From 8ab1af867d31eb93eb748eff7009287750417cf1 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Mon, 2 Dec 2019 18:43:57 +0100
Subject: [PATCH] parse lga output from binary stream
---
modules/bindings/pymod/lga.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/modules/bindings/pymod/lga.py b/modules/bindings/pymod/lga.py
index 7ab23e854..59f5d53fb 100644
--- a/modules/bindings/pymod/lga.py
+++ b/modules/bindings/pymod/lga.py
@@ -109,7 +109,9 @@ def GDT(pdb1, pdb2, chain1='', chain2='', reference_length=None, lga_bin=None):
expanded_cmd=command % params
lga_proc=subprocess.Popen(expanded_cmd, shell=True,
stdout=subprocess.PIPE)
+ stdout, _ = lga_proc.communicate()
+
length=reference_length or max(pdb1.residue_count, pdb2.residue_count)
- result=_ParseLGAOutput(lga_proc.stdout.readlines(), reference_length)
+ result=_ParseLGAOutput(stdout.decode().splitlines(), reference_length)
os.system('rm -r %s' % temp_d)
return result
--
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