def test_init_expect_conflicting_options(self):
"""Test PBAlignRunner.__init__() with a config file and --algorithmOptions
and expect a ValueError for conflicting options."""
argumentList = [
'--algorithmOptions', '-minMatch 10 -useccsall', '--configFile',
self.configFile, self.queryFile, self.referenceFile, self.cmph5Out
]
pbobj = PBAlignRunner(argumentList=argumentList)
with self.assertRaises(ValueError) as cm:
# Expect a ValueError since -minMatch and --minAnchorSize conflicts.
pbobj.start()
def test_init_expect_conflicting_options(self):
"""Test PBAlignRunner.__init__() with a config file and --algorithmOptions
and expect a ValueError for conflicting options."""
argumentList = ['--algorithmOptions', '-minMatch 10 -useccsall',
'--configFile', self.configFile,
self.queryFile, self.referenceFile,
self.cmph5Out]
pbobj = PBAlignRunner(argumentList = argumentList)
with self.assertRaises(ValueError) as cm:
# Expect a ValueError since -minMatch and --minAnchorSize conflicts.
pbobj.start()
def test_init_with_algorithmOptions(self):
"""Test PBAlignRunner.__init__() with --algorithmOptions."""
argumentList = ['--algorithmOptions', '-minMatch 10 -useccsall',
self.queryFile, self.referenceFile,
self.cmph5Out]
pbobj = PBAlignRunner(argumentList = argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init(self):
"""Test PBAlignRunner.__init__()."""
argumentList = ['--minAccuracy', '70', '--maxDivergence', '30',
self.queryFile, self.referenceFile,
self.samOut]
pbobj = PBAlignRunner(argumentList = argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init_with_algorithmOptions(self):
"""Test PBAlignRunner.__init__() with --algorithmOptions."""
argumentList = [
'--algorithmOptions', '-minMatch 10 -useccsall', self.queryFile,
self.referenceFile, self.cmph5Out
]
pbobj = PBAlignRunner(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init(self):
"""Test PBAlignRunner.__init__()."""
argumentList = [
'--minAccuracy', '70', '--maxDivergence', '30', self.queryFile,
self.referenceFile, self.samOut
]
pbobj = PBAlignRunner(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init_with_config_algorithmOptions(self):
"""Test PBAlignRunner.__init__() with a config file and --algorithmOptions."""
argumentList = ['--algorithmOptions', '-maxMatch 20 -nCandidates 30',
'--configFile', self.configFile,
self.queryFile, self.referenceFile,
self.cmph5Out]
pbobj = PBAlignRunner(argumentList = argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init_xml(self):
"""Test PBAlignRunner.__init__() to XML."""
argumentList = ['--minAccuracy', '70', '--maxDivergence', '30',
self.queryFile, self.referenceFile,
self.xmlOut]
pbobj = PBAlignRunner(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
aln = AlignmentSet(self.xmlOut)
self.assertEqual(aln.externalResources[0].reference,
ReferenceSet(self.referenceFile).toExternalFiles()[0])
def test_init_with_config_algorithmOptions(self):
"""Test PBAlignRunner.__init__() with a config file and --algorithmOptions."""
argumentList = [
'--algorithmOptions', '-maxMatch 20 -nCandidates 30',
'--configFile', self.configFile, self.queryFile,
self.referenceFile, self.cmph5Out
]
pbobj = PBAlignRunner(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
def test_init_xml(self):
"""Test PBAlignRunner.__init__() to XML."""
argumentList = [
'--minAccuracy', '70', '--maxDivergence', '30', self.queryFile,
self.referenceFile, self.xmlOut
]
pbobj = PBAlignRunner(argumentList=argumentList)
self.assertEqual(pbobj.start(), 0)
aln = AlignmentSet(self.xmlOut)
self.assertEqual(aln.externalResources[0].reference,
ReferenceSet(self.referenceFile).toExternalFiles()[0])