def write(self):
if hasattr(self, 'result'):
errors.directorymake(self.outdir)
for rec in self.result:
filename = fileIO.join_path(self.outdir, rec.name) + '.phy'
rec.write_phylip(filename, interleaved=True)
for i in range(self.num_classes):
tree = self.class_trees[i+1]
name = 'tree{0:0>{1}}.nwk'.format(i+1, len(str(self.num_classes)))
filename = fileIO.join_path(self.outdir, name)
tree.write_to_file(filename)
filename = fileIO.join_path(self.outdir, 'true_partition.txt')
with open(filename, 'w') as partition_file:
partition_file.write(repr(self.true_partition))
def write(self):
if hasattr(self, 'result'):
errors.directorymake(self.outdir)
for rec in self.result:
filename = fileIO.join_path(self.outdir, rec.name) + '.phy'
rec.write_phylip(filename, interleaved=True)
for i in range(self.num_classes):
tree = self.class_trees[i + 1]
name = 'tree{0:0>{1}}.nwk'.format(i + 1,
len(str(self.num_classes)))
filename = fileIO.join_path(self.outdir, name)
tree.write_to_file(filename)
filename = fileIO.join_path(self.outdir, 'true_partition.txt')
with open(filename, 'w') as partition_file:
partition_file.write(repr(self.true_partition))
def make_alf_dirs(self):
alf_dirs = {}
for k in range(self.num_classes):
dirname = fileIO.join_path(self.tmpdir,
'class{0:0>1}'.format(k + 1))
alf_dirs[k + 1] = errors.directorymake(dirname)
self.alf_dirs = alf_dirs
def make_alf_dirs(self):
alf_dirs = {}
for k in range(self.num_classes):
dirname = fileIO.join_path(self.tmpdir, 'class{0:0>1}'.format(
k+1))
alf_dirs[k+1] = errors.directorymake(dirname)
self.alf_dirs = alf_dirs
def __init__(
self,
class_list,
permutations_list,
nspecies,
tmpdir,
datatype='protein',
master_tree_generator_method='yule',
master_tree=None,
class_tree_permuter='nni',
gene_length_kappa=1.7719,
gene_length_theta=279.9,
gene_length_min=10,
outdir='./'
):
# default
errors.optioncheck(master_tree_generator_method, ['yule', 'coal',
'rtree', 'custom'])
errors.optioncheck(class_tree_permuter, ['nni', 'spr', 'lgt', 'genetree'
])
if master_tree is None and master_tree_generator_method == 'custom':
raise Exception('No custom tree was specified')
self.num_classes = len(class_list)
self.num_genes = sum(class_list)
self.class_list = class_list
if master_tree is None:
tree = self.generate_master_tree(master_tree_generator_method,
nspecies)
self.master_tree = tree
self.num_species = nspecies
else:
self.master_tree = master_tree
if len(master_tree) != nspecies:
msg = [
'Warning: supplied tree has {0} taxa.'.format(
len(master_tree)),
'Required number is {0}.\n'.format(nspecies),
'Resetting number of species to match the supplied tree.'
]
print ''.join(msg)
self.num_species = nspecies
self.set_gene_lengths(gene_length_kappa, gene_length_theta,
gene_length_min)
self.permuter = class_tree_permuter
self.permutations_list = permutations_list
self.datatype = datatype
self.tmpdir = errors.directorymake(tmpdir)
self.outdir = outdir
self.generate_class_trees() # sets self.class_trees dict
self.make_alf_dirs() # sets self.alf_dirs dict
self.write_alf_params()
self.get_true_partition()