def make_alf_dirs_(self):
""" DEPRECATED """
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):
""" DEPRECATED """
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 write(self):
if hasattr(self, 'result'):
errors.directorymake(self.outdir)
errors.directorymake(fileIO.join_path(self.outdir,
'base_class_trees'))
errors.directorymake(fileIO.join_path(self.outdir,
'gene_trees'))
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 = 'base_tree_class{0:0>{1}}.nwk'.format(i+1,
len(str(self.num_classes)))
filename = fileIO.join_path(self.outdir, 'base_class_trees',
name)
tree.write_to_file(filename)
for i, tree in enumerate(self.gene_trees, start=1):
filename = fileIO.join_path(self.outdir, 'gene_trees',
tree.name+'.nwk')
tree.write_to_file(filename)
self.master_tree.write_to_file(fileIO.join_path(self.outdir,
'master_tree.nwk'))
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)
errors.directorymake(
fileIO.join_path(self.outdir, 'base_class_trees'))
errors.directorymake(fileIO.join_path(self.outdir, 'gene_trees'))
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 = 'base_tree_class{0:0>{1}}.nwk'.format(
i + 1, len(str(self.num_classes)))
filename = fileIO.join_path(self.outdir, 'base_class_trees',
name)
tree.write_to_file(filename)
for i, tree in enumerate(self.gene_trees, start=1):
filename = fileIO.join_path(self.outdir, 'gene_trees',
tree.name + '.nwk')
tree.write_to_file(filename)
self.master_tree.write_to_file(
fileIO.join_path(self.outdir, 'master_tree.nwk'))
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)
errors.directorymake(fileIO.join_path(self.outdir, "base_class_trees"))
errors.directorymake(fileIO.join_path(self.outdir, "gene_trees"))
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 = "base_tree_class{0:0>{1}}.nwk".format(i + 1, len(str(self.num_classes)))
filename = fileIO.join_path(self.outdir, "base_class_trees", name)
tree.write_to_file(filename)
for i, tree in enumerate(self.gene_trees, start=1):
filename = fileIO.join_path(self.outdir, "gene_trees", tree.name + ".nwk")
tree.write_to_file(filename)
self.master_tree.write_to_file(fileIO.join_path(self.outdir, "master_tree.nwk"))
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 i, g in enumerate(self.gene_trees, start=1):
dirname = fileIO.join_path(self.tmpdir, g.name)
alf_dirs[i] = errors.directorymake(dirname)
self.alf_dirs = alf_dirs
def make_alf_dirs(self):
alf_dirs = {}
for i, g in enumerate(self.gene_trees, start=1):
dirname = fileIO.join_path(self.tmpdir, g.name)
alf_dirs[i] = errors.directorymake(dirname)
self.alf_dirs = alf_dirs
