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Merged
RobbinBouwmeester merged 5 commits into from
Sep 17, 2025
Merged

More updates #8

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330065a
add coefficient_bounds
rodvrees Aug 20, 2025
e9ccb41
Add coefficient_bounds param
rodvrees Aug 20, 2025
274816a
updates
rodvrees Aug 25, 2025
3c1b12b
Add DIA-NN features
rodvrees Sep 3, 2025
0c0ab89
Add DIA-NN feature generator
rodvrees Sep 5, 2025
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Empty file removed TESTING_STATUS.md
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32 changes: 0 additions & 32 deletions WORKFLOW_VISUALIZATION.md
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1 change: 1 addition & 0 deletions config_manager.py
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Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ def save(self, path: str) -> None:
"read_correlation",
"dlc_transfer_learn",
"fdr_init_search",
"coefficient_bounds",
]
},
"sage_basic": self.sage_basic,
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49 changes: 25 additions & 24 deletions configs/config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
"bucket_size": 1024,
"enzyme": {
"missed_cleavages": 2,
"min_len": 6,
"min_len": 7,
"max_len": 30,
"cleave_at": "KR",
"restrict": "P",
Expand Down Expand Up @@ -68,15 +68,15 @@
"database": {
"bucket_size": 10240,
"enzyme": {
"missed_cleavages": 2,
"min_len": 6,
"missed_cleavages": 1,
"min_len": 7,
"max_len": 30,
"cleave_at": "$"
},
"fragment_min_mz": 50,
"fragment_max_mz": 2500,
"fragment_min_mz": 200,
"fragment_max_mz": 1800,
"peptide_min_mass": 300,
"peptide_max_mass": 5000,
"peptide_max_mass": 7200,
"ion_kinds": [
"b",
"y"
Expand All @@ -88,15 +88,15 @@
"variable_mods": {
"M": [15.9949]
},
"max_variable_mods": 2,
"max_variable_mods": 1,
"decoy_tag": "rev_",
"generate_decoys": true,
"generate_decoys": false,
"fasta": "fasta/ecoli_22032024.fasta"
},
"precursor_tol": {
"da": [
-40,
40
"ppm": [
-50,
50
]
},
"fragment_tol": {
Expand All @@ -111,37 +111,38 @@
],
"isotope_errors": [
-1,
1
3
],
"deisotope": true,
"deisotope": false,
"annotate_matches": true,
"chimera": true,
"chimera": false,
"predict_rt": false,
"wide_window": true,
"min_peaks": 0,
"max_peaks": 10000,
"min_matched_peaks": 5,
"min_peaks": 15,
"max_peaks": 100000000,
"min_matched_peaks": 1,
"max_fragment_charge": 1,
"report_psms": 12,
"report_psms": 200,
"output_directory": "./",
"mzml_paths": [
"mzml_files/LFQ_Orbitrap_AIF_Ecoli_01.mzML"
]
},
"mumdia": {
"write_deeplc_pickle": true,
"write_ms2pip_pickle": true,
"write_deeplc_pickle": false,
"write_ms2pip_pickle": false,
"write_correlation_pickles": true,
"write_initial_search_pickle": true,
"write_full_search_pickle": true,
"read_deeplc_pickle": true,
"read_ms2pip_pickle": true,
"read_correlation_pickles": true,
"read_full_search_pickles": true,
"read_initial_search_pickle": true,
"read_correlation_pickles": false,
"read_full_search_pickles": false,
"read_initial_search_pickle": false,
"remove_intermediate_files": false,
"dlc_transfer_learn": false,
"fdr_init_search": 0.01,
"coefficient_bounds": 1,
"fdr_init_search": 0.0001,
"rescoring_features": [
"distribution_correlation_matrix_psm_ids",
"distribution_correlation_matrix_frag_ids",
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