Public package
src/offtarget_benchmark/common.py Normalizes guide sequences, off-target sequences, and chromosome names before truth and prediction tables are matched.src/offtarget_benchmark/layout.py Defines the repository paths used by scripts and notebooks.src/offtarget_benchmark/benchmark_tables.py Reads the benchmark truth table and standardized prediction contracts, validates required columns, normalizes comparable fields, and removes duplicate prediction rows.src/offtarget_benchmark/benchmark_metrics.py Computes guide-level recall, overall tool summaries, precision-recall curves, paired statistical summaries, and tool-combination tables.src/offtarget_benchmark/benchmark_outputs.py Writes the quality-control table and compact Markdown report for a benchmark run.src/offtarget_benchmark/benchmark_runner.py Coordinates one benchmark run from input CSVs to result tables.src/offtarget_benchmark/cli.py Provides command-line access to the benchmark workflow.src/offtarget_benchmark/docs_runtime.py Supplies the small path and display helpers used inside Quarto notebooks.
Top-level directories
data/ Manuscript truth data and local placeholders for files distributed through Zenodo.results/ Benchmark run outputs. The manuscript run is stored under results/benchmark_runs/manuscript_primary/.docs/ Quarto project, figure notebooks, generated figure files, and rendered HTML.scripts/ Short command wrappers for benchmark execution and documentation rendering.
Generated outputs
results/benchmark_runs/manuscript_primary/ CSV tables and the Markdown report written by the benchmark runner.docs/generated_figures/ PNG files written when the figure notebooks execute.docs/_site/ Rendered HTML site produced by Quarto.