Merge pull request #302 from Proteobench/fragpipe_parse_win_path_on_unix

🐛 Fix FragPipe parameter parsing

proteobench/io/params/fragger.py

@@ -11,7 +11,7 @@
 import re
 from collections import namedtuple
 from io import BytesIO
-from pathlib import Path
+from pathlib import PureWindowsPath
 
 import pandas as pd
 
@@ -79,7 +79,7 @@ def extract_params(file: BytesIO) -> ProteoBenchParameters:
     params.search_engine = "MSFragger"
 
     msfragger_executable = fragpipe_params.loc["fragpipe-config.bin-msfragger"]
-    msfragger_executable = Path(msfragger_executable).name
+    msfragger_executable = PureWindowsPath(msfragger_executable).name
     match = re.search(VERSION_NO_PATTERN, msfragger_executable)
 
     if match:
@@ -133,9 +133,19 @@ def extract_params(file: BytesIO) -> ProteoBenchParameters:
         _, data = read_fragpipe_workflow(f)
     df = pd.DataFrame.from_records(data, columns=Parameter._fields).set_index(Parameter._fields[0])
     df.to_csv(file.with_suffix(".csv"))
+    with open(file, "rb") as f:
+        params = extract_params(f)
+    pprint(params.__dict__)
+    series = pd.Series(params.__dict__)
+    series.to_csv(file.parent / f"{file.stem}_extracted_params.csv")
 
+    file = pathlib.Path("../../../test/params/fragpipe_win_paths.workflow")
+    with open(file, "rb") as f:
+        _, data = read_fragpipe_workflow(f)
+    df = pd.DataFrame.from_records(data, columns=Parameter._fields).set_index(Parameter._fields[0])
+    df.to_csv(file.with_suffix(".csv"))
     with open(file, "rb") as f:
         params = extract_params(f)
     pprint(params.__dict__)
     series = pd.Series(params.__dict__)
-    series.to_csv(file.parent / "fragger_extracted_params.csv")
+    series.to_csv(file.parent / f"{file.stem}_extracted_params.csv")

