def outgroup(self, options):
"""Reroot tree with outgroup."""
check_file_exists(options.taxonomy_file)
self.logger.info('Identifying genomes from the specified outgroup.')
outgroup = set()
for genome_id, taxa in Taxonomy().read(options.taxonomy_file).iteritems():
if options.outgroup_taxon in taxa:
outgroup.add(genome_id)
self.logger.info('Identifying %d genomes in the outgroup.' % len(outgroup))
reroot = RerootTree()
reroot.root_with_outgroup(options.input_tree, options.output_tree, outgroup)
def outgroup(self, options):
"""Reroot tree with outgroup."""
check_file_exists(options.taxonomy_file)
self.logger.info('Identifying genomes from the specified outgroup.')
outgroup = set()
for genome_id, taxa in Taxonomy().read(options.taxonomy_file).items():
if options.outgroup_taxon in taxa:
outgroup.add(genome_id)
self.logger.info('Identifying %d genomes in the outgroup.' % len(outgroup))
reroot = RerootTree()
reroot.root_with_outgroup(options.input_tree, options.output_tree, outgroup)
def midpoint(self, options):
""""Midpoint root tree."""
reroot = RerootTree()
reroot.midpoint(options.input_tree, options.output_tree)
def midpoint(self, options):
""""Midpoint root tree."""
reroot = RerootTree()
reroot.midpoint(options.input_tree, options.output_tree)