def testChangeTranslate(self):
f = """#NEXUS
Begin taxa ;
dimensions ntax = 4;
taxlabels a b c d ;
end;
begin trees;
translate
1 a,
2 b,
3 c,
4 d;
tree t = (1,2,(3,4));
end;
begin trees;
translate
1 d,
2 b,
3 c,
4 a;
tree t = (4,2,(3,1));
end;
"""
d = Dataset()
d.read(StringIO(f), format="NEXUS")
t = d.trees_blocks[0][0]
s = d.trees_blocks[1][0]
self.assertEqual(t.taxa_block, s.taxa_block)
encode_splits(s)
encode_splits(t)
self.assertEqual(treedists.symmetric_difference(t, s), 0)
def testTaxaWithUnderscoreRead(self):
rd = dendropy.tests.data_source_path("rana.nex")
rt = dendropy.tests.data_source_path("rana.tre")
d = Dataset()
d.read(open(rd, "rU"), format="NEXUS")
self.assertEqual(len(d.taxa_blocks[0]), 64)
d.read_trees(open(rt, "rU"), format="NEXUS")
self.assertEqual(len(d.taxa_blocks[0]), 64)
if conf_file is None:
sys.exit("Expecting a conf file template for GARLI")
data_file = opts.data_filepath
intree_file = opts.intree_filepath
if data_file is None:
sys.exit("Data file must be specified")
if intree_file is None:
sys.exit("Input tree file must be specified")
for f in [data_file, intree_file, conf_file]:
if not os.path.exists(f):
sys.exit("%s does not exist" % f)
conf = read_garli_conf(open(conf_file, "rU"))
write_garli_conf(sys.stdout, conf)
d = Dataset()
d.read(open(data_file, "rU"), format="NEXUS")
taxa = d.taxa_blocks[0]
full_taxa_mask = taxa.all_taxa_bitmask()
for n, taxon in enumerate(taxa):
TAXON_TO_TRANSLATE[taxon] = str(n + 1)
_LOG.debug("%s = full_taxa_mask" % bin(full_taxa_mask))
assert (len(d.taxa_blocks) == 1)
characters = d.char_blocks[0]
assert (len(d.char_blocks) == 1)
assert (len(characters) == len(taxa))
inp_trees = d.read_trees(open(intree_file, "rU"), format="NEXUS")
assert (inp_trees)
current_taxon_mask = None
for tree in inp_trees:
assert tree.taxa_block is taxa
encode_splits(tree)
_LOG.setLevel(logging.DEBUG)
data_file = opts.data_filepath
intree_file = opts.intree_filepath
if data_file is None:
sys.exit("Data file must be specified")
if intree_file is None:
sys.exit("Input tree file must be specified")
for f in [data_file, intree_file, conf_file]:
if not os.path.exists(f):
sys.exit("%s does not exist" % f)
garli = GarliConf()
garli.read_garli_conf(open(conf_file, "rU"))
full_dataset = Dataset()
full_dataset.read(open(data_file, "rU"), format="NEXUS")
assert(len(full_dataset.taxa_blocks) == 1)
taxa = full_dataset.taxa_blocks[0]
full_taxa_mask = taxa.all_taxa_bitmask()
for n, taxon in enumerate(taxa):
TAXON_TO_TRANSLATE[taxon] = str(n + 1)
_LOG.debug("%s = full_taxa_mask" % bin(full_taxa_mask))
garli.datafname = os.path.join("data.nex")
raw_trees = full_dataset.read_trees(open(intree_file, "rU"), format="NEXUS")
assert(raw_trees)
current_taxon_mask = None
# read initial trees and verify that they have the correct set of taxa
_LOG.setLevel(logging.DEBUG)
data_file = opts.data_filepath
intree_file = opts.intree_filepath
if data_file is None:
sys.exit("Data file must be specified")
if intree_file is None:
sys.exit("Input tree file must be specified")
for f in [data_file, intree_file, conf_file]:
if not os.path.exists(f):
sys.exit("%s does not exist" % f)
garli = GarliConf()
garli.read_garli_conf(open(conf_file, "rU"))
full_dataset = Dataset()
full_dataset.read(open(data_file, "rU"), format="NEXUS")
assert (len(full_dataset.taxa_blocks) == 1)
taxa = full_dataset.taxa_blocks[0]
full_taxa_mask = taxa.all_taxa_bitmask()
for n, taxon in enumerate(taxa):
TAXON_TO_TRANSLATE[taxon] = str(n + 1)
_LOG.debug("%s = full_taxa_mask" % bin(full_taxa_mask))
garli.datafname = os.path.join("data.nex")
raw_trees = full_dataset.read_trees(open(intree_file, "rU"),
format="NEXUS")
assert (raw_trees)
current_taxon_mask = None
# read initial trees and verify that they have the correct set of taxa
