Allow for mixed-case prime editing input, fix pinellolab#187

edilytics · Jan 5, 2022 · e999079 · e999079
1 parent 4acdcdd
commit e999079
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -1101,8 +1101,8 @@ def rreplace(s, old, new):
 
             #check that the pegRNA aligns to the reference (and not the RC)
             amp_incentive = np.zeros(len(amplicon_seq_arr[0])+1,dtype=int)
-            f1,f2,fw_score=CRISPResso2Align.global_align(pegRNA_spacer_seq,amplicon_seq_arr[0],matrix=aln_matrix,gap_incentive=amp_incentive,gap_open=args.needleman_wunsch_gap_open,gap_extend=args.needleman_wunsch_gap_extend,)
-            r1,r2,rv_score=CRISPResso2Align.global_align(pegRNA_spacer_seq,CRISPRessoShared.reverse_complement(amplicon_seq_arr[0]),matrix=aln_matrix,gap_incentive=amp_incentive,gap_open=args.needleman_wunsch_gap_open,gap_extend=args.needleman_wunsch_gap_extend,)
+            f1,f2,fw_score=CRISPResso2Align.global_align(pegRNA_spacer_seq,amplicon_seq_arr[0].upper(),matrix=aln_matrix,gap_incentive=amp_incentive,gap_open=args.needleman_wunsch_gap_open,gap_extend=args.needleman_wunsch_gap_extend,)
+            r1,r2,rv_score=CRISPResso2Align.global_align(pegRNA_spacer_seq,CRISPRessoShared.reverse_complement(amplicon_seq_arr[0].upper()),matrix=aln_matrix,gap_incentive=amp_incentive,gap_open=args.needleman_wunsch_gap_open,gap_extend=args.needleman_wunsch_gap_extend,)
             if rv_score > fw_score:
                 raise CRISPRessoShared.BadParameterException('The prime editing pegRNA spacer sequence appears to be given in the 3\'->5\' order. The prime editing pegRNA spacer sequence (--prime_editing_pegRNA_spacer_seq) must be given in the RNA 5\'->3\' order.')