Could not parse PSM from row: `{'peptidoform': 'FLLDNPYTHTYSYSC[UNIMOD:4]SGSAITC[UNIMOD:4]SSK/3', 'spectrum_id': 'controllerType=0 controllerNumber=1 scan=20427', 'run': 'S125.mzML', 'collection': '', 'is_decoy': 'False', 'score': '2.9572053911350387', 'qvalue': '0.00021482277121374866', 'pep': '5.146920190023498e-11', 'precursor_mz': '953.7585583654032', 'retention_time': '58.930706', 'ion_mobility': '', 'protein_list': "['sp|P04054|PA21B_HUMAN', 'tr|F8W062|F8W062_HUMAN']", 'rank': '1', 'source': 'sage', 'provenance:sage_filename': '/public/conode54/PRIDE_DATA/PXD017467/SAGE_v0.15.0-beta.1_metaprot/S125/results.sage.tsv', 'provenance:before_rescoring_score': '0.84745425', 'provenance:before_rescoring_qvalue': '0.00023261223', 'provenance:before_rescoring_pep': '', 'provenance:before_rescoring_rank': '1', 'meta:peptide_score': '2.9572053911350387', 'meta:peptide_qvalue': '0.00025031289111389235', 'meta:peptide_pep': '1.4215369598075943e-10', 'rescoring:expmass': '2858.2522', 'rescoring:calcmass': '2858.2524', 'rescoring:peptide_len': '25.0', 'rescoring:missed_cleavages': '0.0', 'rescoring:isotope_error': '0.0', 'rescoring:precursor_ppm': '-0.08541605', 'rescoring:fragment_ppm': '1.7353373', 'rescoring:hyperscore': '112.49561465256966', 'rescoring:delta_next': '70.73682215740779', 'rescoring:delta_best': '0.0', 'rescoring:delta_rt_model': '0.002063036', 'rescoring:aligned_rt': '0.4640213', 'rescoring:predicted_rt': '0.46195826', 'rescoring:matched_peaks': '37.0', 'rescoring:longest_b': '6.0', 'rescoring:longest_y': '22.0', 'rescoring:longest_y_pct': '0.88', 'rescoring:matched_intensity_pct': '48.41939', 'rescoring:scored_candidates': '8522.0', 'rescoring:poisson': '-25.52627202007773', 'rescoring:ms2_intensity': '12826951.0', 'rescoring:charge_n': '3', 'rescoring:charge_2': '0', 'rescoring:charge_3': '1', 'rescoring:charge_4': '0', 'rescoring:charge_5': '0', 'rescoring:charge_6': '0', 'rescoring:charge_7': '0', 'rescoring:charge_8': '0', 'rescoring:abs_ms1_error_ppm': '0.1908999718867049', 'rescoring:search_engine_score': '0.84745425', 'rescoring:theoretical_mass': '2858.2543919133236', 'rescoring:experimental_mass': '2858.2538456957736', 'rescoring:mass_error': '-0.0005462175499815203', 'rescoring:pep_len': '25', 'rescoring:spec_pearson_norm': '0.41176846903453584', 'rescoring:ionb_pearson_norm': '0.8770021168585164', 'rescoring:iony_pearson_norm': '0.13635298969485898', 'rescoring:spec_mse_norm': '3.6064644', 'rescoring:ionb_mse_norm': '0.5797898', 'rescoring:iony_mse_norm': '6.633139', 'rescoring:min_abs_diff_norm': '0.0', 'rescoring:max_abs_diff_norm': '4.561179', 'rescoring:abs_diff_Q1_norm': '0.0160219669342041', 'rescoring:abs_diff_Q2_norm': '0.6835975646972656', 'rescoring:abs_diff_Q3_norm': '2.23032808303833', 'rescoring:mean_abs_diff_norm': '1.2642136', 'rescoring:std_abs_diff_norm': '1.4171199', 'rescoring:ionb_min_abs_diff_norm': '0.0', 