class Test(unittest.TestCase):
x = None
def setUp(self):
self.x = ExhaustiveAlgorithm()
self.x.options.alignment_file = open(
"data/q2-fragment-insertion/reference_alignment_tiny.fasta", "r")
self.x.options.info_file = open(
"data/q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info",
"r")
self.x.options.tree_file = open(
"data/q2-fragment-insertion/reference_phylogeny_tiny.nwk", "r")
self.x.options.outdir = tempfile.mkdtemp()
def tearDown(self):
self.x.options.alignment_file.close()
self.x.options.info_file.close()
self.x.options.tree_file.close()
self.x.options.fragment_file.close()
shutil.rmtree(self.x.options.outdir, ignore_errors=True)
def test_id_collision_working(self):
self.x.options.fragment_file = open(
"data/q2-fragment-insertion/input_fragments.fasta", "r")
self.x.run()
self.assertTrue(self.x.results is not None)
def test_id_collision_collision(self):
self.x.options.fragment_file = open(
"data/q2-fragment-insertion/input_fragments_collide.fasta", "r")
with self.assertRaisesRegex(
ValueError,
' whose names overlap with names in your reference'):
self.x.run()
self.assertTrue(self.x.results is None)
class Test(unittest.TestCase):
x = None
def resetSepp(self):
sepp.scheduler._jobPool = None
self.x = ExhaustiveAlgorithm()
self.x.options.alignment_file = open(
get_data_path(
"q2-fragment-insertion/reference_alignment_tiny.fasta"), "r")
self.x.options.info_file = open(
get_data_path(
"q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info"),
"r")
self.x.options.tree_file = open(
get_data_path(
"q2-fragment-insertion/reference_phylogeny_tiny.nwk"), "r")
self.x.options.outdir = tempfile.mkdtemp()
suff_bit = "-64" if sys.maxsize > 2**32 else "-32"
if platform.system() == 'Darwin':
suff_bit = ""
for prog in ['hmmalign', 'hmmbuild', 'hmmsearch', 'pplacer']:
setattr(self.x.options, prog, Namespace(
path=get_data_path("../../../tools/bundled/%s/%s%s" % (
platform.system(), prog, suff_bit))))
def setUp(self):
# ensure necessary settings are made
sys.argv = [sys.argv[0], "-c", get_data_path("configs/test2.config")]
self.resetSepp()
def tearDown(self):
shutil.rmtree(self.x.options.outdir, ignore_errors=True)
self.resetSepp()
def test_diamMid(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.options.maxDiam = 0.1
self.x.options.fragmentChunkSize = 1
self.x.options.decomp_strategy = "midpoint"
self.x.run()
self.assertTrue(self.x.results is not None)
def test_diamCent(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.options.maxDiam = 0.1
self.x.options.fragmentChunkSize = 1
self.x.options.decomp_strategy = "centroid"
self.x.run()
self.assertTrue(self.x.results is not None)
class Test(unittest.TestCase):
x = None
def resetSepp(self):
sepp.scheduler._jobPool = None
self.x = ExhaustiveAlgorithm()
self.x.options.alignment_file = open(
get_data_path(
"q2-fragment-insertion/reference_alignment_tiny.fasta"), "r")
self.x.options.info_file = open(
get_data_path(
"q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info"),
"r")
self.x.options.tree_file = open(
get_data_path(
"q2-fragment-insertion/reference_phylogeny_tiny.nwk"), "r")
self.x.options.outdir = tempfile.mkdtemp()
suff_bit = "-64" if sys.maxsize > 2**32 else "-32"
if platform.system() == 'Darwin':
suff_bit = ""
for prog in ['hmmalign', 'hmmbuild', 'hmmsearch', 'pplacer']:
setattr(
self.x.options, prog,
Namespace(
path=get_data_path("../../../tools/bundled/%s/%s%s" %
(platform.system(), prog, suff_bit))))
def setUp(self):
# ensure necessary settings are made
sys.argv = [sys.argv[0], "-c", get_data_path("configs/test2.config")]
self.resetSepp()
def tearDown(self):
shutil.rmtree(self.x.options.outdir, ignore_errors=True)
self.resetSepp()
def test_diamMid(self):
self.x.options.fragment_file = open(
get_data_path("q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.options.maxDiam = 0.1
self.x.options.fragmentChunkSize = 1
self.x.options.decomp_strategy = "midpoint"
self.x.run()
self.assertTrue(self.x.results is not None)
def test_diamCent(self):
self.x.options.fragment_file = open(
get_data_path("q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.options.maxDiam = 0.1
self.x.options.fragmentChunkSize = 1
self.x.options.decomp_strategy = "centroid"
self.x.run()
self.assertTrue(self.x.results is not None)
class Test(unittest.TestCase):
x = None
def resetSepp(self):
# ensure necessary settings are made
sepp.scheduler._jobPool = None
sepp.scheduler._parser = None
self.x = ExhaustiveAlgorithm()
self.x.options.alignment_file = open(
get_data_path(
