def buildTree(conf, stree, gene2species):
params = Spidir.readParams(conf["param"])
if "correcttree" in conf:
conf["correcthash"] = phylo.hash_tree(conf["correcttree"])
if "dist" in conf:
for i in range(len(conf["dist"])):
distfile = conf["dist"][i]
labels, distmat = phylip.read_dist_matrix(distfile)
# read in different labels if needed
if "labels" in conf:
labels = Spidir.readLabels(conf["labels"][i])
conf["aln"] = fasta.read_fasta(conf["labels"][i])
tree, logl = Spidir.spidir(conf, distmat, labels, stree,
gene2species, params)
tree.write(Spidir.outTreeFile(conf))
# test for correctness
if "correcttree" in conf:
correctTree = conf["correcttree"]
phylo.hash_order_tree(correctTree)
phylo.hash_order_tree(tree)
thash1 = phylo.hash_tree(tree)
thash2 = phylo.hash_tree(correctTree)
print "spidir: "
treelib.draw_tree(tree, maxlen=5, minlen=5)
print
print "correct:"
treelib.draw_tree(correctTree, maxlen=5, minlen=5)
print
if len(tree.leaves()) > 3:
rferror = Spidir.robinson_foulds_error(correctTree, tree)
else:
rferror = 0.0
if thash1 == thash2:
print "CORRECT TREE FOUND"
else:
print "WRONG TREE FOUND (RF: %f)" % rferror