'rescoring:ionb_max_abs_diff_norm': '1.7314601', 'rescoring:ionb_abs_diff_Q1_norm': '0.0', 'rescoring:ionb_abs_diff_Q2_norm': '0.20105409622192383', 'rescoring:ionb_abs_diff_Q3_norm': '1.0487935543060303', 'rescoring:ionb_mean_abs_diff_norm': '0.4999725', 'rescoring:ionb_std_abs_diff_norm': '0.5742972', 'rescoring:iony_min_abs_diff_norm': '0.0', 'rescoring:iony_max_abs_diff_norm': '4.561179', 'rescoring:iony_abs_diff_Q1_norm': '0.07674789428710938', 'rescoring:iony_abs_diff_Q2_norm': '2.3137617111206055', 'rescoring:iony_abs_diff_Q3_norm': '3.6162989139556885', 'rescoring:iony_mean_abs_diff_norm': '2.0284545', 'rescoring:iony_std_abs_diff_norm': '1.5869817', 'rescoring:dotprod_norm': '3793.8372', 'rescoring:dotprod_ionb_norm': '2041.9648', 'rescoring:dotprod_iony_norm': '1751.8724', 'rescoring:cos_norm': '0.9841335', 'rescoring:cos_ionb_norm': '0.99780524', 'rescoring:cos_iony_norm': '0.9737345', 'rescoring:spec_pearson': '0.4075273035417464', 'rescoring:ionb_pearson': '0.9715361377308136', 'rescoring:iony_pearson': '0.08303439472257342', 'rescoring:spec_spearman': '0.5942017236284886', 'rescoring:ionb_spearman': '0.8769619065815095', 'rescoring:iony_spearman': '0.4309882163304796', 'rescoring:spec_mse': '7.106519e-05', 'rescoring:ionb_mse': '2.3426217e-06', 'rescoring:iony_mse': '0.00013978775', 'rescoring:min_abs_diff_iontype': '0', 'rescoring:max_abs_diff_iontype': '1', 'rescoring:min_abs_diff': '0.0', 'rescoring:max_abs_diff': '0.027292702', 'rescoring:abs_diff_Q1': '1.1167983757331967e-05', 'rescoring:abs_diff_Q2': '0.0011718226014636457', 'rescoring:abs_diff_Q3': '0.004071362316608429', 'rescoring:mean_abs_diff': '0.00444896', 'rescoring:std_abs_diff': '0.007160443', 'rescoring:ionb_min_abs_diff': '0.0', 'rescoring:ionb_max_abs_diff': '0.0037855804', 'rescoring:ionb_abs_diff_Q1': '0.0', 'rescoring:ionb_abs_diff_Q2': '0.0003011640510521829', 'rescoring:ionb_abs_diff_Q3': '0.0015936261625029147', 'rescoring:ionb_mean_abs_diff': '0.0009635142', 'rescoring:ionb_std_abs_diff': '0.0011892274', 'rescoring:iony_min_abs_diff': '0.0', 'rescoring:iony_max_abs_diff': '0.027292702', 'rescoring:iony_abs_diff_Q1': '0.0001691115612629801', 'rescoring:iony_abs_diff_Q2': '0.004288671771064401', 'rescoring:iony_abs_diff_Q3': '0.012014004169031978', 'rescoring:iony_mean_abs_diff': '0.007934406', 'rescoring:iony_std_abs_diff': '0.008765441', 'rescoring:dotprod': '0.0008882334', 'rescoring:dotprod_ionb': '0.0007298068', 'rescoring:dotprod_iony': '0.00015842658', 'rescoring:cos': '0.47489032', 'rescoring:cos_ionb': '0.96307445', 'rescoring:cos_iony': '0.36226457', 'rescoring:observed_retention_time': '58.930706', 'rescoring:predicted_retention_time': '60.47186694662293', 'rescoring:rt_diff': '1.5411609466229308', 'rescoring:observed_retention_time_best': '58.930706', 'rescoring:predicted_retention_time_best': '60.47186694662293', 'rescoring:rt_diff_best': '1.5411609466229308'}`