"q2-fragment-insertion/reference_alignment_tiny.fasta"), "r")
self.x.options.info_file = open(
get_data_path(
"q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info"),
"r")
self.x.options.tree_file = open(
get_data_path(
"q2-fragment-insertion/reference_phylogeny_tiny.nwk"), "r")
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.options.outdir = tempfile.mkdtemp()
self.x.options.placement_size = 20
def setUp(self):
sys.argv = [sys.argv[0]]
self.resetSepp()
self._checkpointfile = tempfile.mktemp()
def tearDown(self):
shutil.rmtree(self.x.options.outdir, ignore_errors=True)
self.resetSepp()
def test_make_checkpoints(self):
self.x.options.checkpoint = set_checkpoint(self._checkpointfile)
self.x.options.checkpoint_interval = 5
self.x.run()
self.assertTrue(self.x.results is not None)
class Test(unittest.TestCase):
x = None
def setUp(self):
# ensure necessary settings are made
sepp.scheduler._jobPool = None
sys.argv = [sys.argv[0], "-c", get_data_path("configs/test2.config")]
self.x = ExhaustiveAlgorithm()
self.x.options.alignment_file = open(
get_data_path(
"q2-fragment-insertion/reference_alignment_tiny.fasta"), "r")
self.x.options.info_file = open(
get_data_path(
"q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info"),
"r")
self.x.options.tree_file = open(
get_data_path(
"q2-fragment-insertion/reference_phylogeny_tiny.nwk"), "r")
self.x.options.outdir = tempfile.mkdtemp()
suff_bit = "-64" if sys.maxsize > 2**32 else "-32"
if platform.system() == 'Darwin':
suff_bit = ""
for prog in ['hmmalign', 'hmmbuild', 'hmmsearch', 'pplacer']:
setattr(
self.x.options, prog,
Namespace(
path=get_data_path("../../../tools/bundled/%s/%s%s" %
(platform.system(), prog, suff_bit))))
def tearDown(self):
self.x.options.alignment_file.close()
self.x.options.info_file.close()
self.x.options.tree_file.close()
self.x.options.fragment_file.close()
sepp.scheduler._jobPool = None
shutil.rmtree(self.x.options.outdir, ignore_errors=True)
def test_id_collision_working(self):
self.x.options.fragment_file = open(
get_data_path("q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.run()
self.assertTrue(self.x.results is not None)
def test_id_collision_collision(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments_collide.fasta"), "r")
with self.assertRaisesRegex(
ValueError,
' whose names overlap with names in your reference'):
self.x.run()
self.assertTrue(self.x.results is None)
def test_seqnames_whitespaces(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments_spaces.fasta"), "r")
with self.assertRaisesRegex(ValueError,
"contain either whitespaces: "):
self.x.run()
self.assertTrue(self.x.results is None)
class Test(unittest.TestCase):
x = None
def setUp(self):
# ensure necessary settings are made
sepp.scheduler._jobPool = None
sys.argv = [sys.argv[0], "-c", get_data_path("configs/test2.config")]
self.x = ExhaustiveAlgorithm()
self.x.options.alignment_file = open(
get_data_path(
"q2-fragment-insertion/reference_alignment_tiny.fasta"), "r")
self.x.options.info_file = open(
get_data_path(
"q2-fragment-insertion/RAxML_info-reference-gg-raxml-bl.info"),
"r")
self.x.options.tree_file = open(
get_data_path(
"q2-fragment-insertion/reference_phylogeny_tiny.nwk"), "r")
self.x.options.outdir = tempfile.mkdtemp()
suff_bit = "-64" if sys.maxsize > 2**32 else "-32"
if platform.system() == 'Darwin':
suff_bit = ""
for prog in ['hmmalign', 'hmmbuild', 'hmmsearch', 'pplacer']:
setattr(self.x.options, prog, Namespace(
path=get_data_path("../../../tools/bundled/%s/%s%s" % (
platform.system(), prog, suff_bit))))
def tearDown(self):
self.x.options.alignment_file.close()
self.x.options.info_file.close()
self.x.options.tree_file.close()
self.x.options.fragment_file.close()
sepp.scheduler._jobPool = None
shutil.rmtree(self.x.options.outdir, ignore_errors=True)
def test_id_collision_working(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments.fasta"), "r")
self.x.run()
self.assertTrue(self.x.results is not None)
def test_id_collision_collision(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments_collide.fasta"), "r")
with self.assertRaisesRegex(
ValueError,
' whose names overlap with names in your reference'):
self.x.run()
self.assertTrue(self.x.results is None)
def test_seqnames_whitespaces(self):
self.x.options.fragment_file = open(
get_data_path(
"q2-fragment-insertion/input_fragments_spaces.fasta"), "r")
with self.assertRaisesRegex(
ValueError,
"contain either whitespaces: "):
self.x.run()
self.assertTrue(self.x.results is None)