bio-genome-engineering-grna-design

but works well across species for Cas9

def crisprscan_score(guide_35mer): '''Score using CRISPRscan model

Input: 35-mer (6bp upstream + 20bp guide + 3bp PAM + 6bp downstream)
Output: Activity score 0-100

Requires the crisprscan package:
pip install crisprscan
'''
try:
    import crisprscan
    return crisprscan.score(guide_35mer)
except ImportError:
    # Fallback to simplified scoring
    return score_guide_activity(guide_35mer[6:26]) * 100

## Design Workflow

**Goal:** Design the top N guide RNAs for a target gene, optionally restricted to coding exon regions.

**Approach:** Scan both strands for PAM sites, optionally filter to guides within exon coordinates, score each guide for on-target activity using GC content and position-weight criteria, and return the highest-scoring candidates.