Convert cols to numeric for PE

pinellolab · Oct 20, 2021 · cabebbe · cabebbe
1 parent c2bdd96
commit cabebbe
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/CRISPResso2/CRISPRessoCORE.py b/CRISPResso2/CRISPRessoCORE.py
@@ -4316,7 +4316,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                     for nuc in ['A', 'C', 'G', 'T', 'N', '-']:
                         nuc_pcts.append(np.concatenate(([ref_name, nuc], np.array(ref1_all_base_count_vectors[ref_name+"_"+nuc]).astype(np.float)/tot)))
                 colnames = ['Batch', 'Nucleotide']+list(refs[ref_names[0]]['sequence'])
-                pe_nucleotide_percentage_summary_df = pd.DataFrame(nuc_pcts, columns=colnames)
+                pe_nucleotide_percentage_summary_df = pd.DataFrame(nuc_pcts, columns=colnames).apply(pd.to_numeric,errors='ignore')
 
                 mod_pcts = []
                 for ref_name in ref_names_for_pe:
@@ -4328,7 +4328,7 @@ def get_scaffold_len(row, scaffold_start_loc, scaffold_seq):
                     mod_pcts.append(np.concatenate(([ref_name, 'All_modifications'], np.array(ref1_all_indelsub_count_vectors[ref_name]).astype(np.float)/tot)))
                     mod_pcts.append(np.concatenate(([ref_name, 'Total'], [counts_total[ref_name]]*refs[ref_names_for_pe[0]]['sequence_length'])))
                 colnames = ['Batch', 'Modification']+list(refs[ref_names_for_pe[0]]['sequence'])
-                pe_modification_percentage_summary_df = pd.DataFrame(mod_pcts, columns=colnames)
+                pe_modification_percentage_summary_df = pd.DataFrame(mod_pcts, columns=colnames).apply(pd.to_numeric,errors='ignore')
                 sgRNA_intervals = refs[ref_names_for_pe[0]]['sgRNA_intervals']
                 sgRNA_names = refs[ref_names_for_pe[0]]['sgRNA_names']
                 sgRNA_mismatches = refs[ref_names_for_pe[0]]['sgRNA_mismatches']