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

@@ -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)