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(self.taxon_set, out)
out.write('\n')
nw.write_taxa_block(self.contained_trees.taxon_set, out)
if self.contained_trees.taxon_set.label:
domain_title = self.contained_trees.taxon_set.label
else:
domain_title = self.contained_trees.taxon_set.oid
contained_taxon_set = self.contained_trees.taxon_set
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(
dataobject.TreeList([self], taxon_set=self.taxon_set), out)
out.write('\n')
nw.write_trees_block(
dataobject.TreeList(self.contained_trees,
taxon_set=contained_taxon_set,
label=contained_label), out)
out.write('\n')
def clear(self):
"""
Clears all contained trees and mapped edges.
"""
self.contained_trees = dataobject.TreeList(
taxon_set=self._contained_to_containing_taxon_map.domain_taxa)
self.clear_contained_edges()
def _set_contained_trees(self, trees):
if hasattr(trees, 'taxon_set'):
if self._contained_taxon_set is None:
self._contained_taxon_set = trees.taxon_set
elif self._contained_taxon_set is not trees.taxon_set:
raise ValueError(
"'contained_taxon_set' of ContainingTree is not the same TaxonSet object of 'contained_trees'"
)
self._contained_trees = dataobject.TreeList(
trees, taxon_set=self._contained_taxon_set)
if self._contained_taxon_set is None:
self._contained_taxon_set = self._contained_trees.taxon_set
def _get_contained_trees(self):
if self._contained_trees is None:
self._contained_trees = dataobject.TreeList(
taxon_set=self._contained_taxon_set)
return self._contained_trees
def read_filepath_into_dataset(self, file_path):
_LOG.debug("Creating MultiFormatReader")
ncl_nxs_reader_handle = nclwrapper.MultiFormatReader()
_LOG.debug("Setting MultiFormatReader's WarningOutput Level")
ncl_nxs_reader_handle.SetWarningOutputLevel(
DENDROPY_NCL_WARNING_LEVEL)
_LOG.debug(
"Calling MultiFormatReader.cullIdenticalTaxaBlocks(True)")
ncl_nxs_reader_handle.cullIdenticalTaxaBlocks(True)
if self.dataset is None:
self.dataset = dataobject.DataSet()
if self.attached_taxon_set is not None and len(
self.attached_taxon_set) == 0:
self._taxa_to_fill = self.attached_taxon_set
else:
self._taxa_to_fill = None
if self.attached_taxon_set is not None:
self._register_taxa_context(ncl_nxs_reader_handle,
[self.attached_taxon_set])
_LOG.debug("Calling MultiFormatReader.ReadFilepath(%s, %s)" %
(file_path, self.format))
ncl_nxs_reader_handle.ReadFilepath(file_path, self.format)
_LOG.debug("Calling MultiFormatReader.GetNumTaxaBlocks()")
num_taxa_blocks = ncl_nxs_reader_handle.GetNumTaxaBlocks()
for i in xrange(num_taxa_blocks):
_LOG.debug("Calling MultiFormatReader.GetTaxaBlock(%d)" % i)
ncl_tb = ncl_nxs_reader_handle.GetTaxaBlock(i)
taxa_block = self._ncl_taxa_block_to_native(ncl_tb)
self.dataset.add(taxa_block)
#nab = ncl_nxs_reader_handle.GetNumAssumptionsBlocks(ncl_tb)
#for k in xrange(nab):
# a = ncl_nxs_reader_handle.GetAssumptionsBlock(ncl_tb, k)
# cs = a.GetTaxSetNames()
# print "TaxSets have the names " , str(cs)
_LOG.debug(
"Calling MultiFormatReader.GetNumCharactersBlocks()")
num_char_blocks = ncl_nxs_reader_handle.GetNumCharactersBlocks(
ncl_tb)
for j in xrange(num_char_blocks):
_LOG.debug(
"Calling MultiFormatReader.GetCharactersBlock(taxablock, %d)"
% j)
ncl_cb = ncl_nxs_reader_handle.GetCharactersBlock(
ncl_tb, j)
char_block = self._ncl_characters_block_to_native(
taxa_block, ncl_cb, ncl_nxs_reader_handle)
if char_block:
self.dataset.add(char_block)
_LOG.debug("Calling MultiFormatReader.GetNumTreesBlocks()")
ntrb = ncl_nxs_reader_handle.GetNumTreesBlocks(ncl_tb)
for j in xrange(ntrb):
trees_block = dataobject.TreeList()
trees_block.taxon_set = taxa_block
_LOG.debug("Calling MultiFormatReader.GetTreesBlock(%d)" %
j)
ncl_trb = ncl_nxs_reader_handle.GetTreesBlock(ncl_tb, j)
for k in xrange(ncl_trb.GetNumTrees()):
ftd = ncl_trb.GetFullTreeDescription(k)
tokens = ftd.GetTreeTokens()
rooted_flag = ftd.IsRooted()
t = self._ncl_tree_tokens_to_native_tree(
ncl_tb,
taxa_block,
tokens,
rooted_flag=rooted_flag)
if t:
trees_block.append(t)
self.dataset.add(trees_block)
return self.dataset