ZFN Off-Target Ranking

⚠️ EXPERIMENTAL. The ZFN arm has known unfixed defects tracked in #82; do not use ZFN output for any decision without independent validation. Relevant to ranking specifically: the exported worst_site_score / best_offtarget_score fields are inverted (minimum and maximum site score respectively, whereas the highest-scoring off-target is the most dangerous), and the region tie-break can be fed a wrong region because a site inside a large containing gene may be classified intergenic. See ZFN Module Guide.

siRNAforge provides deterministic ZFN off-target ordering via sirnaforge.zfn.rank.rank_sites.

Policy

When two sites have equal score, tie-breaks are applied in this order:

  1. Region priority: exon > promoter > intron > intergenic > unknown

  2. Chromosomal location (chromosome, then start_1based, then end_1based)

  3. Stable fallback by site_id

This policy is designed to match PROGNOS-style ranking behavior used by the ZFN regression tests.

API

from sirnaforge.zfn.rank import rank_sites

ranked = rank_sites(sites, params)

  • sites: sequence of ZFNOffTargetSite

  • params: optional ZFNDesignParameters (reserved for algorithm-specific extension)

  • returns: new list[ZFNOffTargetSite] sorted by rank