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Commit 3bd0466f authored by Studer Gabriel's avatar Studer Gabriel
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undo temporary depug output for CI investigation

parent 1d7038b8
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...@@ -611,23 +611,18 @@ class HHblits: ...@@ -611,23 +611,18 @@ class HHblits:
sout, serr = job.communicate() sout, serr = job.communicate()
lines = sout.decode().splitlines() lines = sout.decode().splitlines()
ost.LogError("SecStruct stdout :")
for line in lines: for line in lines:
ost.LogError(line.strip())
ost.LogVerbose(line.strip()) ost.LogVerbose(line.strip())
if 'error' in line.lower(): if 'error' in line.lower():
raise RuntimeError('Predicting secondary structure for MSA '+ raise RuntimeError('Predicting secondary structure for MSA '+
'(%s) failed, on command: %s' % (a3m_file, line)) '(%s) failed, on command: %s' % (a3m_file, line))
ost.LogError("SecStruct stderr:")
lines = serr.decode().splitlines() lines = serr.decode().splitlines()
for line in lines: for line in lines:
ost.LogError(line.strip())
ost.LogError(line.strip()) ost.LogError(line.strip())
if 'error' in line.lower(): if 'error' in line.lower():
raise RuntimeError('Predicting secondary structure for MSA '+ raise RuntimeError('Predicting secondary structure for MSA '+
'(%s) failed, on command: %s' % (a3m_file, line)) '(%s) failed, on command: %s' % (a3m_file, line))
ost.LogError("SecStruct done")
return a3m_file return a3m_file
......
...@@ -133,13 +133,6 @@ class TestHHblitsBindings(unittest.TestCase): ...@@ -133,13 +133,6 @@ class TestHHblitsBindings(unittest.TestCase):
'TSKYR') 'TSKYR')
self.hh = hhblits.HHblits(query_seq, self.hhroot) self.hh = hhblits.HHblits(query_seq, self.hhroot)
a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/unittestdb') a3m = self.hh.BuildQueryMSA('testfiles/hhblitsdb/unittestdb')
ost.LogError("Im the bad guy")
with open(a3m) as fh:
for line in fh.readlines():
ost.LogError(line)
ost.LogError("Bad guy over n out")
self.assertTrue(filecmp.cmp(a3m, "testfiles/testali_two.a3m")) self.assertTrue(filecmp.cmp(a3m, "testfiles/testali_two.a3m"))
def testA3mToProfileFileName(self): def testA3mToProfileFileName(self):
......
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