From 8d1a0447c7abaea3716d551a8e383543dbc75f30 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 20 Nov 2019 11:35:35 +0100
Subject: [PATCH] set universal_newlines flag in Popen
This enables string encoding in passed streams => stdout and stderr
---
modules/bindings/pymod/blast.py | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/blast.py b/modules/bindings/pymod/blast.py
index 788d46025..7ecff0896 100644
--- a/modules/bindings/pymod/blast.py
+++ b/modules/bindings/pymod/blast.py
@@ -192,7 +192,7 @@ def BlastVersion(blast_location=None):
pattern=re.compile(r'\s*Package: blast (\d+\.\d+\.\d+),\s+')
blast_pipe=subprocess.Popen(args, stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
+ stderr=subprocess.PIPE, universal_newlines=True)
lines=blast_pipe.stdout.readlines()
for line in lines:
@@ -264,7 +264,8 @@ def Blast(query, database, gap_open=11, gap_ext=1, matrix='BLOSUM62',
ost.LogInfo('running BLAST (%s)' % ' '.join(args))
blast_pipe=subprocess.Popen(args, stderr=subprocess.PIPE,
- stdout=subprocess.PIPE, stdin=subprocess.PIPE)
+ stdout=subprocess.PIPE, stdin=subprocess.PIPE,
+ universal_newlines=True)
if isinstance(query, str):
stdout, stderr=blast_pipe.communicate(query)
else:
--
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