Could not parse PSM from row: `{'peptidoform': 'SGGGGDIHQGFQSLLTEVNK/3', 'spectrum_id': 'controllerType=0 controllerNumber=1 scan=20798', 'run': 'S125.mzML', 'collection': '', 'is_decoy': 'False', 'score': '2.8332554673605084', 'qvalue': '0.00021482277121374866', 'pep': '1.275577482626966e-10', 'precursor_mz': '682.0081583654033', 'retention_time': '59.916965', 'ion_mobility': '', 'protein_list': "['sp|P35237|SPB6_HUMAN', 'tr|A0A024QZX5|A0A024QZX5_HUMAN', 'tr|A0A087X1N8|A0A087X1N8_HUMAN', 'tr|A0A2R8Y6A7|A0A2R8Y6A7_HUMAN', 'tr|A0A2R8YD12|A0A2R8YD12_HUMAN']", 'rank': '1', 'source': 'sage', 'provenance:sage_filename': '/public/conode54/PRIDE_DATA/PXD017467/SAGE_v0.15.0-beta.1_metaprot/S125/results.sage.tsv', 'provenance:before_rescoring_score': '0.75979227', 'provenance:before_rescoring_qvalue': '0.00023261223', 'provenance:before_rescoring_pep': '', 'provenance:before_rescoring_rank': '1', 'meta:peptide_score': '2.8332554673605084', 'meta:peptide_qvalue': '0.00025031289111389235', 'meta:peptide_pep': '3.3869088227872117e-10', 'rescoring:expmass': '2043.001', 'rescoring:calcmass': '2043.0022', 'rescoring:peptide_len': '20.0', 'rescoring:missed_cleavages': '0.0', 'rescoring:isotope_error': '0.0', 'rescoring:precursor_ppm': '-0.59750473', 'rescoring:fragment_ppm': '1.2863699', 'rescoring:hyperscore': '89.82319038790175', 'rescoring:delta_next': '52.446143404365536', 'rescoring:delta_best': '0.0', 'rescoring:delta_rt_model': '0.0459615', 'rescoring:aligned_rt': '0.47178712', 'rescoring:predicted_rt': '0.42582563', 'rescoring:matched_peaks': '31.0', 'rescoring:longest_b': '8.0', 'rescoring:longest_y': '18.0', 'rescoring:longest_y_pct': '0.9', 'rescoring:matched_intensity_pct': '57.948303', 'rescoring:scored_candidates': '38796.0', 'rescoring:poisson': '-27.440751494204765', 'rescoring:ms2_intensity': '2815706.5', 'rescoring:charge_n': '3', 'rescoring:charge_2': '0', 'rescoring:charge_3': '1', 'rescoring:charge_4': '0', 'rescoring:charge_5': '0', 'rescoring:charge_6': '0', 'rescoring:charge_7': '0', 'rescoring:charge_8': '0', 'rescoring:abs_ms1_error_ppm': '0.5531489030157593', 'rescoring:search_engine_score': '0.75979227', 'rescoring:theoretical_mass': '2043.003777452594', 'rescoring:experimental_mass': '2043.0026456957742', 'rescoring:mass_error': '-0.0011317568198592198', 'rescoring:pep_len': '20', 'rescoring:spec_pearson_norm': '0.910760446395035', 'rescoring:ionb_pearson_norm': '0.9293791611764727', 'rescoring:iony_pearson_norm': '0.9037716798843634', 'rescoring:spec_mse_norm': '1.2809498', 'rescoring:ionb_mse_norm': '1.0397781', 'rescoring:iony_mse_norm': '1.5221218', 'rescoring:min_abs_diff_norm': '0.0', 'rescoring:max_abs_diff_norm': '2.2099862', 'rescoring:abs_diff_Q1_norm': '0.03599715232849121', 'rescoring:abs_diff_Q2_norm': '0.7622203826904297', 'rescoring:abs_diff_Q3_norm': '1.4571452140808105', 'rescoring:mean_abs_diff_norm': '0.860406', 'rescoring:std_abs_diff_norm': '0.73529005', 