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PyProphet / pyprophet

PyProphet: Semi-supervised learning and scoring of OpenSWATH results.
http://www.openswath.org
BSD 3-Clause "New" or "Revised" License
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pyprophet ipf error #88

Closed summerghw closed 3 years ago

summerghw commented 4 years ago

Hi, when i try to use pyprophet, this error appear: root@61d6818b7369:/data/ftp.peptideatlas.org# pyprophet ipf --in=merged.osw Info: Starting IPF (Inference of PeptidoForms). Info: Reading precursor-level data. Info: Preparing precursor-level data. Info: Conducting precursor-level inference. Traceback (most recent call last): File "/usr/local/bin/pyprophet", line 10, in <module> sys.exit(cli()) File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 764, in __call__ return self.main(*args, **kwargs) File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 1163, in invoke rv.append(sub_ctx.command.invoke(sub_ctx)) File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, **ctx.params) File "/usr/local/lib/python3.5/dist-packages/click/core.py", line 555, in invoke return callback(*args, **kwargs) File "/usr/local/lib/python3.5/dist-packages/pyprophet/main.py", line 122, in ipf infer_peptidoforms(infile, outfile, ipf_ms1_scoring, ipf_ms2_scoring, ipf_h0, ipf_grouped_fdr, ipf_max_precursor_pep, ipf_max_peakgroup_pep, ipf_max_precursor_peakgroup_pep, ipf_max_transition_pep) File "/usr/local/lib/python3.5/dist-packages/pyprophet/ipf.py", line 366, in infer_peptidoforms precursor_data = precursor_inference(precursor_table, ipf_ms1_scoring, ipf_ms2_scoring, ipf_max_precursor_pep, ipf_max_precursor_peakgroup_pep) File "/usr/local/lib/python3.5/dist-packages/pyprophet/ipf.py", line 323, in precursor_inference prec_pp_data = apply_bm(precursor_data_bm) File "/usr/local/lib/python3.5/dist-packages/pyprophet/ipf.py", line 284, in apply_bm pp_data.columns = ['feature_id','hypothesis','likelihood_prior'] File "/usr/local/lib/python3.5/dist-packages/pandas/core/generic.py", line 5080, in __setattr__ return object.__setattr__(self, name, value) File "pandas/_libs/properties.pyx", line 69, in pandas._libs.properties.AxisProperty.__set__ File "/usr/local/lib/python3.5/dist-packages/pandas/core/generic.py", line 638, in _set_axis self._data.set_axis(axis, labels) File "/usr/local/lib/python3.5/dist-packages/pandas/core/internals/managers.py", line 155, in set_axis 'values have {new} elements'.format(old=old_len, new=new_len)) ValueError: Length mismatch: Expected axis has 2 elements, new values have 3 elements could you help, thank you a lot

grosenberger commented 4 years ago

Could you please provide further information so I can try to reproduce the issue? Ideally the following information would be available:

summerghw commented 4 years ago

1.software version: pyprophet, version 2.1.3 2.openswath cmd OpenSwathAssayGenerator-in greenmonkey.TraML \ -out greenmonkey_optimized.TraML \ -swath_windows_file greenmonkey_windos.txt \ -enable_ipf \ -unimod_file unimod_phospho.xml \ -min_transitions 6 \ -max_transitions 6 \ -allowed_fragment_types b,y \ -allowed_fragment_charges 1,2,3,4 \ -enable_detection_specific_losses \ -enable_detection_unspecific_losses \ -precursor_mz_threshold 0.025 \ -precursor_lower_mz_limit 400 \ -precursor_upper_mz_limit 1200 \ -product_mz_threshold 0.025 \ -product_lower_mz_limit 350 \ -product_upper_mz_limit 2000 \ -max_num_alternative_localizations 10000 \ -disable_identification_ms2_precursors \ -disable_identification_specific_losses \ -enable_identification_unspecific_losses \ -enable_swath_specifity OpenSwathDecoyGenerator -in greenmonkey_optimized.TraML \ -allowed_fragment_types b,y \ -allowed_fragment_charges 1,2,3,4 \ -enable_detection_specific_losses \ -enable_detection_unspecific_losses \ -product_mz_threshold 0.025 \ -out greenmonkey_optimized_decoys.TraML TargetedFileConverter -in greenmonkey_optimized.TraML \ -out greenmonkey_optimized.PQP #!/bin/bash date for i in 'less mzML.list' do { OpenSwathWorkflow -in ${i} -tr greenmonkey_optimized_decoys.PQP -swath_windows_file greenmonkey_windows_analysis.txt -use_ms1_traces -enable_uis_scoring -out_tsv osw_${i} ; }& done wait date

pyprophet cmd pyprophet merge --template=greenmonkey_optimized_decoys.PQP --out=merged.osw *.osw pyprophet score --in=merged.osw --level=ms1 \ score --in=merged.osw --level=ms2 \ score --in=merged.osw --level=transition

pyprophet peptide --in=merged.osw --context=run-specific \ peptide --in=merged.osw --context=experiment-wide \ peptide --in=merged.osw --context=global

pyprophet protein --in=merged.osw --context=run-specific \ protein --in=merged.osw --context=experiment-wide \ protein --in=merged.osw --context=global

pyprophet ipf --in=merged.osw

pyprophet export --in=merged.osw --out=legacy.tsv

3.merge.osw https://pan.baidu.com/s/1zUosy167qVOpo5jh5EBjhw passwd: vf3g when i try to export ,there is no new file, i tryed to use pyprophet export --in=merged.osw --out=legacy.tsv --max_rs_peakgroup_qvalue 1 --max_global_protein_qvalue 1 --max_global_peptide_qvalue 1 --max_transition_pep 1 but still not work. is that means my library is not correct.

grosenberger commented 4 years ago

I unfortunately have issues to access the link and to download the files. But here are a few comments to the parameters:

OpenSwathAssayGenerator -in library.tsv -out library_targets.pqp -min_transitions 6 -max_transitions 6 -enable_ipf -unimod_file unimod_phospho.xml -disable_identification_ms2_precursors -disable_identification_specific_losses OpenSwathDecoyGenerator -in $cache/library_targets.pqp -out $cache/library.pqp