test/params/fragpipe_win_paths.csv

@@ -0,0 +1,328 @@
+name,value,comment
+database.db-path,Q\:\\MISC_PERSONAL\\Bart\\Proteobench\\20240417\\2024-04-17-decoys-ProteoBenchFASTA_DDAQuantification.fasta.fas,
+crystalc.run-crystalc,false,
+database.decoy-tag,rev_,
+diann.fragpipe.cmd-opts,,
+diann.generate-msstats,true,
+diann.heavy,,
+diann.library,,
+diann.light,,
+diann.medium,,
+diann.q-value,0.01,
+diann.quantification-strategy,3,
+diann.quantification-strategy-2,QuantUMS (high accuracy),
+diann.run-dia-nn,false,
+diann.run-dia-plex,false,
+diann.run-specific-protein-q-value,false,
+diann.unrelated-runs,false,
+diann.use-predicted-spectra,true,
+diaumpire.AdjustFragIntensity,true,
+diaumpire.BoostComplementaryIon,false,
+diaumpire.CorrThreshold,0,
+diaumpire.DeltaApex,0.2,
+diaumpire.ExportPrecursorPeak,false,
+diaumpire.Q1,true,
+diaumpire.Q2,true,
+diaumpire.Q3,true,
+diaumpire.RFmax,500,
+diaumpire.RPmax,25,
+diaumpire.RTOverlap,0.3,
+diaumpire.SE.EstimateBG,false,
+diaumpire.SE.IsoPattern,0.3,
+diaumpire.SE.MS1PPM,10,
+diaumpire.SE.MS2PPM,20,
+diaumpire.SE.MS2SN,1.1,
+diaumpire.SE.MassDefectFilter,true,
+diaumpire.SE.MassDefectOffset,0.1,
+diaumpire.SE.NoMissedScan,1,
+diaumpire.SE.SN,1.1,
+diaumpire.run-diaumpire,false,
+fpop.fpop-tmt,false,
+fpop.label_control,,
+fpop.label_fpop,,
+fpop.region_size,1,
+fpop.run-fpop,false,
+fpop.subtract-control,false,
+fragpipe-config.bin-diann,C\:\\Users\\brvpuyve\\Downloads\\FragPipe-21.1\\fragpipe\\tools\\diann\\1.8.2_beta_8\\win\\DiaNN.exe,
+fragpipe-config.bin-ionquant,C\:\\Users\\brvpuyve\\Downloads\\FragPipe-21.1\\fragpipe\\tools\\IonQuant-1.10.12.jar,
+fragpipe-config.bin-msfragger,C\:\\Users\\brvpuyve\\Downloads\\FragPipe-21.1\\fragpipe\\tools\\MSFragger-4.0\\MSFragger-4.0.jar,
+fragpipe-config.bin-philosopher,C\:\\Users\\brvpuyve\\Downloads\\philosopher_v5.1.0_windows_amd64\\philosopher.exe,
+fragpipe-config.bin-python,C\:\\Users\\brvpuyve\\Anaconda3\\python.exe,
+freequant.mz-tol,10,
+freequant.rt-tol,0.4,
+freequant.run-freequant,false,
+ionquant.excludemods,,
+ionquant.heavy,,
+ionquant.imtol,0.05,
+ionquant.ionfdr,0.01,
+ionquant.light,,
+ionquant.locprob,0.75,
+ionquant.maxlfq,1,
+ionquant.mbr,1,
+ionquant.mbrimtol,0.05,
+ionquant.mbrmincorr,0,
+ionquant.mbrrttol,1,
+ionquant.mbrtoprun,10,
+ionquant.medium,,
+ionquant.minfreq,0,
+ionquant.minions,2,
+ionquant.minisotopes,2,
+ionquant.minscans,3,
+ionquant.mztol,10,
+ionquant.normalization,1,
+ionquant.peptidefdr,1,
+ionquant.proteinfdr,1,
+ionquant.requantify,1,
+ionquant.rttol,0.4,
+ionquant.run-ionquant,true,
+ionquant.tp,0,
+ionquant.uniqueness,0,
+ionquant.use-labeling,false,
+ionquant.use-lfq,true,
+ionquant.writeindex,0,
+msbooster.predict-rt,true,
+msbooster.predict-spectra,true,
+msbooster.run-msbooster,true,
+msbooster.use-correlated-features,false,
+msfragger.Y_type_masses,,
+msfragger.activation_types,all,
+msfragger.allowed_missed_cleavage_1,2,
+msfragger.allowed_missed_cleavage_2,2,
+msfragger.calibrate_mass,2,
+msfragger.check_spectral_files,true,
+msfragger.clip_nTerm_M,true,
+msfragger.deisotope,1,
+msfragger.delta_mass_exclude_ranges,"(-1.5,3.5)",
+msfragger.deneutralloss,1,
+msfragger.diagnostic_fragments,,
+msfragger.diagnostic_intensity_filter,0,
+msfragger.digest_max_length,50,
+msfragger.digest_min_length,7,
+msfragger.fragment_ion_series,"b,y",
+msfragger.fragment_mass_tolerance,0.02,
+msfragger.fragment_mass_units,0,
+msfragger.group_variable,0,
+msfragger.intensity_transform,0,
+msfragger.ion_series_definitions,,
+msfragger.isotope_error,0/1/2,
+msfragger.labile_search_mode,off,
+msfragger.localize_delta_mass,false,
+msfragger.mass_diff_to_variable_mod,0,
+msfragger.mass_offsets,0,
+msfragger.mass_offsets_detailed,,
+msfragger.max_fragment_charge,2,
+msfragger.max_variable_mods_combinations,5000,
+msfragger.max_variable_mods_per_peptide,3,
+msfragger.min_fragments_modelling,2,
+msfragger.min_matched_fragments,4,
