 0.0625 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0625 0.0625 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0625 0.0625 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0625 0.0625 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 27 columns] +[100 rows x 30 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-True-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-True-False].out index 20406b3..bf6924f 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-True-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-False-True-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_peptide_experiment_wide m_score_peptide_global m_score_peptide_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0033 0.0033 0.0033 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0033 0.0033 0.0033 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0033 0.0033 0.0033 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0033 0.0033 0.0033 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0033 0.0033 0.0033 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0033 0.0033 0.0033 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0033 0.0033 0.0033 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0033 0.0033 0.0033 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0033 0.0033 0.0033 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0033 0.0033 0.0033 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_peptide_experiment_wide m_score_peptide_global m_score_peptide_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0033 0.0033 0.0033 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0033 0.0033 0.0033 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0033 0.0033 0.0033 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0033 0.0033 0.0033 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0033 0.0033 0.0033 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0033 0.0033 0.0033 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0033 0.0033 0.0033 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0033 0.0033 0.0033 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0033 0.0033 0.0033 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0033 0.0033 0.0033 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 28 columns] +[100 rows x 31 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-True-False-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-True-False-False].out index f8f9d27..a56e8c0 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-True-False-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[parquet-True-False-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 41.0;787.0;969.0;36907.0;479.0;60.0;1426.0;30.... 223.0;12510.0;10322.0;251772.0;5557.0;500.0;99... 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;520.0;181.0;1338.0;294.0;20.0;232.0;10.0;1... 150.0;13418.0;3123.0;9325.0;2329.0;100.0;4328.... 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;541.0;294.0;1060.0;90.0;0.0;190.0;30.0;429... 50.0;5415.0;1984.0;6992.0;1344.0;60.0;1748.0;1... 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;702.0;334.0;386.0;241.0;10.0;212.0;20.0;29... 10.0;4454.0;1675.0;2411.0;1323.0;60.0;1121.0;1... 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;592.0;397.0;743.0;427.0;20.0;222.0;0.0;348... 30.0;10869.0;5111.0;8116.0;33319.0;271.0;6193.... 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 439.0;20367.0;40.0;19321.0;968.0;120.0;4323.0;... 3589.0;89094.0;571.0;85016.0;4040.0;965.0;2048... 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 224.0;847.0;10.0;582.0;30.0;50.0;295.0;531.0;5... 2071.0;5859.0;141.0;4805.0;321.0;503.0;2775.0;... 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 283.0;913.0;50.0;1597.0;60.0;50.0;643.0;937.0;... 4611.0;12157.0;330.0;11363.0;594.0;1098.0;5460... 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 397.0;263.0;50.0;520.0;162.0;80.0;441.0;296.0;... 4032.0;2661.0;580.0;6989.0;1362.0;732.0;6854.0... 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 306.0;233.0;30.0;510.0;40.0;213.0;406.0;562.0;... 1334.0;1410.0;140.0;2288.0;140.0;1194.0;1952.0... 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 41.0;787.0;969.0;36907.0;479.0;60.0;1426.0;30.... 223.0;12510.0;10322.0;251772.0;5557.0;500.0;99... 117220.7500 854645.0 26.5 2595.5788 5.7301 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1.0 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;520.0;181.0;1338.0;294.0;20.0;232.0;10.0;1... 150.0;13418.0;3123.0;9325.0;2329.0;100.0;4328.... 8790.7810 104006.0 26.5 2595.5733 1.2404 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2.0 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;541.0;294.0;1060.0;90.0;0.0;190.0;30.0;429... 50.0;5415.0;1984.0;6992.0;1344.0;60.0;1748.0;1... 5750.4717 73215.2 26.5 2595.5750 0.8151 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3.0 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;702.0;334.0;386.0;241.0;10.0;212.0;20.0;29... 10.0;4454.0;1675.0;2411.0;1323.0;60.0;1121.0;1... 4036.5600 25862.3 26.5 2595.5754 0.6777 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4.0 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;592.0;397.0;743.0;427.0;20.0;222.0;0.0;348... 30.0;10869.0;5111.0;8116.0;33319.0;271.0;6193.... 10419.7430 241873.0 26.5 2595.5778 -0.1013 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5.0 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 439.0;20367.0;40.0;19321.0;968.0;120.0;4323.0;... 3589.0;89094.0;571.0;85016.0;4040.0;965.0;2048... 269150.5600 1192530.0 16.3 2245.2318 5.6532 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1.0 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 224.0;847.0;10.0;582.0;30.0;50.0;295.0;531.0;5... 2071.0;5859.0;141.0;4805.0;321.0;503.0;2775.0;... 