From b12ef172a0ec4f0af1f84b89739e18c4f5ad970c Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 10 Feb 2012 16:15:18 +0100
Subject: [PATCH] blast binding looks now both for .pin and .pal database file
---
modules/bindings/pymod/blast.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 054bff58c..8f14d64dc 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -136,7 +136,8 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
:type query: :class:`seq.ConstSequenceHandle`
:param database: The filename of the sequence database. Make sure that
- formatdb has been run on the database and the <database>.pin file exists.
+ formatdb has been run on the database and the <database>.pin or
+ <database>.pal file exists.
:param matrix: The substitution matrix to be used. Must be one of 'BLOSUM45',
'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70'.
:param gap_open: Gap opening penalty. Note that only a subset of gap opening
@@ -155,7 +156,7 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
subst_mats=('BLOSUM45', 'BLOSUM62', 'BLOSUM80', 'PAM30', 'PAM70',)
if matrix not in subst_mats:
raise ValueError('matrix must be one of %s' % ', '.join(subst_mats))
- if not os.path.exists('%s.pin' % database):
+ if not os.path.exists('%s.pin' % database) and not os.path.exists('%s.pal' % database):
raise IOError("Database %s does not exist" % database)
blastall_exe=settings.Locate('blastall', explicit_file_name=blast_location)
args=[blastall_exe, '-d', database, '-p', 'blastp',
--
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