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I've noticed you're CFD scoring for each individual off-target sequence is the same. Try this fix.......
def calc_cfd_e(sg,wt,pam,mm_scores,pam_scores):
score = 1
wt = wt.replace('T','U')
sg = sg.replace('T','U')
#wt_list = list(wt)
#sg_list = list(sg)
shorter, longer = sorted([sg, wt], key=len)
for i in range(-len(shorter), 0):
if (sg[i] != =wt[i]):
key = 'r' + sg[i] + ':d' + revcom(wt[i]) + ',' + str(20 + i + 1)
score *= mm_scores[key]
score *= pam_scores[pam[-2:]]
#for i,wl in enumerate(wt_list):
# try:
# key = 'r'+sg_list[i]+':d'+revcom(wl)+','+str(i+1)
# score*= mm_scores[key]
# except KeyError:
# continue
#score*=pam_scores[pam]
return (score)
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