def kernelOfTest(self, trees):
expected = trees[-1]
input = trees[:-1]
_LOG.debug('input = %s' % str(input))
output = inplace_strict_consensus_merge(input)
encode_splits(output)
encode_splits(expected)
if symmetric_difference(expected, output) != 0:
self.fail("\n%s\n!=\n%s" % (str(output), str(expected)))
def kernelOfTest(self, trees):
expected = trees[-1]
input = trees[:-1]
_LOG.debug('input = %s' % str(input))
output = inplace_strict_consensus_merge(input)
encode_splits(output)
encode_splits(expected)
if symmetric_difference(expected, output) != 0:
self.fail("\n%s\n!=\n%s" % (str(output), str(expected)))
'--schema',
dest='schema',
type='str',
default="newick",
help='The format/schema of the input data')
parser.add_option('-g',
'--gordon',
dest='gordons',
action="store_true",
default=False,
help="Specify to use the Gordon's strict consensus")
(options, args) = parser.parse_args()
if len(args) == 0:
sys.exit("Expecting a filename as an argument")
schema = options.schema.upper()
trees = []
taxon_set = TaxonSet()
dataset = DataSet(taxon_set=taxon_set)
if schema == "PHYLIP":
schema = "NEWICK"
for f in args:
fo = open(f, "rU")
dataset.read(stream=fo, schema=schema)
for tl in dataset.tree_lists:
trees.extend(tl)
o = inplace_strict_consensus_merge(trees,
gordons_supertree=options.gordons)
sys.stdout.write("%s;\n" % str(o))
verbose = False
from dendropy.scm import inplace_strict_consensus_merge
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser()
parser.add_option('-s', '--schema', dest='schema',
type='str', default="newick", help='The format/schema of the input data')
parser.add_option('-g', '--gordon', dest='gordons',
action="store_true", default=False, help="Specify to use the Gordon's strict consensus")
(options, args) = parser.parse_args()
if len(args) == 0:
sys.exit("Expecting a filename as an argument")
schema = options.schema.upper()
trees = []
taxon_set = TaxonSet()
dataset = DataSet(taxon_set=taxon_set)
if schema == "PHYLIP":
schema = "NEWICK"
for f in args:
fo = open(f, "rU")
dataset.read(stream=fo, schema=schema)
for tl in dataset.tree_lists:
trees.extend(tl)
o = inplace_strict_consensus_merge(trees, gordons_supertree=options.gordons)
sys.stdout.write("%s;\n" % str(o))
