def validate(self, options):
"""Validate command"""
check_file_exists(options.taxonomy_file)
taxonomy = Taxonomy()
t = taxonomy.read(options.taxonomy_file)
errors = taxonomy.validate(t,
check_prefixes=not options.no_prefix,
check_ranks=not options.no_all_ranks,
check_hierarchy=not options.no_hierarhcy,
check_species=not options.no_species,
check_group_names=True,
check_duplicate_names=True,
report_errors=True)
invalid_ranks, invalid_prefixes, invalid_species_name, invalid_hierarchies, invalid_group_name = errors
if sum([len(e) for e in errors]) == 0:
self.logger.info('No errors identified in taxonomy file.')
else:
self.logger.info('Identified %d incomplete taxonomy strings.' %
len(invalid_ranks))
self.logger.info('Identified %d rank prefix errors.' %
len(invalid_prefixes))
self.logger.info('Identified %d invalid species names.' %
len(invalid_species_name))
self.logger.info('Identified %d taxa with multiple parents.' %
len(invalid_hierarchies))
self.logger.info('Identified %d invalid group names.' %
len(invalid_group_name))
def validate(self, options):
"""Check taxonomy file is formatted as expected."""
check_file_exists(options.input_taxonomy)
taxonomy = Taxonomy()
t = taxonomy.read(options.input_taxonomy)
taxonomy.validate(t,
check_prefixes=True,
check_ranks=True,
check_hierarchy=True,
check_species=True,
check_group_names=True,
check_duplicate_names=True,
report_errors=True)
self.logger.info('Finished performing validation tests.')
def validate(self, options):
"""Validate command"""
check_file_exists(options.taxonomy_file)
taxonomy = Taxonomy()
t = taxonomy.read(options.taxonomy_file)
errors = taxonomy.validate(t,
not options.no_prefix,
not options.no_all_ranks,
not options.no_hierarhcy,
not options.no_species,
True)
invalid_ranks, invalid_prefixes, invalid_species_name, invalid_hierarchies = errors
if sum([len(e) for e in errors]) == 0:
self.logger.info('No errors identified in taxonomy file.')
else:
self.logger.info('Identified %d incomplete taxonomy strings.' % len(invalid_ranks))
self.logger.info('Identified %d rank prefix errors.' % len(invalid_prefixes))
self.logger.info('Identified %d invalid species names.' % len(invalid_species_name))
self.logger.info('Identified %d taxa with multiple parents.' % len(invalid_hierarchies))
def check_tree(self, options):
"""Validate taxonomy of decorated tree and check for polyphyletic groups."""
check_file_exists(options.decorated_tree)
# validate taxonomy
taxonomy = Taxonomy()
if options.taxonomy_file:
t = taxonomy.read(options.taxonomy_file)
else:
t = taxonomy.read_from_tree(options.decorated_tree)
taxonomy.validate(t,
check_prefixes=True,
check_ranks=True,
check_hierarchy=True,
check_species=True,
check_group_names=True,
check_duplicate_names=True,
report_errors=True)
# check for polyphyletic groups
polyphyletic_groups = set()
tree = dendropy.Tree.get_from_path(options.decorated_tree,
schema='newick',
rooting="force-rooted",
preserve_underscores=True)
if options.taxonomy_file:
# reduce taxonomy to taxa in tree and map taxon labels to Taxon objects
reduced_taxonomy = {}
taxon_map = {}
for leaf in tree.leaf_node_iter():
reduced_taxonomy[leaf.taxon.label] = t[leaf.taxon.label]
taxon_map[leaf.taxon.label] = leaf.taxon
# find taxa with an MRCA spanning additional taxa
for rank_label in Taxonomy.rank_labels[1:]:
extant_taxa = taxonomy.extant_taxa_for_rank(
rank_label, reduced_taxonomy)
for taxon, taxa_ids in extant_taxa.items():
mrca = tree.mrca(taxa=[taxon_map[t] for t in taxa_ids])
mrca_leaf_count = sum([1 for leaf in mrca.leaf_iter()])
if mrca_leaf_count != len(taxa_ids):
polyphyletic_groups.add(taxon)
else:
# find duplicate taxon labels in tree
taxa = set()
for node in tree.preorder_node_iter(lambda n: not n.is_leaf()):
_support, taxon_label, _aux_info = parse_label(node.label)
if taxon_label:
for taxon in [t.strip() for t in taxon_label.split(';')]:
if taxon in taxa:
polyphyletic_groups.add(taxon)
taxa.add(taxon)
if len(polyphyletic_groups):
print('')
print('Tree contains polyphyletic groups:')
for taxon in polyphyletic_groups:
print('%s' % (taxon))
self.logger.info('Finished performing validation tests.')
