def tree_collection(self,
niters=5,
keep_topology=False,
quiet=True,
tmpdir=None,
taxon_set=None,
guide_tree=None,
set_as_record_tree=True):
import tree_collection
if tmpdir is not None:
tmpdir = tmpdir
elif self.tmpdir is not None:
tmpdir = self.tmpdir
else:
tmpdir = TMPDIR
gt = None
if guide_tree is not None:
gt = guide_tree
elif self.tree is not None:
gt = self.tree
else:
self.bionj(tmpdir)
gt = self.tree
if gt is None:
raise Exception('Couldn\'t generate a guide tree')
if self.dv <= []:
self.dv_matrix(tmpdir)
if not gt.is_rooted:
gt.reroot_at_midpoint()
if not gt.is_rooted:
raise Exception('Couldn\'t root the guide tree' )
dv, gm, lab = self._get_tree_collection_strings()
output_tree, score = tree_collection.compute(dv, gm, lab, gt.newick,
niters, keep_topology,
quiet)
if taxon_set is not None:
result = TrClTree(output_tree, score, program='tree_collection',
name=self.name, output='',
taxon_set=taxon_set)
else:
result = TrClTree(output_tree, score, program='tree_collection',
name=self.name, output='')
if set_as_record_tree:
self.tree = result
return result
#!/usr/bin/env python
from __future__ import print_function
import tree_collection
mat = open('/Users/kgori/git_repos/gitolite/treesoflife/data/DistVar.txt').read()
map_ = open('/Users/kgori/git_repos/gitolite/treesoflife/data/GenomeMap.txt').read()
lab = open('/Users/kgori/git_repos/gitolite/treesoflife/data/Labels.txt').read()
tre = open('/Users/kgori/git_repos/gitolite/treesoflife/data/Tree.nwk').read()
print('Running test 1 - fit initial tree...')
result = tree_collection.compute(mat, map_, lab, tre,
iter=8,
keep_topology=True,
quiet=False)
print(type(result))
print(result[0])
print(result[1])
print('Running test 2 - optimise tree...')
result = tree_collection.compute(mat, map_, lab, tre,
iter=8,
keep_topology=False,
quiet=False)
print(type(result))
print(result[0])
print(result[1])
#!/usr/bin/env python
import tree_collection
import sys
folder_name = sys.argv[1]
mat = open(folder_name + 'DistVar.txt').read()
map_ = open(folder_name + 'Map.txt').read()
lab = open(folder_name + "Labels.txt").read()
tre = open(folder_name + 'initial_tree.txt').read()
result = tree_collection.compute(mat, map_, lab, tre, 8, False)
with open(r'%s' % folder_name + "tree.txt", 'w') as tree_coll_tree:
tree_coll_tree.write(result[0])
def minsq_task(dv, gm, lab, tree, niters=10):
tree, sse = tree_collection.compute(dv, gm, lab, tree, niters, False, True)
tree = Tree(tree)
tree.deroot()
return dict(tree=tree.newick, sse=sse)
def minsq_task(dv, gm, lab, tree, niters=10, keep_topology=False):
tree, lk = tree_collection.compute(dv, gm, lab, tree, niters, True, keep_topology, False)
tree = Tree(tree)
tree.deroot()
return dict(tree=tree.newick, score=lk)
def minsq_task(dv, gm, lab, tree, niters=10):
tree, sse = tree_collection.compute(dv, gm, lab, tree, niters, False, True)
tree = Tree(tree)
tree.deroot()
return dict(tree=tree.newick, sse=sse)