From c45d1761ce1e281c013a03020068b6df9041e45f Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@stud.unibas.ch>
Date: Tue, 20 Nov 2012 16:32:35 +0100
Subject: [PATCH] suppress terminal output, when running kclust with binding.
---
modules/bindings/pymod/kclust.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/modules/bindings/pymod/kclust.py b/modules/bindings/pymod/kclust.py
index 3a0605be3..f4ace6788 100644
--- a/modules/bindings/pymod/kclust.py
+++ b/modules/bindings/pymod/kclust.py
@@ -99,7 +99,7 @@ def _RunkClust(tmp_dir_name, clustering_thresh, create_alignments):
executable=settings.Locate('kClust')
cmd=[]
- cmd.append('kClust')
+ cmd.append(executable)
cmd.append('-i')
cmd.append(os.path.join(tmp_dir_name,'fastadb.fasta'))
cmd.append('-d')
@@ -108,8 +108,8 @@ def _RunkClust(tmp_dir_name, clustering_thresh, create_alignments):
cmd.append(str(bitscore))
cmd=' '.join(cmd)
- ps=subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
- ps.stdout.readlines()
+ ps=subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+ stdout, stderr = ps.communicate()
result=_ParseOutput(tmp_dir_name)
--
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