Fix pVACvector bug that would result in not all junctional epitopes g…

…etting tested on clipping
griffithlab · Feb 10, 2025 · 0285cbf · 0285cbf
1 parent 0eea407
commit 0285cbf
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Showing 14 changed files with 937 additions and 601 deletions.
diff --git a/pvactools/lib/fasta_generator.py b/pvactools/lib/fasta_generator.py
@@ -402,8 +402,8 @@ def execute(self):
                             if right_clip_length > first_position:
                                 warnings.add("Clipping {} amino acids off the start of peptide {} would clip the best peptide. Skipping.".format(right_clip_length, seq2))
                                 continue
-                        trunc_seq1 = seq1_seq[(len(seq1_seq) - wingspan_length):(len(seq1_seq) - left_clip_length)]
-                        trunc_seq2 = seq2_seq[(0 + right_clip_length):wingspan_length]
+                        trunc_seq1 = seq1_seq[(len(seq1_seq) - wingspan_length - left_clip_length):(len(seq1_seq) - left_clip_length)]
+                        trunc_seq2 = seq2_seq[(0 + right_clip_length):wingspan_length + right_clip_length]
 
                         if self.spacer != 'None':
                             seq_ID = "{}|{}|{}|{}|{}".format(seq1, left_clip_length, self.spacer, right_clip_length, seq2)