def root(self, options):
"""Root tree using outgroup.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
check_file_exists(options.input_tree)
taxonomy = self._read_taxonomy_files(options)
self.logger.info(f'Identifying genomes from the specified outgroup: {options.outgroup_taxon}')
outgroup = set()
for genome_id, taxa in taxonomy.items():
if options.outgroup_taxon in taxa:
outgroup.add(genome_id)
reroot = RerootTree()
reroot.root_with_outgroup(options.input_tree,
options.output_tree,
outgroup)
self.logger.info('Done.')
def root(self, options):
"""Root tree using outgroup.
Parameters
----------
options : argparse.Namespace
The CLI arguments input by the user.
"""
self.logger.warning("Tree rooting is still under development!")
check_file_exists(options.input_tree)
if options.custom_taxonomy_file:
check_file_exists(options.custom_taxonomy_file)
taxonomy = Taxonomy().read(options.custom_taxonomy_file)
else:
taxonomy = Taxonomy().read(Config.TAXONOMY_FILE)
self.logger.info('Identifying genomes from the specified outgroup.')
outgroup = set()
for genome_id, taxa in taxonomy.items():
if options.outgroup_taxon in taxa:
outgroup.add(genome_id)
reroot = RerootTree()
reroot.root_with_outgroup(options.input_tree, options.output_tree,
outgroup)
# Symlink to the tree summary file, if not run independently
if hasattr(options, 'suffix'):
if options.suffix == 'bac120':
symlink_f(
PATH_BAC120_ROOTED_TREE.format(prefix=options.prefix),
os.path.join(
options.out_dir,
os.path.basename(
PATH_AR122_ROOTED_TREE.format(
prefix=options.prefix))))
elif options.suffix == 'ar122':
symlink_f(
PATH_AR122_ROOTED_TREE.format(prefix=options.prefix),
os.path.join(
options.out_dir,
os.path.basename(
PATH_AR122_ROOTED_TREE.format(
prefix=options.prefix))))
else:
raise GenomeMarkerSetUnknown(
'There was an error determining the marker set.')
self.logger.info('Done.')