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)