├── .gitignore ├── MANIFEST.in ├── README.md ├── data ├── __init__.py └── aa_mass_lookup.csv ├── example_mgf ├── example.mgf ├── example_wInvalid.mgf └── example_wScores.mgf ├── requirements.txt ├── setup.py ├── spectralis ├── __init__.py ├── bin_reclassification │ ├── __init__.py │ ├── bin_reclassifier.py │ ├── datasets.py │ ├── models.py │ ├── ms2_binning.py │ ├── peptide2profile.py │ ├── profile2peptide.py │ └── trainer.py ├── denovo_utils │ ├── __constants__.py │ ├── __init__.py │ └── __utils__.py ├── evolutionary_algorithm │ ├── __init__.py │ ├── ea_optimizer.py │ ├── input_from_csv.py │ └── seq_initializer.py ├── lev_scoring │ ├── __init__.py │ ├── counting_features.py │ ├── ms2_comparison.py │ ├── scorer.py │ └── similarity_features.py ├── main.py └── spectralis_master.py └── spectralis_config.yaml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gagneurlab/spectralis/HEAD/.gitignore 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