'rescoring:ionb_min_abs_diff_norm': '0.0013017654', 'rescoring:ionb_max_abs_diff_norm': '1.7479038', 'rescoring:ionb_abs_diff_Q1_norm': '0.06224393844604492', 'rescoring:ionb_abs_diff_Q2_norm': '0.6541690826416016', 'rescoring:ionb_abs_diff_Q3_norm': '1.4193768501281738', 'rescoring:ionb_mean_abs_diff_norm': '0.78739315', 'rescoring:ionb_std_abs_diff_norm': '0.6479121', 'rescoring:iony_min_abs_diff_norm': '0.0', 'rescoring:iony_max_abs_diff_norm': '2.2099862', 'rescoring:iony_abs_diff_Q1_norm': '0.012955665588378906', 'rescoring:iony_abs_diff_Q2_norm': '0.7855844497680664', 'rescoring:iony_abs_diff_Q3_norm': '1.5957486629486084', 'rescoring:iony_mean_abs_diff_norm': '0.93341887', 'rescoring:iony_std_abs_diff_norm': '0.8067534', 'rescoring:dotprod_norm': '2676.7527', 'rescoring:dotprod_ionb_norm': '1449.67', 'rescoring:dotprod_iony_norm': '1227.083', 'rescoring:cos_norm': '0.9942359', 'rescoring:cos_ionb_norm': '0.99588186', 'rescoring:cos_iony_norm': '0.99237776', 'rescoring:spec_pearson': '0.8376676013502923', 'rescoring:ionb_pearson': '0.9641323719935002', 'rescoring:iony_pearson': '0.8020847760154302', 'rescoring:spec_spearman': '0.9225440633748869', 'rescoring:ionb_spearman': '0.921155373492619', 'rescoring:iony_spearman': '0.9208629798824227', 'rescoring:spec_mse': '0.000116645104', 'rescoring:ionb_mse': '2.6876502e-05', 'rescoring:iony_mse': '0.00020641368', 'rescoring:min_abs_diff_iontype': '1', 'rescoring:max_abs_diff_iontype': '1', 'rescoring:min_abs_diff': '0.0', 'rescoring:max_abs_diff': '0.046071827', 'rescoring:abs_diff_Q1': '2.5274493964388967e-05', 'rescoring:abs_diff_Q2': '0.0023476206697523594', 'rescoring:abs_diff_Q3': '0.005975590436719358', 'rescoring:mean_abs_diff': '0.0054772515', 'rescoring:std_abs_diff': '0.009308319', 'rescoring:ionb_min_abs_diff': '9.026844e-07', 'rescoring:ionb_max_abs_diff': '0.018601516', 'rescoring:ionb_abs_diff_Q1': '4.414957948029041e-05', 'rescoring:ionb_abs_diff_Q2': '0.0010216772789135575', 'rescoring:ionb_abs_diff_Q3': '0.003766025649383664', 'rescoring:ionb_mean_abs_diff': '0.0029510926', 'rescoring:ionb_std_abs_diff': '0.004262341', 'rescoring:iony_min_abs_diff': '0.0', 'rescoring:iony_max_abs_diff': '0.046071827', 'rescoring:iony_abs_diff_Q1': '9.02422470971942e-06', 'rescoring:iony_abs_diff_Q2': '0.003311329986900091', 'rescoring:iony_abs_diff_Q3': '0.007248033070936799', 'rescoring:iony_mean_abs_diff': '0.008003411', 'rescoring:iony_std_abs_diff': '0.011931432', 'rescoring:dotprod': '0.0028044768', 'rescoring:dotprod_ionb': '0.00031696752', 'rescoring:dotprod_iony': '0.002487509', 'rescoring:cos': '0.8855172', 'rescoring:cos_ionb': '0.97616076', 'rescoring:cos_iony': '0.8761408', 'rescoring:observed_retention_time': '59.916965', 'rescoring:predicted_retention_time': '61.663453635700805', 'rescoring:rt_diff': '1.746488635700807', 'rescoring:observed_retention_time_best': '59.916965', 'rescoring:predicted_retention_time_best': '61.663453635700805', 'rescoring:rt_diff_best': '1.746488635700807'}`
