From b6cfdc93c9f0b267f66ceaa5c791dc66b6547b9d Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Thu, 9 Mar 2017 11:17:07 +0100
Subject: [PATCH] Testing
---
modules/bindings/pymod/hhblits.py | 6 +++++-
modules/bindings/tests/test_hhblits.py | 10 ----------
2 files changed, 5 insertions(+), 11 deletions(-)
diff --git a/modules/bindings/pymod/hhblits.py b/modules/bindings/pymod/hhblits.py
index 83adafdec..68e8a7f67 100644
--- a/modules/bindings/pymod/hhblits.py
+++ b/modules/bindings/pymod/hhblits.py
@@ -577,13 +577,17 @@ class HHblits:
job = subprocess.Popen(addss_cmd, shell=True, cwd=self.working_dir,
env=env, stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
- sout, _ = job.communicate()
+ sout, serr = job.communicate()
lines = sout.splitlines()
for line in lines:
if 'error' in line.lower():
ost.LogWarning('Predicting secondary structure for MSA '+
'(%s) failed, on command: %s' % (a3m_file, line))
return a3m_file
+ print "BIENCHEN", line
+ lines = serr.splitlines()
+ for line in lines:
+ print "BIENCHEN", line
return a3m_file
def A3MToProfile(self, a3m_file, hhm_file=None):
diff --git a/modules/bindings/tests/test_hhblits.py b/modules/bindings/tests/test_hhblits.py
index f1d2d4042..c396528b8 100644
--- a/modules/bindings/tests/test_hhblits.py
+++ b/modules/bindings/tests/test_hhblits.py
@@ -115,16 +115,6 @@ class TestHHblitsBindings(unittest.TestCase):
'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot)
a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/hhblitsdb')
- print "A3M"
- with open(a3m) as fh:
- for line in fh:
- line = line.strip()
- print line
- print "TESTFILE"
- with open("testfiles/testali.a3m") as fh:
- for line in fh:
- line = line.strip()
- print line
self.assertTrue(filecmp.cmp(a3m, "testfiles/testali.a3m"))
def testA3mToProfileFileName(self):
--
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