def write_as_mesquite(self, out, **kwargs):
"""
For debugging purposes, write out a Mesquite-format file.
"""
from dendropy.dataio import nexuswriter
nw = nexuswriter.NexusWriter(**kwargs)
nw.is_write_block_titles = True
out.write("#NEXUS\n\n")
nw._write_taxa_block(out, self.taxon_namespace)
out.write('\n')
nw._write_taxa_block(out, self.contained_trees.taxon_namespace)
if self.contained_trees.taxon_namespace.label:
domain_title = self.contained_trees.taxon_namespace.label
else:
domain_title = self.contained_trees.taxon_namespace.oid
contained_taxon_namespace = self.contained_trees.taxon_namespace
contained_label = self.contained_trees.label
out.write('\n')
self._contained_to_containing_taxon_map.write_mesquite_association_block(
out)
out.write('\n')
nw._write_trees_block(
out, dendropy.TreeList([self],
taxon_namespace=self.taxon_namespace))
out.write('\n')
nw._write_trees_block(
out,
dendropy.TreeList(self.contained_trees,
taxon_namespace=contained_taxon_namespace,
label=contained_label))
out.write('\n')
def __init__(self,
suppress_standard_preamble=False,
ignore_error_returncode=False,
strip_extraneous_prompts_from_stderr=True,
strip_extraneous_prompts_from_stdout=True,
cwd=None,
env=None,
paup_path=PAUP_PATH):
self.suppress_standard_preamble = suppress_standard_preamble
self.ignore_error_returncode = ignore_error_returncode
self.strip_extraneous_prompts_from_stderr = strip_extraneous_prompts_from_stderr
self.strip_extraneous_prompts_from_stdout = strip_extraneous_prompts_from_stdout
self.cwd = cwd
self.env = env
self.paup_path = paup_path
self._nexus_writer = nexuswriter.NexusWriter()
self.commands = []