Could not parse PSM from row: `{'peptidoform': 'HSYTASYDIYDLNKR/3', 'spectrum_id': 'controllerType=0 controllerNumber=1 scan=14202', 'run': 'S125.mzML', 'collection': '', 'is_decoy': 'False', 'score': '2.526217973536679', 'qvalue': '0.00021482277121374866', 'pep': '1.2080439560140989e-09', 'precursor_mz': '615.9640583654033', 'retention_time': '42.379105', 'ion_mobility': '', 'protein_list': "['sp|P27487|DPP4_HUMAN', 'tr|A0A7I2V2I2|A0A7I2V2I2_HUMAN', 'tr|A0A7I2V2R5|A0A7I2V2R5_HUMAN', 'tr|A0A7I2V2X8|A0A7I2V2X8_HUMAN', 'tr|F8WE17|F8WE17_HUMAN']", 'rank': '1', 'source': 'sage', 'provenance:sage_filename': '/public/conode54/PRIDE_DATA/PXD017467/SAGE_v0.15.0-beta.1_metaprot/S125/results.sage.tsv', 'provenance:before_rescoring_score': '0.75256574', 'provenance:before_rescoring_qvalue': '0.00023261223', 'provenance:before_rescoring_pep': '', 'provenance:before_rescoring_rank': '1', 'meta:peptide_score': '2.526217973536679', 'meta:peptide_qvalue': '0.00025031289111389235', 'meta:peptide_pep': '2.9092832161275775e-09', 'rescoring:expmass': '1844.8687', 'rescoring:calcmass': '1844.8694', 'rescoring:peptide_len': '15.0', 'rescoring:missed_cleavages': '1.0', 'rescoring:isotope_error': '0.0', 'rescoring:precursor_ppm': '-0.3970048', 'rescoring:fragment_ppm': '0.919254', 'rescoring:hyperscore': '88.12938410605383', 'rescoring:delta_next': '47.856982096219454', 'rescoring:delta_best': '0.0', 'rescoring:delta_rt_model': '0.00078237057', 'rescoring:aligned_rt': '0.33369374', 'rescoring:predicted_rt': '0.33291137', 'rescoring:matched_peaks': '30.0', 'rescoring:longest_b': '8.0', 'rescoring:longest_y': '13.0', 'rescoring:longest_y_pct': '0.8666667', 'rescoring:matched_intensity_pct': '35.734142', 'rescoring:scored_candidates': '22757.0', 'rescoring:poisson': '-25.830992151500485', 'rescoring:ms2_intensity': '2615455.0', 'rescoring:charge_n': '3', 'rescoring:charge_2': '0', 'rescoring:charge_3': '1', 'rescoring:charge_4': '0', 'rescoring:charge_5': '0', 'rescoring:charge_6': '0', 'rescoring:charge_7': '0', 'rescoring:charge_8': '0', 'rescoring:abs_ms1_error_ppm': '0.3391333737134869', 'rescoring:search_engine_score': '0.75256574', 'rescoring:theoretical_mass': '1844.870972377894', 'rescoring:experimental_mass': '1844.870345695774', 'rescoring:mass_error': '-0.0006266821201279527', 'rescoring:pep_len': '15', 'rescoring:spec_pearson_norm': '0.9211873388502895', 'rescoring:ionb_pearson_norm': '0.9312531115434698', 'rescoring:iony_pearson_norm': '0.9266800443281002', 'rescoring:spec_mse_norm': '0.6551733', 'rescoring:ionb_mse_norm': '0.7134226', 'rescoring:iony_mse_norm': '0.596924', 'rescoring:min_abs_diff_norm': '0.01346302', 'rescoring:max_abs_diff_norm': '1.6076927', 'rescoring:abs_diff_Q1_norm': '0.13090264797210693', 'rescoring:abs_diff_Q2_norm': '0.44056224822998047', 