9656.7600 89588.0 16.3 2245.2345 0.3846 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2.0 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 283.0;913.0;50.0;1597.0;60.0;50.0;643.0;937.0;... 4611.0;12157.0;330.0;11363.0;594.0;1098.0;5460... 10568.0810 85676.6 16.3 2245.2373 0.3343 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3.0 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 397.0;263.0;50.0;520.0;162.0;80.0;441.0;296.0;... 4032.0;2661.0;580.0;6989.0;1362.0;732.0;6854.0... 6480.8610 75465.1 16.3 2245.2345 -0.0155 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4.0 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 306.0;233.0;30.0;510.0;40.0;213.0;406.0;562.0;... 1334.0;1410.0;140.0;2288.0;140.0;1194.0;1952.0... 10810.2700 56553.9 16.3 2245.2307 -1.8782 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5.0 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 28 columns] +[100 rows x 31 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-False].out index 7540ce7..14d9122 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 25 columns] +[100 rows x 28 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-True].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-True].out index 13284eb..c237bc4 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-True].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-False-True].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_protein_experiment_wide m_score_protein_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0625 0.0625 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0625 0.0625 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0625 0.0625 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0625 0.0625 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0625 0.0625 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0625 0.0625 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0625 0.0625 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0625 0.0625 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0625 0.0625 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0625 0.0625 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_protein_experiment_wide m_score_protein_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0625 0.0625 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0625 0.0625 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0625 0.0625 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0625 0.0625 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0625 0.0625 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0625 0.0625 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0625 0.0625 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0625 0.0625 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0625 0.0625 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0625 0.0625 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 27 columns] +[100 rows x 30 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-True-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-True-False].out index e81a8b3..d33d347 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-True-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-False-True-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_peptide_experiment_wide m_score_peptide_global m_score_peptide_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0033 0.0033 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0033 0.0033 0.0033 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0033 0.0033 0.0033 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0033 0.0033 0.0033 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0033 0.0033 0.0033 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0033 0.0033 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0033 0.0033 0.0033 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0033 0.0033 0.0033 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0033 0.0033 0.0033 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0033 0.0033 0.0033 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score m_score_peptide_experiment_wide m_score_peptide_global m_score_peptide_run_specific mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 0.0033 0.0033 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 0.0033 0.0033 0.0033 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 0.0033 0.0033 0.0033 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 0.0033 0.0033 0.0033 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 0.0033 0.0033 0.0033 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 0.0033 0.0033 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 0.0033 0.0033 0.0033 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 0.0033 0.0033 0.0033 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 0.0033 0.0033 0.0033 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 0.0033 0.0033 0.0033 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 28 columns] +[100 rows x 31 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-True-False-False].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-True-False-False].out index 7d752c0..ea2540e 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-True-False-False].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_analysis[split_parquet-True-False-False].out @@ -1,14 +1,14 @@ - Charge FullPeptideName Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id -0 2 ADSTGTLVITDPTR(UniMod:267) 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 41.0;787.0;969.0;36907.0;479.0;60.0;1426.0;30.... 223.0;12510.0;10322.0;251772.0;5557.0;500.0;99... 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 -1 2 ADSTGTLVITDPTR(UniMod:267) 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;520.0;181.0;1338.0;294.0;20.0;232.0;10.0;1... 