From 33e8b86a6ec1d167266b5df956d4a15f0660ddea Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 17:00:32 +0100
Subject: [PATCH] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/ialign.py | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/ialign.py b/modules/bindings/pymod/ialign.py
index 2c6090102..176a5dbe4 100644
--- a/modules/bindings/pymod/ialign.py
+++ b/modules/bindings/pymod/ialign.py
@@ -140,9 +140,12 @@ def _RuniAlign(ialign, tmp_dir, options={}):
else:
ialign_path=settings.Locate('ialign.pl', explicit_file_name=ialign)
command="\"%s\" \"%s\" \"%s\" %s" % (ialign_path, model1_filename, model2_filename, cmd_opts)
- ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+
+ ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE,
+ universal_newlines=True)
ps.wait()
lines=ps.stdout.readlines()
+
if (len(lines))<22:
_CleanupFiles(tmp_dir)
#for l in lines:
--
GitLab