From 9a9938993f5a0493e42f9b13a0e3834816ae246a Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 22 Jan 2013 09:17:59 +0000
Subject: [PATCH] Temporarily disable frameshift detection (#124)
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@666 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/describe.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 44e62646..4ca3f453 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -256,6 +256,10 @@ def fitFS(peptide, altPeptide, FS):
@arg FS: Frame shift table.
@type FS: dict
"""
+ # Todo: This is a temporary fix to prevent crashing on frameshift
+ # detection (I think bug #124).
+ return False
+
if len(peptide) < len(altPeptide):
return False
@@ -766,7 +770,7 @@ def protein_description(M, s1, s2, s1_start, s1_end, s2_start, s2_end):
if (fitFS(s1[s1_start + 1:], s2[s2_start + 1:], FS1) or
fitFS(s1[s1_start + 1:], s2[s2_start + 1:], FS2) or
fitFS(s2[s2_start + 1:], s1[s1_start + 2:], FS1) or
- fitFS(s2[s2_start + 1:], s1[s1_start + 2:], FS2)):
+ fitFS(s2[s2_start + 1:], s1[s1_start + 2:], FS2)):
return [RawVar(DNA=False, start=s1_start + 1, deleted=s1[s1_start],
inserted=s2[s2_start], term=len(s2) - s2_start, type="fs")]
#if
--
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