150.0;13418.0;3123.0;9325.0;2329.0;100.0;4328.... 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 -2 2 ADSTGTLVITDPTR(UniMod:267) 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;541.0;294.0;1060.0;90.0;0.0;190.0;30.0;429... 50.0;5415.0;1984.0;6992.0;1344.0;60.0;1748.0;1... 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 -3 2 ADSTGTLVITDPTR(UniMod:267) 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;702.0;334.0;386.0;241.0;10.0;212.0;20.0;29... 10.0;4454.0;1675.0;2411.0;1323.0;60.0;1121.0;1... 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 -4 2 ADSTGTLVITDPTR(UniMod:267) 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;592.0;397.0;743.0;427.0;20.0;222.0;0.0;348... 30.0;10869.0;5111.0;8116.0;33319.0;271.0;6193.... 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 VYVYAVDQTR(UniMod:267) 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 439.0;20367.0;40.0;19321.0;968.0;120.0;4323.0;... 3589.0;89094.0;571.0;85016.0;4040.0;965.0;2048... 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 -96 2 VYVYAVDQTR(UniMod:267) 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 224.0;847.0;10.0;582.0;30.0;50.0;295.0;531.0;5... 2071.0;5859.0;141.0;4805.0;321.0;503.0;2775.0;... 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 -97 2 VYVYAVDQTR(UniMod:267) 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 283.0;913.0;50.0;1597.0;60.0;50.0;643.0;937.0;... 4611.0;12157.0;330.0;11363.0;594.0;1098.0;5460... 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 -98 2 VYVYAVDQTR(UniMod:267) 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 397.0;263.0;50.0;520.0;162.0;80.0;441.0;296.0;... 4032.0;2661.0;580.0;6989.0;1362.0;732.0;6854.0... 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 -99 2 VYVYAVDQTR(UniMod:267) 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 306.0;233.0;30.0;510.0;40.0;213.0;406.0;562.0;... 1334.0;1410.0;140.0;2288.0;140.0;1194.0;1952.0... 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 + Charge EXP_IM FullPeptideName IM_leftWidth IM_rightWidth Intensity ProteinName RT Sequence aggr_Fragment_Annotation aggr_Peak_Apex aggr_Peak_Area aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_iRT assay_rt d_score decoy delta_iRT delta_rt filename iRT id leftWidth m_score mz peak_group_rank pep rightWidth run_id transition_group_id +0 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 207283.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2661.55 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 41.0;787.0;969.0;36907.0;479.0;60.0;1426.0;30.... 223.0;12510.0;10322.0;251772.0;5557.0;500.0;99... 117220.7482 854645.0 26.5 2595.5788 5.7301 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz 28.4379 -4409520928686189639 2640.5100 0.0033 728.8795 1 0.0031 2705.3701 -8670811102654834151 0 +1 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 6385.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2605.74 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;520.0;181.0;1338.0;294.0;20.0;232.0;10.0;1... 150.0;13418.0;3123.0;9325.0;2329.0;100.0;4328.... 8790.7812 104006.0 26.5 2595.5733 1.2404 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 26.8198 260819276075322832 2575.6399 0.0685 728.8795 2 1.0000 2623.4399 -8670811102654834151 0 +2 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 3838.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2708.53 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;541.0;294.0;1060.0;90.0;0.0;190.0;30.0;429... 50.0;5415.0;1984.0;6992.0;1344.0;60.0;1748.0;1... 5750.4716 73215.2 26.5 2595.5750 0.8151 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 29.8002 8534214264242363560 2705.3701 0.2018 728.8795 3 1.0000 2736.0901 -8670811102654834151 0 +3 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 2693.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2795.06 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;702.0;334.0;386.0;241.0;10.0;212.0;20.0;29... 10.0;4454.0;1675.0;2411.0;1323.0;60.0;1121.0;1... 4036.5600 25862.3 26.5 2595.5754 0.6777 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 32.3092 6932937885234622359 2790.7200 0.2018 728.8795 4 1.0000 2811.2000 -8670811102654834151 0 +4 2 NaN ADSTGTLVITDPTR(UniMod:267) NaN NaN 5180.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2832.77 ADSTGTLVITDPTR 1363_y6_2;1348_b8_2;1343_b4_1;1359_y3_1;1365_y... 0.0;592.0;397.0;743.0;427.0;20.0;222.0;0.0;348... 30.0;10869.0;5111.0;8116.0;33319.0;271.0;6193.... 10419.7435 241873.0 26.5 2595.5778 -0.1013 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 33.4026 5163914660633416481 2811.2000 0.4692 728.8795 5 1.0000 2855.5801 -8670811102654834151 0 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 597887.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2230.18 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 439.0;20367.0;40.0;19321.0;968.0;120.0;4323.0;... 3589.0;89094.0;571.0;85016.0;4040.0;965.0;2048... 269150.5777 1192530.0 16.3 2245.2318 5.6532 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 15.9300 6870255268859409918 2213.2600 0.0033 612.3184 1 0.0031 2247.3999 -8670811102654834151 19 +96 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 16553.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2317.38 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 224.0;847.0;10.0;582.0;30.0;50.0;295.0;531.0;5... 2071.0;5859.0;141.0;4805.0;321.0;503.0;2775.0;... 9656.7598 89588.0 16.3 2245.2345 0.3846 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 18.4584 6262215160571261022 2302.0200 0.2507 612.3184 2 1.0000 2332.7400 -8670811102654834151 19 +97 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 20746.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2120.97 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 283.0;913.0;50.0;1597.0;60.0;50.0;643.0;937.0;... 