debugging lines

CRISPResso2/CRISPRessoCORE.py

@@ -4309,6 +4309,7 @@ def count_alternate_alleles(sub_base_vectors, ref_name, ref_sequence, ref_total_
                         'annotate_wildtype_allele': args.annotate_wildtype_allele,
                         'custom_colors': custom_config["colors"],
                     }
+                    CRISPRessoPlot.plot_alleles_table(**plot_9_input)
                     debug('Plotting allele distribution around cut for {0}'.format(ref_name))
                     plot(CRISPRessoPlot.plot_alleles_table, plot_9_input)
                     crispresso2_info['results']['refs'][ref_name]['plot_9_roots'].append(os.path.basename(fig_filename_root))

CRISPResso2/CRISPRessoPlot.py

@@ -2659,6 +2659,7 @@ def prep_alleles_table(df_alleles, reference_seq, MAX_N_ROWS, MIN_FREQUENCY):
 
     re_find_indels=re.compile("(-*-)")
     idx_row=0
+    breakpoint()
     for idx, row in df_alleles[df_alleles['%Reads']>=MIN_FREQUENCY][:MAX_N_ROWS].iterrows():
         X.append(seq_to_numbers(idx.upper()))
         annot.append(list(idx))
@@ -2758,6 +2759,7 @@ def plot_alleles_heatmap(reference_seq,fig_filename_root,X,annot,y_labels,insert
     -custom_colors: dict of colors to plot (e.g. colors['A'] = (1,0,0,0.4) # red,blue,green,alpha )
     """
     plot_nuc_len=len(reference_seq)
+    breakpoint()
 
     # make a color map of fixed colors
     alpha=0.4
@@ -3061,6 +3063,7 @@ def plot_alleles_table(reference_seq,df_alleles,fig_filename_root,MIN_FREQUENCY=
     annotate_wildtype_allele: string to add to the end of the wildtype allele (e.g. ** or '')
     """
     X, annot, y_labels, insertion_dict, per_element_annot_kws, is_reference = prep_alleles_table(df_alleles, reference_seq, MAX_N_ROWS, MIN_FREQUENCY)
+    breakpoint()
     if annotate_wildtype_allele != '':
         for ix, is_ref in enumerate(is_reference):
             if is_ref: