Fix plot window cloning from Ref1 to HDR

Plot window for sgRNA will be the same length after cloning even if the window is shorter or longer after comparing between ref1 and HDR.
pinellolab · Nov 14, 2020 · 88b6e9c · 88b6e9c
1 parent 7403a46
commit 88b6e9c
Showing 1 changed file with 7 additions and 10 deletions.
diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -1646,9 +1646,11 @@ def get_prime_editing_guides(this_amp_seq,this_amp_name,ref0_seq,prime_edited_se
 
                     this_sgRNA_intervals = []
                     this_sgRNA_mismatches = []
+                    this_sgRNA_plot_idxs = []
                     for idx,(sgRNA_interval_start,sgRNA_interval_end) in enumerate(refs[clone_ref_name]['sgRNA_intervals']):
                         this_sgRNA_intervals.append((s1inds[sgRNA_interval_start],s1inds[sgRNA_interval_end]))
 
+                        sgRNA_cut_point_this = s1inds[refs[clone_ref_name]['sgRNA_cut_points'][idx]]
                         sgRNA_seq_clone = refs[clone_ref_name]['sequence'][sgRNA_interval_start:sgRNA_interval_end+1]
                         sgRNA_seq_this = refs[ref_name]['sequence'][s1inds[sgRNA_interval_start]:s1inds[sgRNA_interval_end]+1]
                         sgRNA_seq_orig_seq = refs[clone_ref_name]['sgRNA_orig_sequences'][idx]
@@ -1659,15 +1661,11 @@ def get_prime_editing_guides(this_amp_seq,this_amp_name,ref0_seq,prime_edited_se
                             best_aln_mismatches = rv_mismatches
                         this_sgRNA_mismatches.append(sorted(best_aln_mismatches))
 
-
-                    this_sgRNA_plot_idxs = []
-                    for plot_idx_list in refs[clone_ref_name]['sgRNA_plot_idxs']:
-                        if len(plot_idx_list) > 0:
-                            st = s1inds[plot_idx_list[0]]
-                            en = s1inds[plot_idx_list[-1]]
-                            this_sgRNA_plot_idxs.append(sorted(list(range(st,en+1))))
-                        else:
-                            this_sgRNA_plot_idxs.append([])
+                        ref_seq_length = len(refs[ref_name]['sequence'])
+                        window_around_cut=max(1,args.plot_window_size)
+                        st=max(0,sgRNA_cut_point_this-window_around_cut+1)
+                        en=min(ref_seq_length-1,sgRNA_cut_point_this+window_around_cut+1)
+                        this_sgRNA_plot_idxs.append(sorted(list(range(st,en))))
 
                     old_this_sgRNA_plot_idxs = []
                     for plot_idx_list in refs[clone_ref_name]['sgRNA_plot_idxs']:
@@ -4393,7 +4391,6 @@ def count_alternate_alleles(sub_base_vectors,ref_name,ref_sequence,ref_total_aln
                         crispresso2_info['refs'][ref_name]['plot_10d_captions'].append("Figure 10d: Log2 nucleotide frequencies for each position in the plotting window around the " + sgRNA_legend + ". The quantification window is outlined by the dotted box.")
                         crispresso2_info['refs'][ref_name]['plot_10d_datas'].append([])
 
-
                         fig_filename_root = _jp('10e.'+ref_plot_name+'Selected_conversion_at_'+args.conversion_nuc_from+'s_around_'+sgRNA_label)
                         CRISPRessoPlot.plot_conversion_at_sel_nucs(
                             df_subs = plot_nuc_pcts,