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CRISPR M1: base-editing design mode (CBE/ABE + iSTOP + AA consequence)
Tengo Gzirishvili +1: Claude Opus 4.8Promotes the base-editor flag into a first-class design mode that out-classes tools which only flag editability. Backend (dee/core/base_editor.py, new): - Editor library: BE4max/BE3/evoCDA (CBE C→T), ABE8e/ABE7.10 (ABE A→G), each with activity window + per-position profile (Komor/Koblan/ Thuronyi/Gaudelli/Richter). - predict_base_edits(): edits in window, per-position efficiency, bystander detection, editability score. - codon_consequence(): frame-aware AA call — silent/missense/nonsense/ stop-loss + CRISPR-STOP / iSTOP detection. Returns None (never guesses) on alignment mismatch or incomplete codon. find_guides() gains mode="base_edit" + base_editor= kwargs (defaults keep every existing caller unchanged). New Guide fields are all defaulted. AA consequence fills only when a reading frame is trusted — gene_symbol+ organism aligned to CDS, or the input is itself a clean coding sequence (_looks_like_cds). Base editing is SpCas9-only; annotation is gated to it.…dd2d535