From d27c07b04e3b230457368e592974081f911bb094 Mon Sep 17 00:00:00 2001
From: gongyixiao <5620765+gongyixiao@users.noreply.github.com>
Date: Thu, 16 Jul 2020 13:47:17 -0400
Subject: [PATCH 1/2] better handling for no mutation input maf

add header to empty maf file and empty .all_neoantigen_predictions.txt
---
 neoantigen.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/neoantigen.py b/neoantigen.py
index 4464cf6..1d51390 100644
--- a/neoantigen.py
+++ b/neoantigen.py
@@ -295,9 +295,22 @@ def main():
 
         # create empty neoantigens.maf file if there are no mutations
         if n_muts == 0:
-            logger.info('No mutations in this tumor. Creating empty .neoantigens.maf file')
+            logger.info('No mutations in this tumor. Creating empty .neoantigens.maf and .all_neoantigen_predictions.txt file')
             logger.info('Exiting neoantigen pipeline')
-            execute_cmd('touch ' + sample_path_pfx + '.neoantigens.maf')
+            maf_df_empty = maf_df
+            maf_df_empty['neo_maf_identifier_key'] = ''
+            maf_df_empty['neo_best_icore_peptide'] = ''
+            maf_df_empty['neo_best_rank'] = ''
+            maf_df_empty['neo_best_binding_affinity'] = ''
+            maf_df_empty['neo_best_binder_class'] = ''
+            maf_df_empty['neo_best_is_in_wt_peptidome'] = ''
+            maf_df_empty['neo_best_algorithm'] = ''
+            maf_df_empty['neo_best_hla_allele'] = ''
+            maf_df_empty['neo_n_peptides_evaluated'] = ''
+            maf_df_empty['neo_n_strong_binders'] = ''
+            maf_df_empty['neo_n_weak_binders'] = ''
+            maf_df_empty.to_csv(sample_path_pfx + '.neoantigens.maf' , sep='\t', index=False)
+            execute_cmd('touch ' + sample_path_pfx + '.all_neoantigen_predictions.txt')
             exit(1)
 
     except Exception:

From 945d26b0e7289e2ed3b4a4cb1866a1f27443ff2d Mon Sep 17 00:00:00 2001
From: gongyixiao <5620765+gongyixiao@users.noreply.github.com>
Date: Thu, 16 Jul 2020 13:50:29 -0400
Subject: [PATCH 2/2] change exit code to 0

---
 neoantigen.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/neoantigen.py b/neoantigen.py
index 1d51390..e798c68 100644
--- a/neoantigen.py
+++ b/neoantigen.py
@@ -311,7 +311,7 @@ def main():
             maf_df_empty['neo_n_weak_binders'] = ''
             maf_df_empty.to_csv(sample_path_pfx + '.neoantigens.maf' , sep='\t', index=False)
             execute_cmd('touch ' + sample_path_pfx + '.all_neoantigen_predictions.txt')
-            exit(1)
+            exit(0)
 
     except Exception:
         logger.error('Error while generating mutated peptides')