4611.0;12157.0;330.0;11363.0;594.0;1098.0;5460... 10568.0806 85676.6 16.3 2245.2373 0.3343 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz 12.7632 -610141049182829192 2100.6001 0.4000 612.3184 3 1.0000 2141.5701 -8670811102654834151 19 +98 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 48058.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2291.53 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 397.0;263.0;50.0;520.0;162.0;80.0;441.0;296.0;... 4032.0;2661.0;580.0;6989.0;1362.0;732.0;6854.0... 6480.8607 75465.1 16.3 2245.2345 -0.0155 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 17.7088 2043199813358518344 2267.8799 0.4692 612.3184 4 1.0000 2298.6101 -8670811102654834151 19 +99 2 NaN VYVYAVDQTR(UniMod:267) NaN NaN 10959.0 AQUA4SWATH_HMLangeA;AQUA4SWATH_HMLangeA;AQUA4S... 2538.15 VYVYAVDQTR 1817_y6_2;1803_b3_1;1808_b7_2;1813_y3_1;1819_y... 306.0;233.0;30.0;510.0;40.0;213.0;406.0;562.0;... 1334.0;1410.0;140.0;2288.0;140.0;1194.0;1952.0... 10810.2698 56553.9 16.3 2245.2307 -1.8782 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz 24.8599 -5430403952310232561 2520.5100 0.4692 612.3184 5 1.0000 2544.4099 -8670811102654834151 19 -[100 rows x 28 columns] +[100 rows x 31 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[osw].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[osw].out index 467460f..a54378c 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[osw].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[osw].out @@ -1,14 +1,14 @@ - Charge Intensity RT aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_RT assay_rt decoy delta_RT delta_rt filename id leftWidth mz rightWidth run_id transition_group_id var_ms1_isotope_correlation_score var_ms1_isotope_overlap_score var_ms1_massdev_score var_ms1_xcorr_coelution var_ms1_xcorr_shape var_ms2_bseries_score var_ms2_dotprod_score var_ms2_elution_model_fit_score var_ms2_intensity_score var_ms2_isotope_correlation_score var_ms2_isotope_overlap_score var_ms2_library_corr var_ms2_library_dotprod var_ms2_library_manhattan var_ms2_library_rmsd var_ms2_library_rootmeansquare var_ms2_library_sangle var_ms2_log_sn_score var_ms2_manhattan_score var_ms2_massdev_score var_ms2_massdev_score_weighted var_ms2_norm_rt_score var_ms2_sonar_lag var_ms2_sonar_log_diff var_ms2_sonar_log_sn var_ms2_sonar_log_trend var_ms2_sonar_rsq var_ms2_sonar_shape var_ms2_xcorr_coelution var_ms2_xcorr_coelution_weighted var_ms2_xcorr_shape var_ms2_xcorr_shape_weighted var_ms2_yseries_score -0 2 207283.0 2661.55 117220.7482 854645.0 26.5 2595.5788 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz -4409520928686189639 2640.5100 728.8795 2705.3701 -8670811102654834151 0 0.9835 0.1247 1.3707 0.0000 0.9907 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 -1 2 6385.0 2605.74 8790.7812 104006.0 26.5 2595.5733 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 260819276075322832 2575.6399 728.8795 2623.4399 -8670811102654834151 0 0.9555 0.2667 5.4202 5.1430 0.6532 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 -2 2 3838.0 2708.53 5750.4716 73215.2 26.5 2595.5750 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 8534214264242363560 2705.3701 728.8795 2736.0901 -8670811102654834151 0 -0.3692 0.7498 7.1610 6.7500 0.4827 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 -3 2 5180.0 2832.77 10419.7435 241873.0 26.5 2595.5778 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 5163914660633416481 2811.2000 728.8795 2855.5801 -8670811102654834151 0 0.6123 0.4707 8.9907 4.0083 0.5985 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 -4 2 2693.0 2795.06 4036.5600 25862.3 26.5 2595.5754 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 6932937885234622359 2790.7200 728.8795 2811.2000 -8670811102654834151 0 0.1872 2.4435 1.8505 4.0083 0.6422 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 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 597887.0 2230.18 269150.5777 1192530.0 16.3 2245.2318 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 6870255268859409918 2213.2600 612.3184 2247.3999 -8670811102654834151 19 0.9939 0.1300 2.0203 0.0000 0.9990 8.0 0.7684 NaN 0.6626 0.9928 0.0000 0.8658 0.9884 0.1569 0.0719 0.0725 0.2613 4.7826 0.7659 1.6355 1.5429 0.0037 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9992 0.9993 8.0 -96 2 48058.0 2291.53 6480.8607 75465.1 16.3 2245.2345 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 2043199813358518344 2267.8799 612.3184 2298.6101 -8670811102654834151 19 0.7397 3.0841 3.4962 5.3116 0.4407 5.0 0.6916 NaN 0.0533 0.7474 0.0866 -0.3525 0.8138 0.5478 0.2791 0.3394 1.0605 1.2194 0.8070 2.2562 2.3997 0.0141 NaN NaN NaN NaN NaN NaN 4.4101 1.9926 0.7236 0.7141 7.0 -97 2 16553.0 2317.38 9656.7598 89588.0 16.3 2245.2345 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 6262215160571261022 2302.0200 612.3184 2332.7400 -8670811102654834151 19 0.4212 0.8821 2.1071 7.7080 0.4296 4.0 0.7153 NaN 0.0183 0.0829 0.2014 -0.0107 0.9622 0.2794 0.1337 0.1370 0.5120 0.2548 0.7596 1.9435 1.6447 0.0216 NaN NaN NaN NaN NaN NaN 0.7830 0.1896 0.7600 0.7459 7.0 -98 2 20746.0 2120.97 10568.0806 85676.6 16.3 2245.2373 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz -610141049182829192 2100.6001 612.3184 2141.5701 -8670811102654834151 19 0.5016 0.9312 12.3692 1.8165 0.6723 4.0 0.7176 NaN 0.0230 0.6551 0.4036 0.5606 0.9754 0.2021 0.0921 0.1010 0.3719 0.7732 0.7428 4.7941 2.9011 0.0354 NaN NaN NaN NaN NaN NaN 2.5491 1.1289 0.8015 0.7928 5.0 -99 2 10959.0 2538.15 10810.2698 56553.9 16.3 2245.2307 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz -5430403952310232561 2520.5100 612.3184 2544.4099 -8670811102654834151 19 0.7016 0.5650 8.3246 1.8165 0.5954 2.0 0.6942 NaN 0.0121 0.4590 0.6792 -0.1524 0.9216 0.3502 0.1629 0.1915 0.6979 0.6856 0.7628 4.0046 