'rescoring:abs_diff_Q3_norm': '1.0282604694366455', 'rescoring:mean_abs_diff_norm': '0.6026467', 'rescoring:std_abs_diff_norm': '0.54036134', 'rescoring:ionb_min_abs_diff_norm': '0.01346302', 'rescoring:ionb_max_abs_diff_norm': '1.6076927', 'rescoring:ionb_abs_diff_Q1_norm': '0.12889623641967773', 'rescoring:ionb_abs_diff_Q2_norm': '0.4005255699157715', 'rescoring:ionb_abs_diff_Q3_norm': '0.9863555431365967', 'rescoring:ionb_mean_abs_diff_norm': '0.61105007', 'rescoring:ionb_std_abs_diff_norm': '0.58312976', 'rescoring:iony_min_abs_diff_norm': '0.022177696', 'rescoring:iony_max_abs_diff_norm': '1.4913979', 'rescoring:iony_abs_diff_Q1_norm': '0.1476057767868042', 'rescoring:iony_abs_diff_Q2_norm': '0.44056224822998047', 'rescoring:iony_abs_diff_Q3_norm': '0.9950416088104248', 'rescoring:iony_mean_abs_diff_norm': '0.5942431', 'rescoring:iony_std_abs_diff_norm': '0.49376026', 'rescoring:dotprod_norm': '1826.4756', 'rescoring:dotprod_ionb_norm': '997.2679', 'rescoring:dotprod_iony_norm': '829.20764', 'rescoring:cos_norm': '0.9961801', 'rescoring:cos_ionb_norm': '0.9962752', 'rescoring:cos_iony_norm': '0.9960694', 'rescoring:spec_pearson': '0.8402039927026685', 'rescoring:ionb_pearson': '0.842033929435886', 'rescoring:iony_pearson': '0.8679565771477882', 'rescoring:spec_spearman': '0.9382519123417841', 'rescoring:ionb_spearman': '0.9756157806107449', 'rescoring:iony_spearman': '0.9514441515604878', 'rescoring:spec_mse': '6.343032e-05', 'rescoring:ionb_mse': '5.9857495e-05', 'rescoring:iony_mse': '6.7003144e-05', 'rescoring:min_abs_diff_iontype': '0', 'rescoring:max_abs_diff_iontype': '1', 'rescoring:min_abs_diff': '9.375508e-06', 'rescoring:max_abs_diff': '0.027109118', 'rescoring:abs_diff_Q1': '0.00022254808573052287', 'rescoring:abs_diff_Q2': '0.00153104099445045', 'rescoring:abs_diff_Q3': '0.004575862199999392', 'rescoring:mean_abs_diff': '0.0041583027', 'rescoring:std_abs_diff': '0.0067925574', 'rescoring:ionb_min_abs_diff': '9.375508e-06', 'rescoring:ionb_max_abs_diff': '0.025847232', 'rescoring:ionb_abs_diff_Q1': '0.00022654057829640806', 'rescoring:ionb_abs_diff_Q2': '0.000960308185312897', 'rescoring:ionb_abs_diff_Q3': '0.0036672039423137903', 'rescoring:ionb_mean_abs_diff': '0.003679257', 'rescoring:ionb_std_abs_diff': '0.006805921', 'rescoring:iony_min_abs_diff': '1.5491154e-05', 'rescoring:iony_max_abs_diff': '0.027109118', 'rescoring:iony_abs_diff_Q1': '0.0006274663319345564', 'rescoring:iony_abs_diff_Q2': '0.0024233314907178283', 'rescoring:iony_abs_diff_Q3': '0.004654044983908534', 'rescoring:iony_mean_abs_diff': '0.004637348', 'rescoring:iony_std_abs_diff': '0.0067452323', 'rescoring:dotprod': '0.0034486693', 'rescoring:dotprod_ionb': '0.0006779208', 'rescoring:dotprod_iony': '0.0027707485', 'rescoring:cos': '0.89578646', 'rescoring:cos_ionb': '0.89138514', 'rescoring:cos_iony': '0.921435', 'rescoring:observed_retention_time': '42.379105', 'rescoring:predicted_retention_time': '42.25716830430793', 'rescoring:rt_diff': '0.12193669569207088', 'rescoring:observed_retention_time_best': '42.379105', 'rescoring:predicted_retention_time_best': '42.25716830430793', 'rescoring:rt_diff_best': '0.12193669569207088'}`
