def test_smap_error(self): mul = MulRFModel(extra = None) gene2species = phylo.read_gene2species("../../../examples/test/nonBinaryAll.smap") stree = treelib.read_tree('../../../examples/test/24Hits.stree') gtree = treelib.read_tree('../../../examples/test/24Hits.gtree') with self.assertRaises(Exception): mul.optimize_model(gtree, stree, None)
def test_nonbinary_trees(self): mul = MulRFModel(extra = None) gene2species = phylo.read_gene2species("../../../examples/test/nonBinaryAll.smap") stree = treelib.read_tree('../../../examples/test/nonBinaryAll.stree') gtree = treelib.read_tree('../../../examples/test/nonBinaryAll.gtree') mul.stree = stree mul.gene2species = gene2species self.assertEqual(mul.compute_cost(gtree), 6)
def test_null_trees(self): mul = MulRFModel(extra = None) stree = treelib.read_tree('../../../examples/test/EmptyTree.stree') gtree = treelib.read_tree('../../../examples/test/EmptyTree.stree') gene2species = phylo.read_gene2species("../../../examples/test/24Hits.smap") mul.stree = stree mul.gene2species = gene2species with self.assertRaises(AttributeError): mul.compute_cost(gtree)
def test_deep(self): deep = DeepCoalescenceModel(extra = None) gene2species = phylo.read_gene2species("../../../examples/test/24Hits.smap") stree = treelib.read_tree('../../../examples/test/test1.stree') gtree = treelib.read_tree('../../../examples/test/test1.gtree') deep.stree = stree deep.gene2species = gene2species self.assertEqual(deep.compute_cost(gtree), 2)
def test_single_node(self): sNode = treelib.TreeNode() gNode = treelib.TreeNode() mul = MulRFModel(extra = None) gene2species = phylo.read_gene2species("../../../examples/test/nonBinaryAll.smap") mul.stree = sNode mul.gene2species = gene2species with self.assertRaises(AttributeError): mul.compute_cost(gNode)
def test_birthDeathPrior_large(self): """test birth death prior for large trees""" l = 0.000732 u = 0.000859 maxdoom = 20 stree = treelib.read_tree("test/data/fungi.stree") gene2species = phylo.read_gene2species("test/data/fungi.smap") tree = treelib.read_tree("test/data/fungi/10169/10169.tree") recon = phylo.reconcile(tree, stree, gene2species) p = c_calcBirthDeathPrior(tree, stree, recon, l, u, maxdoom) print p self.assert_(p != -INF)
#gene2species = phylo.read_gene2species(conf.smap) stree = treelib1.read_tree(conf.stree) tree = treelib1.read_tree(conf.tree) if conf.names: snames = dict(util.read_delim(conf.names)) else: snames = None if conf.brecon: brecon = phylo.read_brecon(conf.brecon, tree, stree) elif conf.recon: recon, events = phylo.read_recon_events(conf.recon, tree, stree) brecon = phylo.recon_events2brecon(recon, events) else: gene2species = phylo.read_gene2species(conf.smap) recon = phylo.reconcile(tree, stree, gene2species) events = phylo.label_events(tree, recon) brecon = phylo.recon_events2brecon(recon, events) phylo.add_implied_spec_nodes_brecon(tree, brecon) transsvg.draw_tree(tree, brecon, stree, filename=conf.output, snames=snames)
#============================================================================= # parse options conf, args = o.parse_args() #gene2species = phylo.read_gene2species(conf.smap) stree = treelib1.read_tree(conf.stree) tree = treelib1.read_tree(conf.tree) if conf.names: snames = dict(util.read_delim(conf.names)) else: snames = None if conf.brecon: brecon = phylo.read_brecon(conf.brecon, tree, stree) elif conf.recon: recon, events = phylo.read_recon_events(conf.recon, tree, stree) brecon = phylo.recon_events2brecon(recon, events) else: gene2species = phylo.read_gene2species(conf.smap) recon = phylo.reconcile(tree, stree, gene2species) events = phylo.label_events(tree, recon) brecon = phylo.recon_events2brecon(recon, events) phylo.add_implied_spec_nodes_brecon(tree, brecon) transsvg.draw_tree(tree, brecon, stree, filename=conf.output, snames=snames)