4.4541 0.0856 NaN NaN NaN NaN NaN NaN 1.4718 0.6660 0.7586 0.6855 6.0 + Charge EXP_IM IM_leftWidth IM_rightWidth Intensity RT aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_RT assay_rt decoy delta_RT delta_rt filename id leftWidth mz rightWidth run_id transition_group_id var_ms1_isotope_correlation_score var_ms1_isotope_overlap_score var_ms1_massdev_score var_ms1_xcorr_coelution var_ms1_xcorr_shape var_ms2_bseries_score var_ms2_dotprod_score var_ms2_elution_model_fit_score var_ms2_intensity_score var_ms2_isotope_correlation_score var_ms2_isotope_overlap_score var_ms2_library_corr var_ms2_library_dotprod var_ms2_library_manhattan var_ms2_library_rmsd var_ms2_library_rootmeansquare var_ms2_library_sangle var_ms2_log_sn_score var_ms2_manhattan_score var_ms2_massdev_score var_ms2_massdev_score_weighted var_ms2_norm_rt_score var_ms2_sonar_lag var_ms2_sonar_log_diff var_ms2_sonar_log_sn var_ms2_sonar_log_trend var_ms2_sonar_rsq var_ms2_sonar_shape var_ms2_xcorr_coelution var_ms2_xcorr_coelution_weighted var_ms2_xcorr_shape var_ms2_xcorr_shape_weighted var_ms2_yseries_score +0 2 NaN NaN NaN 207283.0 2661.55 117220.7482 854645.0 26.5 2595.5788 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz -4409520928686189639 2640.5100 728.8795 2705.3701 -8670811102654834151 0 0.9835 0.1247 1.3707 0.0000 0.9907 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 +1 2 NaN NaN NaN 6385.0 2605.74 8790.7812 104006.0 26.5 2595.5733 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 260819276075322832 2575.6399 728.8795 2623.4399 -8670811102654834151 0 0.9555 0.2667 5.4202 5.1430 0.6532 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 +2 2 NaN NaN NaN 3838.0 2708.53 5750.4716 73215.2 26.5 2595.5750 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 8534214264242363560 2705.3701 728.8795 2736.0901 -8670811102654834151 0 -0.3692 0.7498 7.1610 6.7500 0.4827 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 +3 2 NaN NaN NaN 5180.0 2832.77 10419.7435 241873.0 26.5 2595.5778 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 5163914660633416481 2811.2000 728.8795 2855.5801 -8670811102654834151 0 0.6123 0.4707 8.9907 4.0083 0.5985 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 +4 2 NaN NaN NaN 2693.0 2795.06 4036.5600 25862.3 26.5 2595.5754 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 6932937885234622359 2790.7200 728.8795 2811.2000 -8670811102654834151 0 0.1872 2.4435 1.8505 4.0083 0.6422 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 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN NaN NaN 597887.0 2230.18 269150.5777 1192530.0 16.3 2245.2318 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 6870255268859409918 2213.2600 612.3184 2247.3999 -8670811102654834151 19 0.9939 0.1300 2.0203 0.0000 0.9990 8.0 0.7684 NaN 0.6626 0.9928 0.0000 0.8658 0.9884 0.1569 0.0719 0.0725 0.2613 4.7826 0.7659 1.6355 1.5429 0.0037 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9992 0.9993 8.0 +96 2 NaN NaN NaN 48058.0 2291.53 6480.8607 75465.1 16.3 2245.2345 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 2043199813358518344 2267.8799 612.3184 2298.6101 -8670811102654834151 19 0.7397 3.0841 3.4962 5.3116 0.4407 5.0 0.6916 NaN 0.0533 0.7474 0.0866 -0.3525 0.8138 0.5478 0.2791 0.3394 1.0605 1.2194 0.8070 2.2562 2.3997 0.0141 NaN NaN NaN NaN NaN NaN 4.4101 1.9926 0.7236 0.7141 7.0 +97 2 NaN NaN NaN 16553.0 2317.38 9656.7598 89588.0 16.3 2245.2345 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 6262215160571261022 2302.0200 612.3184 2332.7400 -8670811102654834151 19 0.4212 0.8821 2.1071 7.7080 0.4296 4.0 0.7153 NaN 0.0183 0.0829 0.2014 -0.0107 0.9622 0.2794 0.1337 0.1370 0.5120 0.2548 0.7596 1.9435 1.6447 0.0216 NaN NaN NaN NaN NaN NaN 0.7830 0.1896 0.7600 0.7459 7.0 +98 2 NaN NaN NaN 20746.0 2120.97 10568.0806 85676.6 16.3 2245.2373 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz -610141049182829192 2100.6001 612.3184 2141.5701 -8670811102654834151 19 0.5016 0.9312 12.3692 1.8165 0.6723 4.0 0.7176 NaN 0.0230 0.6551 0.4036 0.5606 0.9754 0.2021 0.0921 0.1010 0.3719 0.7732 0.7428 4.7941 2.9011 0.0354 NaN NaN NaN NaN NaN NaN 2.5491 1.1289 0.8015 0.7928 5.0 +99 2 NaN NaN NaN 10959.0 2538.15 10810.2698 56553.9 16.3 2245.2307 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz -5430403952310232561 2520.5100 612.3184 2544.4099 -8670811102654834151 19 0.7016 0.5650 8.3246 1.8165 0.5954 2.0 0.6942 NaN 0.0121 0.4590 0.6792 -0.1524 0.9216 0.3502 0.1629 0.1915 0.6979 0.6856 0.7628 4.0046 4.4541 0.0856 NaN NaN NaN NaN NaN NaN 1.4718 0.6660 0.7586 0.6855 6.0 -[100 rows x 50 columns] +[100 rows x 53 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[parquet].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[parquet].out index 3b20073..77a8a52 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[parquet].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[parquet].out @@ -1,14 +1,14 @@ - Charge Intensity RT aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_RT_1 assay_rt decoy delta_RT_1 delta_rt filename id leftWidth mz rightWidth run_id transition_group_id var_ms1__isotope_correlation_score var_ms1__isotope_overlap_score var_ms1__massdev_score var_ms1__xcorr_coelution var_ms1__xcorr_shape var_ms2__bseries_score var_ms2__dotprod_score var_ms2__elution_model_fit_score var_ms2__intensity_score var_ms2__isotope_correlation_score var_ms2__isotope_overlap_score var_ms2__library_corr var_ms2__library_dotprod var_ms2__library_manhattan var_ms2__library_rmsd var_ms2__library_rootmeansquare var_ms2__library_sangle var_ms2__log_sn_score var_ms2__manhattan_score var_ms2__massdev_score var_ms2__massdev_score_weighted var_ms2__norm_rt_score var_ms2__sonar_lag var_ms2__sonar_log_diff var_ms2__sonar_log_sn var_ms2__sonar_log_trend var_ms2__sonar_rsq var_ms2__sonar_shape