---------------------------------------------------------------------------
ValidationError Traceback (most recent call last)
File ~/vcs/psm_utils/psm_utils/io/tsv.py:81, in TSVReader.__iter__(self)
80 try:
---> 81 yield PSM(**self._parse_entry(row))
82 except ValidationError as e:
File ~/vcs/psm_utils/psm_utils/psm.py:103, in PSM.__init__(self, **data)
48 """
49 Initialize a peptide-spectrum match (PSM).
50
(...) 101
102 """
--> 103 super().__init__(**data)
File ~/vcs/psm_utils/.venv/lib/python3.13/site-packages/pydantic/main.py:263, in BaseModel.__init__(self, **data)
262 __tracebackhide__ = True
--> 263 validated_self = self.__pydantic_validator__.validate_python(data, self_instance=self)
264 if self is not validated_self:
ValidationError: 1 validation error for PSM
provenance_data.before_rescoring_pep
Input should be a valid string [type=string_type, input_value=None, input_type=NoneType]
For further information visit https://errors.pydantic.dev/2.13/v/string_type
The above exception was the direct cause of the following exception:
PSMUtilsIOException Traceback (most recent call last)
Cell In[2], line 1
----> 1 psm_utils.io.read_file("/public/conode54/PRIDE_DATA/PXD017467/MS2RESCORE_v3.2.0-alpha-aee8ec7-b1_metaprot/S125/results.sage.ms2rescore.psms.tsv")
File ~/vcs/psm_utils/psm_utils/io/__init__.py:279, in read_file(filename, filetype, *args, **kwargs)
275 raise PSMUtilsIOException(
276 f"Filetype '{filetype}' unknown or not supported for reading."
277 ) from e
278 reader = reader_cls(filename, *args, **kwargs)
--> 279 psm_list = reader.read_file()
280 return psm_list
File ~/vcs/psm_utils/psm_utils/io/_base_classes.py:55, in ReaderBase.read_file(self)
53 def read_file(self) -> PSMList:
54 """Read full PSM file into a PSMList object."""
---> 55 return PSMList(psm_list=[psm for psm in self.__iter__()])
File ~/vcs/psm_utils/psm_utils/io/tsv.py:86, in TSVReader.__iter__(self)
84 logger.warning(f"Could not parse PSM from row: `{row}`")
85 if failed_rows >= 3:
---> 86 raise PSMUtilsIOException(
87 "Could not parse PSM from three consecutive rows. Verify that the "
88 "file is formatted correctly as a psm_utils TSV file or that the "
89 "correct file type reader is used."
90 ) from e
91 else:
92 failed_rows = 0
PSMUtilsIOException: Could not parse PSM from three consecutive rows. Verify that the file is formatted correctly as a psm_utils TSV file or that the correct file type reader is used.
In 4044a55, a regression was introduced, causing issues when trying to read MS2Rescore result files (specifically commit aee8ec7, CompOmics/ms2rescore#178).
Code to reproduce:
Resulting exception:
results.sage.ms2rescore.psms.tsv.gz