├── .github └── workflows │ ├── package_and_test.yml │ ├── publish-to-pypi.yml │ └── publish-to-test-pypi.yml ├── .gitignore ├── .gitmodules ├── .zenodo.json ├── CITATION.cff ├── Dockerfile ├── Dockerfile.anaconda ├── Dockerfile.miniconda ├── Dockerfile.miniforge ├── Dockerfile.viennarna ├── JOSS ├── figure1.png ├── paper.bib └── paper.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── benchmarking ├── MG1655.fna ├── README.md ├── T7_genome.fasta ├── benchmark_ostir.py └── rbscalc_bugfixes.patch ├── calibration ├── README.md ├── input.csv ├── ostir_calibration.R ├── ostir_calibration_python.ipynb ├── output.fit_parameters.csv ├── output.fit_values.csv ├── output.log2_fold_error.png ├── output.predicted_rate_versus_measured_rate.png ├── output.spacing_dG.png └── output.total_dG_versus_measured_rate.png ├── ecoli ├── ecoli_graph.R └── ostir_on_ecoli.py ├── environment.yml ├── img ├── Ecoli_genome_predictions.ai ├── Ecoli_genome_predictions.png ├── deltaG_mRNA.pdf ├── deltaG_mRNA.png ├── deltaG_mRNA_rRNA.pdf ├── deltaG_mRNA_rRNA.png ├── deltaG_spacing.pdf ├── deltaG_spacing.png ├── deltaG_standby.pdf ├── deltaG_standby.png ├── deltaG_start_codon.pdf └── deltaG_start_codon.png ├── ostir ├── ViennaRNA.py ├── __init__.py ├── data_classes.py ├── ostir.py ├── ostir_calculations.py ├── ostir_engine.py ├── ostir_factory.py ├── ostir_farm.py ├── ostir_worker.py ├── rna_turner1999.par ├── rna_turner2004.par └── shortcuts.py ├── pyproject.toml ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── expected ├── Salis2009.csv ├── T7_genome.csv ├── command_line_CSV_input.csv ├── command_line_CSV_input_alternate_columns_and_defaults.csv ├── command_line_FASTA_input.csv └── command_line_string_input.csv ├── input ├── Salis2009.csv ├── T7_genome.fasta ├── command_line_CSV_input.csv ├── command_line_CSV_input_alternate_columns_and_defaults.csv └── command_line_FASTA_input.fa ├── profile_ostir.py └── test_ostir.py /.github/workflows/package_and_test.yml: 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