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Force cloned include_idxs to be np.arrays (otherwise breaks downstrea… #559

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Force cloned include_idxs to be np.arrays (otherwise breaks downstrea… #559

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10 changes: 5 additions & 5 deletions CRISPResso2/CRISPRessoCORE.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3010,8 +3010,8 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited
'exon_len_mods': this_exon_len_mods,
'exon_intervals': this_exon_intervals,
'splicing_positions': this_splicing_positions,
'include_idxs': this_include_idxs,
'exclude_idxs': this_exclude_idxs,
'include_idxs': np.array(this_include_idxs),
'exclude_idxs': np.array(this_exclude_idxs),
'idx_cloned_from': None,
'fw_seeds': seeds,
'rc_seeds': rc_seeds,
Expand Down Expand Up @@ -3183,7 +3183,7 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited
refs[ref_name]['sgRNA_mismatches'] = this_sgRNA_mismatches
refs[ref_name]['sgRNA_orig_sequences'] = refs[clone_ref_name]['sgRNA_orig_sequences']
refs[ref_name]['sgRNA_names'] = refs[clone_ref_name]['sgRNA_names']
refs[ref_name]['include_idxs'] = this_include_idxs
refs[ref_name]['include_idxs'] = np.array(this_include_idxs)
refs[ref_name]['contains_guide'] = refs[clone_ref_name]['contains_guide']

#quantification window coordinates override other options
Expand All @@ -3199,8 +3199,8 @@ def get_prime_editing_guides(this_amp_seq, this_amp_name, ref0_seq, prime_edited
#subtract any indices in 'exclude_idxs' -- e.g. in case some of the cloned include_idxs were near the read ends (excluded)
this_exclude_idxs = sorted(map(int, set(refs[ref_name]['exclude_idxs'])))
this_include_idxs = sorted(map(int, set(np.setdiff1d(this_include_idxs, this_exclude_idxs))))
refs[ref_name]['include_idxs'] = this_include_idxs
refs[ref_name]['exclude_idxs'] = this_exclude_idxs
refs[ref_name]['include_idxs'] = np.array(this_include_idxs)
refs[ref_name]['exclude_idxs'] = np.array(this_exclude_idxs)

if needs_exon_positions and clone_has_exons:
this_exon_positions = set()
Expand Down
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