var_ms2__xcorr_coelution var_ms2__xcorr_coelution_weighted var_ms2__xcorr_shape var_ms2__xcorr_shape_weighted var_ms2__yseries_score -0 2 207283.0 2661.55 117220.7500 854645.0 26.5 2595.5788 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz -4409520928686189639 2640.5100 728.8795 2705.3701 -8670811102654834151 0 0.9835 0.1247 1.3707 0.0000 0.9907 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 -1 2 5180.0 2832.77 10419.7430 241873.0 26.5 2595.5778 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 5163914660633416481 2811.2000 728.8795 2855.5801 -8670811102654834151 0 0.6123 0.4707 8.9907 4.0083 0.5985 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 -2 2 2693.0 2795.06 4036.5600 25862.3 26.5 2595.5754 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 6932937885234622359 2790.7200 728.8795 2811.2000 -8670811102654834151 0 0.1872 2.4435 1.8505 4.0083 0.6422 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 -3 2 6385.0 2605.74 8790.7810 104006.0 26.5 2595.5733 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 260819276075322832 2575.6399 728.8795 2623.4399 -8670811102654834151 0 0.9555 0.2667 5.4202 5.1430 0.6532 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 -4 2 3838.0 2708.53 5750.4717 73215.2 26.5 2595.5750 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 8534214264242363560 2705.3701 728.8795 2736.0901 -8670811102654834151 0 -0.3692 0.7498 7.1610 6.7500 0.4827 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 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 597887.0 2230.18 269150.5600 1192530.0 16.3 2245.2318 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 6870255268859409918 2213.2600 612.3184 2247.3999 -8670811102654834151 19 0.9939 0.1300 2.0203 0.0000 0.9990 8.0 0.7684 NaN 0.6626 0.9928 0.0000 0.8658 0.9884 0.1569 0.0719 0.0725 0.2613 4.7826 0.7659 1.6355 1.5429 0.0037 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9992 0.9993 8.0 -96 2 48058.0 2291.53 6480.8610 75465.1 16.3 2245.2345 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 2043199813358518344 2267.8799 612.3184 2298.6101 -8670811102654834151 19 0.7397 3.0841 3.4962 5.3116 0.4407 5.0 0.6916 NaN 0.0533 0.7474 0.0866 -0.3525 0.8138 0.5478 0.2791 0.3394 1.0605 1.2194 0.8070 2.2562 2.3997 0.0141 NaN NaN NaN NaN NaN NaN 4.4101 1.9926 0.7236 0.7141 7.0 -97 2 16553.0 2317.38 9656.7600 89588.0 16.3 2245.2345 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 6262215160571261022 2302.0200 612.3184 2332.7400 -8670811102654834151 19 0.4212 0.8821 2.1071 7.7080 0.4296 4.0 0.7153 NaN 0.0183 0.0829 0.2014 -0.0107 0.9622 0.2794 0.1337 0.1370 0.5120 0.2548 0.7596 1.9435 1.6447 0.0216 NaN NaN NaN NaN NaN NaN 0.7830 0.1896 0.7600 0.7459 7.0 -98 2 20746.0 2120.97 10568.0810 85676.6 16.3 2245.2373 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz -610141049182829192 2100.6001 612.3184 2141.5701 -8670811102654834151 19 0.5016 0.9312 12.3692 1.8165 0.6723 4.0 0.7176 NaN 0.0230 0.6551 0.4036 0.5606 0.9754 0.2021 0.0921 0.1010 0.3719 0.7732 0.7428 4.7941 2.9011 0.0354 NaN NaN NaN NaN NaN NaN 2.5491 1.1289 0.8015 0.7928 5.0 -99 2 10959.0 2538.15 10810.2700 56553.9 16.3 2245.2307 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz -5430403952310232561 2520.5100 612.3184 2544.4099 -8670811102654834151 19 0.7016 0.5650 8.3246 1.8165 0.5954 2.0 0.6942 NaN 0.0121 0.4590 0.6792 -0.1524 0.9216 0.3502 0.1629 0.1915 0.6979 0.6856 0.7628 4.0046 4.4541 0.0856 NaN NaN NaN NaN NaN NaN 1.4718 0.6660 0.7586 0.6855 6.0 + Charge EXP_IM IM_leftWidth IM_rightWidth Intensity RT aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_RT_1 assay_rt decoy delta_RT_1 delta_rt filename id leftWidth mz rightWidth run_id transition_group_id var_ms1__isotope_correlation_score var_ms1__isotope_overlap_score var_ms1__massdev_score var_ms1__xcorr_coelution var_ms1__xcorr_shape var_ms2__bseries_score var_ms2__dotprod_score var_ms2__elution_model_fit_score var_ms2__intensity_score var_ms2__isotope_correlation_score var_ms2__isotope_overlap_score var_ms2__library_corr var_ms2__library_dotprod var_ms2__library_manhattan var_ms2__library_rmsd var_ms2__library_rootmeansquare var_ms2__library_sangle var_ms2__log_sn_score var_ms2__manhattan_score var_ms2__massdev_score var_ms2__massdev_score_weighted var_ms2__norm_rt_score var_ms2__sonar_lag var_ms2__sonar_log_diff var_ms2__sonar_log_sn var_ms2__sonar_log_trend var_ms2__sonar_rsq var_ms2__sonar_shape var_ms2__xcorr_coelution var_ms2__xcorr_coelution_weighted var_ms2__xcorr_shape var_ms2__xcorr_shape_weighted var_ms2__yseries_score +0 2 NaN NaN NaN 207283.0 2661.55 117220.7500 854645.0 26.5 2595.5788 False 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz -4409520928686189639 2640.5100 728.8795 2705.3701 -8670811102654834151 0 0.9835 0.1247 1.3707 0.0000 0.9907 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 +1 2 NaN NaN NaN 5180.0 2832.77 10419.7430 241873.0 26.5 2595.5778 False 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 5163914660633416481 2811.2000 728.8795 2855.5801 -8670811102654834151 0 0.6123 0.4707 8.9907 4.0083 0.5985 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 +2 2 NaN NaN NaN 2693.0 2795.06 4036.5600 25862.3 26.5 2595.5754 False 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 6932937885234622359 2790.7200 728.8795 2811.2000 -8670811102654834151 0 0.1872 2.4435 1.8505 4.0083 0.6422 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 +3 2 NaN NaN NaN 6385.0 2605.74 8790.7810 104006.0 26.5 2595.5733 False 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 260819276075322832 2575.6399 728.8795 2623.4399 -8670811102654834151 0 0.9555 0.2667 5.4202 5.1430 0.6532 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 +4 2 NaN NaN NaN 3838.0 2708.53 5750.4717 73215.2 26.5 2595.5750 False 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 