From 3afd902dd2d139a7ef1a19556787e8383a2cd9ba Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 17 Jun 2014 18:03:35 +0200
Subject: [PATCH] Handling non-matching hits in BLAST
---
modules/bindings/pymod/blast.py | 8 +++++++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index e2a6f373e..08359de4d 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -83,7 +83,13 @@ def ParseBlastOutput(string, seqid_thres=0, evalue_thres=float("infinity")):
bit_score=float(_GetValue(hsp, 'Hsp_bit-score'))
score=float(_GetValue(hsp, 'Hsp_score'))
evalue=float(_GetValue(hsp, 'Hsp_evalue'))
- identity=float(_GetValue(hsp, 'Hsp_identity'))
+ try:
+ identity=float(_GetValue(hsp, 'Hsp_identity'))
+ except AssertionError:
+ # The Hsp_identity tag is not a 'must' in the BLAST XML format. It
+ # describes the number of matching characters. Hence we assume, if it is
+ # missing, there are 0 matches.
+ identity=0
hsp_align_len=float(_GetValue(hsp, 'Hsp_align-len'))
seqid=identity/hsp_align_len
query_offset=_GetInt(hsp, 'Hsp_query-from')-1
--
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