From da4c8dbf0dd994f1db31051e5a8729f1783253cf Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Fri, 19 Nov 2021 16:59:20 +0100
Subject: [PATCH] prefer makeblastdb (BLAST+) over formatdb (legacy BLAST)
---
modules/bindings/pymod/blast.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index e64e01530..ba82c3397 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -148,12 +148,12 @@ def CreateDB(infasta, dbout, mkdb_cmd=None):
"""
if mkdb_cmd==None:
try:
- exe=settings.Locate('formatdb')
- args=[exe, '-i', infasta, '-n', dbout]
+ exe=settings.Locate('makeblastdb')
+ args=[exe, '-in', infasta, '-out', dbout, '-dbtype', 'prot']
except:
try:
- exe=settings.Locate('makeblastdb')
- args=[exe, '-in', infasta, '-out', dbout, '-dbtype', 'prot']
+ exe=settings.Locate('formatdb')
+ args=[exe, '-i', infasta, '-n', dbout]
except:
raise RuntimeError('could not find makeblastdb/formatdb executable')
else:
--
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