8534214264242363560 2705.3701 728.8795 2736.0901 -8670811102654834151 0 -0.3692 0.7498 7.1610 6.7500 0.4827 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 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN NaN NaN 597887.0 2230.18 269150.5600 1192530.0 16.3 2245.2318 False -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 6870255268859409918 2213.2600 612.3184 2247.3999 -8670811102654834151 19 0.9939 0.1300 2.0203 0.0000 0.9990 8.0 0.7684 NaN 0.6626 0.9928 0.0000 0.8658 0.9884 0.1569 0.0719 0.0725 0.2613 4.7826 0.7659 1.6355 1.5429 0.0037 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9992 0.9993 8.0 +96 2 NaN NaN NaN 48058.0 2291.53 6480.8610 75465.1 16.3 2245.2345 False 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 2043199813358518344 2267.8799 612.3184 2298.6101 -8670811102654834151 19 0.7397 3.0841 3.4962 5.3116 0.4407 5.0 0.6916 NaN 0.0533 0.7474 0.0866 -0.3525 0.8138 0.5478 0.2791 0.3394 1.0605 1.2194 0.8070 2.2562 2.3997 0.0141 NaN NaN NaN NaN NaN NaN 4.4101 1.9926 0.7236 0.7141 7.0 +97 2 NaN NaN NaN 16553.0 2317.38 9656.7600 89588.0 16.3 2245.2345 False 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 6262215160571261022 2302.0200 612.3184 2332.7400 -8670811102654834151 19 0.4212 0.8821 2.1071 7.7080 0.4296 4.0 0.7153 NaN 0.0183 0.0829 0.2014 -0.0107 0.9622 0.2794 0.1337 0.1370 0.5120 0.2548 0.7596 1.9435 1.6447 0.0216 NaN NaN NaN NaN NaN NaN 0.7830 0.1896 0.7600 0.7459 7.0 +98 2 NaN NaN NaN 20746.0 2120.97 10568.0810 85676.6 16.3 2245.2373 False -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz -610141049182829192 2100.6001 612.3184 2141.5701 -8670811102654834151 19 0.5016 0.9312 12.3692 1.8165 0.6723 4.0 0.7176 NaN 0.0230 0.6551 0.4036 0.5606 0.9754 0.2021 0.0921 0.1010 0.3719 0.7732 0.7428 4.7941 2.9011 0.0354 NaN NaN NaN NaN NaN NaN 2.5491 1.1289 0.8015 0.7928 5.0 +99 2 NaN NaN NaN 10959.0 2538.15 10810.2700 56553.9 16.3 2245.2307 False 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz -5430403952310232561 2520.5100 612.3184 2544.4099 -8670811102654834151 19 0.7016 0.5650 8.3246 1.8165 0.5954 2.0 0.6942 NaN 0.0121 0.4590 0.6792 -0.1524 0.9216 0.3502 0.1629 0.1915 0.6979 0.6856 0.7628 4.0046 4.4541 0.0856 NaN NaN NaN NaN NaN NaN 1.4718 0.6660 0.7586 0.6855 6.0 -[100 rows x 50 columns] +[100 rows x 53 columns] diff --git a/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[split_parquet].out b/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[split_parquet].out index c2a9bbd..7d8e360 100644 --- a/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[split_parquet].out +++ b/tests/_regtest_outputs/test_pyprophet_export.test_osw_unscored[split_parquet].out @@ -1,14 +1,14 @@ - Charge Intensity RT aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_RT_1 assay_rt decoy delta_RT_1 delta_rt filename id leftWidth mz rightWidth run_id transition_group_id var_ms1__isotope_correlation_score var_ms1__isotope_overlap_score var_ms1__massdev_score var_ms1__xcorr_coelution var_ms1__xcorr_shape var_ms2__bseries_score var_ms2__dotprod_score var_ms2__elution_model_fit_score var_ms2__intensity_score var_ms2__isotope_correlation_score var_ms2__isotope_overlap_score var_ms2__library_corr var_ms2__library_dotprod var_ms2__library_manhattan var_ms2__library_rmsd var_ms2__library_rootmeansquare var_ms2__library_sangle var_ms2__log_sn_score var_ms2__manhattan_score var_ms2__massdev_score var_ms2__massdev_score_weighted var_ms2__norm_rt_score var_ms2__sonar_lag var_ms2__sonar_log_diff var_ms2__sonar_log_sn var_ms2__sonar_log_trend var_ms2__sonar_rsq var_ms2__sonar_shape var_ms2__xcorr_coelution var_ms2__xcorr_coelution_weighted var_ms2__xcorr_shape var_ms2__xcorr_shape_weighted var_ms2__yseries_score -0 2 207283.0 2661.55 117220.7482 854645.0 26.5 2595.5788 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz -4409520928686189639 2640.5100 728.8795 2705.3701 -8670811102654834151 0 0.9835 0.1247 1.3707 0.0000 0.9907 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 -1 2 5180.0 2832.77 10419.7435 241873.0 26.5 2595.5778 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 5163914660633416481 2811.2000 728.8795 2855.5801 -8670811102654834151 0 0.6123 0.4707 8.9907 4.0083 0.5985 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 -2 2 2693.0 2795.06 4036.5600 25862.3 26.5 2595.5754 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 6932937885234622359 2790.7200 728.8795 2811.2000 -8670811102654834151 0 0.1872 2.4435 1.8505 4.0083 0.6422 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 -3 2 6385.0 2605.74 8790.7812 104006.0 26.5 2595.5733 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 260819276075322832 2575.6399 728.8795 2623.4399 -8670811102654834151 0 0.9555 0.2667 5.4202 5.1430 0.6532 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 -4 2 3838.0 2708.53 5750.4716 73215.2 26.5 2595.5750 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 8534214264242363560 2705.3701 728.8795 2736.0901 -8670811102654834151 0 -0.3692 0.7498 7.1610 6.7500 0.4827 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 -.