From 00f77e8abc3f472b70ce4909f831a412040c81be Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 16 Jan 2019 13:38:33 +0100
Subject: [PATCH] use default argument for db size when creating new blast db
Newer version have a hard limit for maximum file size that has been
exceeded by the arguments provided by the blast binding.
We simply use the default instead. Thanks to Andrius Merkys for the proposed fix.
---
modules/bindings/pymod/blast.py | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 0a51c1ed8..e63007f40 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -149,21 +149,20 @@ def CreateDB(infasta, dbout, mkdb_cmd=None):
if mkdb_cmd==None:
try:
exe=settings.Locate('formatdb')
- args=[exe, '-i', infasta, '-v',str(10000),'-n',dbout]
+ args=[exe, '-i', infasta, '-n', dbout]
except:
try:
exe=settings.Locate('makeblastdb')
- args=[exe, '-in', infasta, ' -max_file_sz 10GB -out', dbout,'-dbtype','prot']
-
+ args=[exe, '-in', infasta, '-out', dbout, '-dbtype', 'prot']
except:
raise RuntimeError('could not find makeblastdb/formatdb executable')
else:
if os.path.basename(mkdb_cmd)=='makeblastdb':
exe=settings.Locate('makeblastdb',explicit_file_name=mkdb_cmd)
- args=[exe, '-in', infasta, ' -max_file_sz 10GB -out', dbout,'-dbtype','prot']
+ args=[exe, '-in', infasta, '-out', dbout, '-dbtype', 'prot']
elif os.path.basename(mkdb_cmd)=='formatdb':
exe=settings.Locate('formatdb',explicit_filename=mkdb_cmd)
- args=[exe, '-i', infasta, '-v',str(10000),'-n',dbout]
+ args=[exe, '-i', infasta, '-n', dbout]
else:
raise IOError('mkdb command must either be the path to formatdb or makeblastdb!')
--
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