fix a bug when no mutated protein identified

Author: ATPs

src/perChrom.py

@@ -686,6 +686,9 @@ def save_mutation_and_proteins(df_transcript3, outprefix):
     # save mutation annotation
     columns_keep = ['protein_id_fasta', 'seqname', 'strand','frameChange','stopGain', 'AA_stopGain', 'stopLoss', 'stopLoss_pos', 'nonStandardStopCodon', 'n_variant_AA', 'n_deletion_AA', 'n_insertion_AA', 'variant_AA', 'insertion_AA', 'deletion_AA', 'len_ref_AA', 'len_alt_AA']
     columns_keep = [e for e in columns_keep if e in df_transcript3.columns]
+    if df_transcript3.shape[0] == 0:
+        print('no protein with AA change')
+        return None
     df_sum_mutations = df_transcript3[(df_transcript3['AA_seq'] != df_transcript3['new_AA']) & (pd.notnull(df_transcript3['new_AA']))][columns_keep]
 
     outfilename = outprefix +'.aa_mutations.csv'