Module Overview#

CFTK currently uses script-style modules under src. Public APIs are still evolving, so this page describes module responsibilities rather than promising stable Python imports.

Command And Configuration#

  • src/cftk.py: command-line parser and dispatcher.

  • src/doctor.py: non-repairing project, reference, input, and tool readiness diagnostics.

  • src/init.py: config validation, sample helpers, output path helpers, and config summary.

  • src/process.py: raw processing steps and CpG matrix merge.

  • src/run_workflow.py: fail-fast beginner stage orchestration, artifact contracts, resume/quarantine decisions, and per-attempt provenance.

  • src/validation_reports.py: installed evidence tables and sanitized figures generated automatically for terminal beginner-run attempts.

  • src/util.py: shared helpers and exact external-command recording.

Analysis Modules#

  • src/analysis/qc.py: QC calculations.

  • src/analysis/power_analysis.py: statistical power analysis.

  • src/analysis/model_power.py and src/analysis/model_power_reference.py: model-development simulation and external aggregate-reference loading.

  • src/analysis/model_power_discovery.py and src/analysis/model_power_operating_characteristics.py: cross-validated discovery power and null-calibrated operating characteristics.

  • src/analysis/differential.py and src/analysis/pca_analysis.py: feature-level differential analysis and PCA.

  • src/analysis/dmr.py: DMR preparation, metilene execution, and annotation handoff.

  • src/analysis/occupancy.py and src/analysis/wps.py: fragmentomics occupancy and WPS features.

  • src/analysis/delfi.py, src/analysis/end_motif.py, and src/analysis/cleavage.py: finaletoolkit-backed fragmentomics features.

  • src/analysis/mesa.py and src/analysis/modality_performance.py: modality performance and MESA modeling.

Visualization And Reporting#

  • src/visualization/: plotting modules for QC, differential analysis, DMR, fragmentomics, MESA, and power analysis.

  • src/report/report_generator.py: self-contained HTML report generation.