+msfragger.min_sequence_matches,2,
+msfragger.minimum_peaks,15,
+msfragger.minimum_ratio,0.01,
+msfragger.misc.fragger.clear-mz-hi,0,
+msfragger.misc.fragger.clear-mz-lo,0,
+msfragger.misc.fragger.digest-mass-hi,5000,
+msfragger.misc.fragger.digest-mass-lo,500,
+msfragger.misc.fragger.enzyme-dropdown-1,stricttrypsin,
+msfragger.misc.fragger.enzyme-dropdown-2,null,
+msfragger.misc.fragger.precursor-charge-hi,4,
+msfragger.misc.fragger.precursor-charge-lo,1,
+msfragger.misc.fragger.remove-precursor-range-hi,1.5,
+msfragger.misc.fragger.remove-precursor-range-lo,-1.5,
+msfragger.misc.slice-db,1,
+msfragger.num_enzyme_termini,2,
+msfragger.output_format,pepXML_pin,
+msfragger.output_max_expect,50,
+msfragger.output_report_topN,1,
+msfragger.output_report_topN_dda_plus,5,
+msfragger.output_report_topN_dia1,5,
+msfragger.override_charge,false,
+msfragger.precursor_mass_lower,-20,
+msfragger.precursor_mass_mode,selected,
+msfragger.precursor_mass_units,1,
+msfragger.precursor_mass_upper,20,
+msfragger.precursor_true_tolerance,10,
+msfragger.precursor_true_units,1,
+msfragger.remainder_fragment_masses,,
+msfragger.remove_precursor_peak,1,
+msfragger.report_alternative_proteins,true,
+msfragger.require_precursor,true,
+msfragger.restrict_deltamass_to,all,
+msfragger.reuse_dia_fragment_peaks,false,
+msfragger.run-msfragger,true,
+msfragger.search_enzyme_cut_1,KR,
+msfragger.search_enzyme_cut_2,,
+msfragger.search_enzyme_name_1,stricttrypsin,
+msfragger.search_enzyme_name_2,null,
+msfragger.search_enzyme_nocut_1,,
+msfragger.search_enzyme_nocut_2,,
+msfragger.search_enzyme_sense_1,C,
+msfragger.search_enzyme_sense_2,C,
+msfragger.table.fix-mods,"0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1",
+msfragger.table.var-mods,"15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1",
+msfragger.track_zero_topN,0,
+msfragger.use_all_mods_in_first_search,false,
+msfragger.use_detailed_offsets,false,
+msfragger.use_topN_peaks,150,
+msfragger.write_calibrated_mzml,false,
+msfragger.write_uncalibrated_mgf,false,
+msfragger.zero_bin_accept_expect,0,
+msfragger.zero_bin_mult_expect,1,
+opair.activation1,HCD,
+opair.activation2,ETD,
+opair.filterOxonium,true,
+opair.glyco_db,,
+opair.max_glycans,4,
+opair.max_isotope_error,2,
+opair.min_isotope_error,0,
+opair.ms1_tol,20,
+opair.ms2_tol,20,
+opair.oxonium_filtering_file,,
+opair.oxonium_minimum_intensity,0.05,
+opair.reverse_scan_order,false,
+opair.run-opair,false,
+opair.single_scan_type,false,
+peptide-prophet.cmd-opts,--decoyprobs --ppm --accmass --nonparam --expectscore,
+peptide-prophet.combine-pepxml,false,
+peptide-prophet.run-peptide-prophet,false,
+percolator.cmd-opts,--only-psms --no-terminate --post-processing-tdc,
+percolator.keep-tsv-files,false,
+percolator.min-prob,0.5,
+percolator.run-percolator,true,
+phi-report.dont-use-prot-proph-file,false,
+phi-report.filter,--sequential --prot 0.01,
+phi-report.pep-level-summary,false,
+phi-report.philosoher-msstats,false,
+phi-report.print-decoys,false,
+phi-report.prot-level-summary,false,
+phi-report.remove-contaminants,false,
+phi-report.run-report,true,
+protein-prophet.cmd-opts,--maxppmdiff 2000000,
+protein-prophet.run-protein-prophet,true,
+ptmprophet.cmdline,"KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 MINPROB\=0.5",
+ptmprophet.run-ptmprophet,false,
+ptmshepherd.adv_params,false,
+ptmshepherd.annotation-common,false,
+ptmshepherd.annotation-custom,false,
+ptmshepherd.annotation-glyco,false,
+ptmshepherd.annotation-unimod,true,
+ptmshepherd.annotation_file,,
+ptmshepherd.annotation_tol,0.01,
+ptmshepherd.cap_y_ions,,
+ptmshepherd.decoy_type,1,
+ptmshepherd.diag_ions,,
+ptmshepherd.diagmine_diagMinFoldChange,3.0,
+ptmshepherd.diagmine_diagMinSpecDiff,00.2,
+ptmshepherd.diagmine_fragMinFoldChange,3.0,
+ptmshepherd.diagmine_fragMinPropensity,00.1,
+ptmshepherd.diagmine_fragMinSpecDiff,00.1,
+ptmshepherd.diagmine_minIonsPerSpec,2,
