From 0e46a276ac4f1bd8ad3cf6c101f2b83ced716413 Mon Sep 17 00:00:00 2001
From: stefan <stefan@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Thu, 17 Jun 2010 15:30:17 +0000
Subject: [PATCH] fixes tmalign and tmtools subprocess calls (works on linux
and windows) please test it on mac
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2418 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/tmtools.py | 16 +++++-----------
1 file changed, 5 insertions(+), 11 deletions(-)
diff --git a/modules/bindings/pymod/tmtools.py b/modules/bindings/pymod/tmtools.py
index a8aae7100..9117b675d 100644
--- a/modules/bindings/pymod/tmtools.py
+++ b/modules/bindings/pymod/tmtools.py
@@ -69,15 +69,12 @@ def _RunTmAlign(tmalign, tmp_dir):
if platform.system() == "Windows":
tmalign_path=settings.Locate('tmalign.exe', explicit_file_name=tmalign)
command="\"%s\" %s %s" %(os.path.normpath(tmalign_path), model1_filename, model2_filename)
- command=command+" > "+tmp_dir+"/tmalign_output"
else:
tmalign_path=settings.Locate('tmalign', explicit_file_name=tmalign)
command="%s '%s' '%s'" %(tmalign_path, model1_filename, model2_filename)
- command=command+" > "+tmp_dir+"/tmalign_output"
- ps=subprocess.call(command, shell=True, stdout=subprocess.PIPE)
- tmalign_f=open(tmp_dir+"/tmalign_output","r")
- lines=tmalign_f.readlines()
- tmalign_f.close()
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+ ps.wait()
+ lines=ps.stdout.readlines()
if (len(lines))<22:
raise RuntimeError("tmalign superposition failed")
return _ParseTmAlign(lines)
@@ -117,15 +114,12 @@ def _RunTmScore(tmscore, tmp_dir):
if platform.system() == "Windows":
tmscore_path=settings.Locate('tmscore.exe', explicit_file_name=tmscore)
command="\"%s\" %s %s" %(os.path.normpath(tmscore_path), model1_filename, model2_filename)
- command=command+" > "+tmp_dir+"/tmscore_output"
else:
tmscore_path=settings.Locate('tmscore', explicit_file_name=tmscore)
command="%s '%s' '%s'" %(tmscore_path, model1_filename, model2_filename)
- command=command+" > "+tmp_dir+"/tmscore_output"
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
- tmscore_f=open(tmp_dir+"/tmscore_output","r")
- lines=tmscore_f.readlines()
- tmscore_f.close()
+ ps.wait()
+ lines=ps.stdout.readlines()
if (len(lines))<22:
raise RuntimeError("tmscore superposition failed")
return _ParseTmScore(lines)
--
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