Merge branch 'hotfix'

griffithlab · Dec 14, 2016 · 095664b · 095664b
2 parents 06f994a + e475eb6
commit 095664b
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/pvacseq/lib/convert_vcf.py b/pvacseq/lib/convert_vcf.py
@@ -242,7 +242,10 @@ def main(args_input = sys.argv[1:]):
                 if consequence is None:
                     continue
                 elif consequence == 'FS':
-                    amino_acid_change_position = transcript['Protein_position']
+                    if transcript['DownstreamProtein'] == '':
+                        continue
+                    else:
+                        amino_acid_change_position = transcript['Protein_position']
                 else:
                     amino_acid_change_position = transcript['Protein_position'] + transcript['Amino_acids']
                 gene_name = transcript['SYMBOL']

diff --git a/pvacseq/lib/parse_output.py b/pvacseq/lib/parse_output.py
@@ -59,12 +59,13 @@ def match_wildtype_and_mutant_entry_for_missense(result, mt_position, wt_results
 def match_wildtype_and_mutant_entry_for_frameshift(result, mt_position, wt_results, previous_result):
     #The WT epitope at the same position is the match
     match_position = mt_position
-
     #Since the MT sequence is longer than the WT sequence, not all MT epitopes have a match
     if match_position not in wt_results:
         result['wt_epitope_seq'] = 'NA'
         result['wt_scores']      = dict.fromkeys(result['mt_scores'].keys(), 'NA')
-        if previous_result['mutation_position'] > 0:
+        if previous_result['mutation_position'] == 'NA':
+            result['mutation_position'] = 'NA'
+        elif previous_result['mutation_position'] > 0:
             result['mutation_position'] = previous_result['mutation_position'] - 1
         else:
             result['mutation_position'] = 0