+ptmshepherd.diagmine_minPeps,25,
+ptmshepherd.diagmine_pepMinFoldChange,3.0,
+ptmshepherd.diagmine_pepMinSpecDiff,00.2,
+ptmshepherd.glyco_adducts,,
+ptmshepherd.glyco_fdr,1.00,
+ptmshepherd.glyco_isotope_max,3,
+ptmshepherd.glyco_isotope_min,-1,
+ptmshepherd.glyco_ppm_tol,50,
+ptmshepherd.glycodatabase,,
+ptmshepherd.histo_smoothbins,2,
+ptmshepherd.iontype_a,false,
+ptmshepherd.iontype_b,true,
+ptmshepherd.iontype_c,false,
+ptmshepherd.iontype_x,false,
+ptmshepherd.iontype_y,true,
+ptmshepherd.iontype_z,false,
+ptmshepherd.localization_allowed_res,,
+ptmshepherd.localization_background,4,
+ptmshepherd.max_adducts,0,
+ptmshepherd.n_glyco,true,
+ptmshepherd.normalization-psms,true,
+ptmshepherd.normalization-scans,false,
+ptmshepherd.output_extended,false,
+ptmshepherd.peakpicking_mass_units,0,
+ptmshepherd.peakpicking_minPsm,10,
+ptmshepherd.peakpicking_promRatio,0.3,
+ptmshepherd.peakpicking_width,0.002,
+ptmshepherd.precursor_mass_units,0,
+ptmshepherd.precursor_tol,0.01,
+ptmshepherd.print_decoys,false,
+ptmshepherd.prob_dhexOx,"2,0.5,0.1",
+ptmshepherd.prob_dhexY,"2,0.5",
+ptmshepherd.prob_neuacOx,"2,0.05,0.2",
+ptmshepherd.prob_neugcOx,"2,0.05,0.2",
+ptmshepherd.prob_phosphoOx,"2,0.05,0.2",
+ptmshepherd.prob_regY,"5,0.5",
+ptmshepherd.prob_sulfoOx,"2,0.05,0.2",
+ptmshepherd.remainder_masses,,
+ptmshepherd.remove_glycan_delta_mass,true,
+ptmshepherd.run-shepherd,false,
+ptmshepherd.run_diagextract_mode,false,
+ptmshepherd.run_diagmine_mode,false,
+ptmshepherd.run_glyco_mode,false,
+ptmshepherd.spectra_maxfragcharge,2,
+ptmshepherd.spectra_ppmtol,20,
+ptmshepherd.varmod_masses,,
+quantitation.run-label-free-quant,true,
+run-psm-validation,true,
+run-validation-tab,true,
+saintexpress.fragpipe.cmd-opts,,
+saintexpress.max-replicates,10,
+saintexpress.run-saint-express,false,
+saintexpress.virtual-controls,100,
+speclibgen.easypqp.extras.max_delta_ppm,15,
+speclibgen.easypqp.extras.max_delta_unimod,0.02,
+speclibgen.easypqp.extras.rt_lowess_fraction,0,
+speclibgen.easypqp.fragment.a,false,
+speclibgen.easypqp.fragment.b,true,
+speclibgen.easypqp.fragment.c,false,
+speclibgen.easypqp.fragment.x,false,
+speclibgen.easypqp.fragment.y,true,
+speclibgen.easypqp.fragment.z,false,
+speclibgen.easypqp.im-cal,Automatic selection of a run as reference IM,
+speclibgen.easypqp.neutral_loss,false,
+speclibgen.easypqp.rt-cal,noiRT,
+speclibgen.easypqp.select-file.text,,
+speclibgen.easypqp.select-im-file.text,,
+speclibgen.keep-intermediate-files,false,
+speclibgen.run-speclibgen,false,
+tab-run.delete_calibrated_mzml,false,
+tab-run.delete_temp_files,false,
+tab-run.sub_mzml_prob_threshold,0.5,
+tab-run.write_sub_mzml,false,
+tmtintegrator.add_Ref,-1,
+tmtintegrator.aggregation_method,0,
+tmtintegrator.allow_overlabel,true,
+tmtintegrator.allow_unlabeled,true,
+tmtintegrator.best_psm,true,
+tmtintegrator.channel_num,TMT-6,
+tmtintegrator.extraction_tool,IonQuant,
+tmtintegrator.glyco_qval,-1,
+tmtintegrator.groupby,0,
+tmtintegrator.log2transformed,true,
+tmtintegrator.max_pep_prob_thres,0,
+tmtintegrator.min_ntt,0,
+tmtintegrator.min_pep_prob,0.9,
+tmtintegrator.min_percent,0.05,
+tmtintegrator.min_purity,0.5,
+tmtintegrator.min_site_prob,-1,
+tmtintegrator.mod_tag,none,
+tmtintegrator.ms1_int,true,
+tmtintegrator.outlier_removal,true,
+tmtintegrator.print_RefInt,false,
+tmtintegrator.prot_exclude,none,
+tmtintegrator.prot_norm,0,
+tmtintegrator.psm_norm,false,
+tmtintegrator.quant_level,2,
+tmtintegrator.ref_tag,Bridge,
+tmtintegrator.run-tmtintegrator,false,
+tmtintegrator.tolerance,20,
+tmtintegrator.top3_pep,true,
+tmtintegrator.unique_gene,0,
+tmtintegrator.unique_pep,false,
+tmtintegrator.use_glycan_composition,false,
+workdir,Q\:\\MISC_PERSONAL\\Bart\\Proteobench\\20240417,
+workflow.input.data-type.im-ms,false,
+workflow.input.data-type.regular-ms,true,
+workflow.misc.save-sdrf,true,
+workflow.ram,0,
+workflow.threads,47,