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... -95 2 597887.0 2230.18 269150.5777 1192530.0 16.3 2245.2318 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 6870255268859409918 2213.2600 612.3184 2247.3999 -8670811102654834151 19 0.9939 0.1300 2.0203 0.0000 0.9990 8.0 0.7684 NaN 0.6626 0.9928 0.0000 0.8658 0.9884 0.1569 0.0719 0.0725 0.2613 4.7826 0.7659 1.6355 1.5429 0.0037 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9992 0.9993 8.0 -96 2 48058.0 2291.53 6480.8607 75465.1 16.3 2245.2345 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 2043199813358518344 2267.8799 612.3184 2298.6101 -8670811102654834151 19 0.7397 3.0841 3.4962 5.3116 0.4407 5.0 0.6916 NaN 0.0533 0.7474 0.0866 -0.3525 0.8138 0.5478 0.2791 0.3394 1.0605 1.2194 0.8070 2.2562 2.3997 0.0141 NaN NaN NaN NaN NaN NaN 4.4101 1.9926 0.7236 0.7141 7.0 -97 2 16553.0 2317.38 9656.7598 89588.0 16.3 2245.2345 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 6262215160571261022 2302.0200 612.3184 2332.7400 -8670811102654834151 19 0.4212 0.8821 2.1071 7.7080 0.4296 4.0 0.7153 NaN 0.0183 0.0829 0.2014 -0.0107 0.9622 0.2794 0.1337 0.1370 0.5120 0.2548 0.7596 1.9435 1.6447 0.0216 NaN NaN NaN NaN NaN NaN 0.7830 0.1896 0.7600 0.7459 7.0 -98 2 20746.0 2120.97 10568.0806 85676.6 16.3 2245.2373 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz -610141049182829192 2100.6001 612.3184 2141.5701 -8670811102654834151 19 0.5016 0.9312 12.3692 1.8165 0.6723 4.0 0.7176 NaN 0.0230 0.6551 0.4036 0.5606 0.9754 0.2021 0.0921 0.1010 0.3719 0.7732 0.7428 4.7941 2.9011 0.0354 NaN NaN NaN NaN NaN NaN 2.5491 1.1289 0.8015 0.7928 5.0 -99 2 10959.0 2538.15 10810.2698 56553.9 16.3 2245.2307 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz -5430403952310232561 2520.5100 612.3184 2544.4099 -8670811102654834151 19 0.7016 0.5650 8.3246 1.8165 0.5954 2.0 0.6942 NaN 0.0121 0.4590 0.6792 -0.1524 0.9216 0.3502 0.1629 0.1915 0.6979 0.6856 0.7628 4.0046 4.4541 0.0856 NaN NaN NaN NaN NaN NaN 1.4718 0.6660 0.7586 0.6855 6.0 + Charge EXP_IM IM_leftWidth IM_rightWidth Intensity RT aggr_prec_Peak_Apex aggr_prec_Peak_Area assay_RT_1 assay_rt decoy delta_RT_1 delta_rt filename id leftWidth mz rightWidth run_id transition_group_id var_ms1__isotope_correlation_score var_ms1__isotope_overlap_score var_ms1__massdev_score var_ms1__xcorr_coelution var_ms1__xcorr_shape var_ms2__bseries_score var_ms2__dotprod_score var_ms2__elution_model_fit_score var_ms2__intensity_score var_ms2__isotope_correlation_score var_ms2__isotope_overlap_score var_ms2__library_corr var_ms2__library_dotprod var_ms2__library_manhattan var_ms2__library_rmsd var_ms2__library_rootmeansquare var_ms2__library_sangle var_ms2__log_sn_score var_ms2__manhattan_score var_ms2__massdev_score var_ms2__massdev_score_weighted var_ms2__norm_rt_score var_ms2__sonar_lag var_ms2__sonar_log_diff var_ms2__sonar_log_sn var_ms2__sonar_log_trend var_ms2__sonar_rsq var_ms2__sonar_shape var_ms2__xcorr_coelution var_ms2__xcorr_coelution_weighted var_ms2__xcorr_shape var_ms2__xcorr_shape_weighted var_ms2__yseries_score +0 2 NaN NaN NaN 207283.0 2661.55 117220.7482 854645.0 26.5 2595.5788 0 1.9379 65.9712 napedro_L120420_010_SW.mzXML.gz -4409520928686189639 2640.5100 728.8795 2705.3701 -8670811102654834151 0 0.9835 0.1247 1.3707 0.0000 0.9907 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 +1 2 NaN NaN NaN 5180.0 2832.77 10419.7435 241873.0 26.5 2595.5778 0 6.9026 237.1922 napedro_L120420_010_SW.mzXML.gz 5163914660633416481 2811.2000 728.8795 2855.5801 -8670811102654834151 0 0.6123 0.4707 8.9907 4.0083 0.5985 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 +2 2 NaN NaN NaN 2693.0 2795.06 4036.5600 25862.3 26.5 2595.5754 0 5.8092 199.4846 napedro_L120420_010_SW.mzXML.gz 6932937885234622359 2790.7200 728.8795 2811.2000 -8670811102654834151 0 0.1872 2.4435 1.8505 4.0083 0.6422 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 +3 2 NaN NaN NaN 6385.0 2605.74 8790.7812 104006.0 26.5 2595.5733 0 0.3198 10.1667 napedro_L120420_010_SW.mzXML.gz 260819276075322832 2575.6399 728.8795 2623.4399 -8670811102654834151 0 0.9555 0.2667 5.4202 5.1430 0.6532 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 +4 2 NaN NaN NaN 3838.0 2708.53 5750.4716 73215.2 26.5 2595.5750 0 3.3002 112.9550 napedro_L120420_010_SW.mzXML.gz 8534214264242363560 2705.3701 728.8795 2736.0901 -8670811102654834151 0 -0.3692 0.7498 7.1610 6.7500 0.4827 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 +.. ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... +95 2 NaN NaN NaN 597887.0 2230.18 269150.5777 1192530.0 16.3 2245.2318 0 -0.3700 -15.0518 napedro_L120420_010_SW.mzXML.gz 6870255268859409918 2213.2600 612.3184 2247.3999 -8670811102654834151 19 0.9939 0.1300 2.0203 0.0000 0.9990 8.0 0.7684 NaN 0.6626 0.9928 0.0000 0.8658 0.9884 0.1569 0.0719 0.0725 0.2613 4.7826 0.7659 1.6355 1.5429 0.0037 NaN NaN NaN NaN NaN NaN 0.0000 0.0000 0.9992 0.9993 8.0 +96 2 NaN NaN NaN 48058.0 2291.53 6480.8607 75465.1 16.3 2245.2345 0 1.4088 46.2955 napedro_L120420_010_SW.mzXML.gz 2043199813358518344 2267.8799 612.3184 2298.6101 -8670811102654834151 19 0.7397 3.0841 3.4962 5.3116 0.4407 5.0 0.6916 NaN 0.0533 0.7474 0.0866 -0.3525 0.8138 0.5478 0.2791 0.3394 1.0605 1.2194 0.8070 2.2562 2.3997 0.0141 NaN NaN NaN NaN NaN NaN 4.4101 1.9926 0.7236 0.7141 7.0 +97 2 NaN NaN NaN 16553.0 2317.38 9656.7598 89588.0 16.3 2245.2345 0 2.1584 72.1455 napedro_L120420_010_SW.mzXML.gz 6262215160571261022 2302.0200 612.3184 2332.7400 -8670811102654834151 19 0.4212 0.8821 2.1071 7.7080 0.4296 4.0 0.7153 NaN 0.0183 0.0829 0.2014 -0.0107 0.9622 0.2794 0.1337 0.1370 0.5120 0.2548 0.7596 1.9435 1.6447 0.0216 NaN NaN NaN NaN NaN NaN 0.7830 0.1896 0.7600 0.7459 7.0 +98 2 NaN NaN NaN 20746.0 2120.97 10568.0806 85676.6 16.3 2245.2373 0 -3.5368 -124.2673 napedro_L120420_010_SW.mzXML.gz -610141049182829192 2100.6001 612.3184 2141.5701 -8670811102654834151 19 0.5016 0.9312 12.3692 1.8165 0.6723 4.0 0.7176 NaN 0.0230 0.6551 0.4036 0.5606 0.9754 0.2021 0.0921 0.1010 0.3719 0.7732 0.7428 4.7941 2.9011 0.0354 NaN NaN NaN NaN NaN NaN 2.5491 1.1289 0.8015 0.7928 5.0 +99 2 NaN NaN NaN 10959.0 2538.15 10810.2698 56553.9 16.3 2245.2307 0 8.5599 292.9193 napedro_L120420_010_SW.mzXML.gz -5430403952310232561 2520.5100 612.3184 2544.4099 -8670811102654834151 19 0.7016 0.5650 8.3246 1.8165 0.5954 2.0 0.6942 NaN 0.0121 0.4590 0.6792 -0.1524 0.9216 0.3502 0.1629 0.1915 0.6979 0.6856 0.7628 4.0046 4.4541 0.0856 NaN NaN NaN NaN NaN NaN 1.4718 0.6660 0.7586 0.6855 6.0 -[100 rows x 50 columns] +[100 rows x 53 columns]