From e92657fdf715afb2113b2fd4c0299e4a83817c77 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Mon, 25 Feb 2019 17:50:10 +0100
Subject: [PATCH] Fix the HHblits parser for large alignments where the format
slightly changes.
---
modules/bindings/pymod/hhblits.py | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index a203a2920..34efe86af 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -254,21 +254,27 @@ def ParseHHblitsOutput(output):
if line[1:].startswith(' ss_dssp'):
continue
if line.startswith('T '):
- end_pos = line.find(' ', 22)
+ for start_pos in range(22, len(line)):
+ if line[start_pos].isalpha() or line[start_pos] == '-':
+ break
+ end_pos = line.find(' ', start_pos)
# this can fail if we didn't skip all other "T ..." lines
if end_pos == -1:
error_str = "Unparsable line '%s' for entry No %d" \
% (line.strip(), entry_index + 1)
raise AssertionError(error_str)
- templ_str += line[22:end_pos]
+ templ_str += line[start_pos:end_pos]
if line.startswith('Q '):
- end_pos = line.find(' ', 22)
+ for start_pos in range(22, len(line)):
+ if line[start_pos].isalpha() or line[start_pos] == '-':
+ break
+ end_pos = line.find(' ', start_pos)
# this can fail if we didn't skip all other "Q ..." lines
if end_pos == -1:
error_str = "Unparsable line '%s' for entry No %d" \
% (line.strip(), entry_index + 1)
raise AssertionError(error_str)
- query_str += line[22:end_pos]
+ query_str += line[start_pos:end_pos]
except StopIteration:
if len(query_str) > 0:
hits[entry_index][0].aln = _MakeAln(query_id,
--
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