return more precise difference in orfs.json

cfe-lab · Jun 30, 2023 · 7b71af3 · 7b71af3
1 parent b508a07
commit 7b71af3
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Showing 4 changed files with 519 additions and 517 deletions.
diff --git a/intact/intact.py b/intact/intact.py
@@ -607,8 +607,10 @@ def get_indel_impact(alignment):
         exp_nucleotides = reference[e.start:e.end].upper()
         if got_nucleotides:
             orf_alignment = aligner.align(exp_nucleotides, got_nucleotides)[0]
+            best_match.distance = -1 * (orf_alignment.score / len(exp_nucleotides))
         else:
             orf_alignment = (exp_nucleotides, "-" * len(exp_nucleotides))
+            best_match.distance = len(exp_nucleotides) ** 2
 
         deletions = max(0, len(exp_protein) - len(got_protein)) * 3
         insertions = max(0, len(got_protein) - len(exp_protein)) * 3