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.')
def tree_tax_diff(self, tree1_file, tree2_file, output_dir):
"""Tabulate differences between two taxonomies on a tree.
Parameters
----------
tree1_file : str
File with tree in Newick format.
tree2_file : str
File with tree in Newick format.
output_dir : str
Output directory.
"""
tree1 = dendropy.Tree.get_from_path(tree1_file,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
tree2 = dendropy.Tree.get_from_path(tree2_file,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
# prune both trees to a set of common taxa
taxa1 = set()
for t in tree1.leaf_node_iter():
taxa1.add(t.taxon.label)
taxa2 = set()
for t in tree2.leaf_node_iter():
taxa2.add(t.taxon.label)
taxa_in_common = taxa1.intersection(taxa2)
self.logger.info('Tree 1 contains %d taxa.' % len(taxa1))
self.logger.info('Tree 2 contains %d taxa.' % len(taxa2))
self.logger.info('Pruning trees to the %d taxa in common.' % len(taxa_in_common))
tree1.retain_taxa_with_labels(taxa_in_common)
tree2.retain_taxa_with_labels(taxa_in_common)
# get named lineages at each taxonomic rank
taxonomy = Taxonomy()
tax1 = taxonomy.read_from_tree(tree1)
tax2 = taxonomy.read_from_tree(tree2)
taxa_at_rank1 = taxonomy.named_lineages_at_rank(tax1)
taxa_at_rank2 = taxonomy.named_lineages_at_rank(tax2)
# identify retained taxonomic names
tax_file_name = os.path.splitext(os.path.basename(tree1_file))[0]
output_file = os.path.join(output_dir, '%s.taxa_diff.tsv' % tax_file_name)
fout = open(output_file, 'w')
fout.write('Rank\tClassification\tTaxonomy 1\tTaxonomy 2\n')
taxon2_accounted_for = defaultdict(set)
for rank, rank_label in enumerate(Taxonomy.rank_labels[0:-1]):
for taxon in taxa_at_rank1[rank]:
# check if taxon has been retained
if taxon in taxa_at_rank2[rank]:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'retained', taxon, taxon))
taxon2_accounted_for[rank].add(taxon)
continue
# check if name was simply corrected by changing suffix
old_taxon = self._change_suffix(taxon, rank, taxa_at_rank2)
if old_taxon:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'corrected', taxon, old_taxon))
taxon2_accounted_for[rank].add(old_taxon)
continue
# check if taxon has been moved up or down in rank
old_taxon, old_rank = self._renamed(taxon, rank, taxa_at_rank2)
if old_taxon:
if rank < old_rank:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'more general', taxon, old_taxon))
elif rank == old_rank:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'corrected', taxon, old_taxon))
else:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'more specific', taxon, old_taxon))
taxon2_accounted_for[old_rank].add(old_taxon)
continue
# otherwise, the taxon appears to be new
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'new', taxon, 'NA'))
# report deprecated taxa
for rank, rank_label in enumerate(Taxonomy.rank_labels[0:-1]):
for taxon in taxa_at_rank2[rank]:
if taxon not in taxon2_accounted_for[rank]:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'deprecated', 'NA', taxon))
fout.close()
# tabulate congruence of taxonomy strings
output_table = os.path.join(output_dir, '%s.perc_diff.tsv' % tax_file_name)
self._tax_diff_table(tax1, tax2, output_table)
def tree_tax_diff(self, tree1_file, tree2_file, output_dir):
"""Tabulate differences between two taxonomies on a tree.
Parameters
----------
tree1_file : str
File with tree in Newick format.
tree2_file : str
File with tree in Newick format.
output_dir : str
Output directory.
"""
tree1 = dendropy.Tree.get_from_path(tree1_file,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
tree2 = dendropy.Tree.get_from_path(tree2_file,
schema='newick',
rooting='force-rooted',
preserve_underscores=True)
# prune both trees to a set of common taxa
taxa1 = set()
for t in tree1.leaf_node_iter():
taxa1.add(t.taxon.label)
taxa2 = set()
for t in tree2.leaf_node_iter():
taxa2.add(t.taxon.label)
taxa_in_common = taxa1.intersection(taxa2)
self.logger.info('Tree 1 contains %d taxa.' % len(taxa1))
self.logger.info('Tree 2 contains %d taxa.' % len(taxa2))
self.logger.info('Pruning trees to the %d taxa in common.' % len(taxa_in_common))
tree1.retain_taxa_with_labels(taxa_in_common)
tree2.retain_taxa_with_labels(taxa_in_common)
# get named lineages at each taxonomic rank
taxonomy = Taxonomy()
tax1 = taxonomy.read_from_tree(tree1)
tax2 = taxonomy.read_from_tree(tree2)
taxa_at_rank1 = taxonomy.named_lineages_at_rank(tax1)
taxa_at_rank2 = taxonomy.named_lineages_at_rank(tax2)
# identify retained taxonomic names
tax_file_name = os.path.splitext(os.path.basename(tree1_file))[0]
output_file = os.path.join(output_dir, '%s.taxa_diff.tsv' % tax_file_name)
fout = open(output_file, 'w')
fout.write('Rank\tClassification\tTaxonomy 1\tTaxonomy 2\n')
taxon2_accounted_for = defaultdict(set)
for rank, rank_label in enumerate(Taxonomy.rank_labels[0:-1]):
for taxon in taxa_at_rank1[rank]:
# check if taxon has been retained
if taxon in taxa_at_rank2[rank]:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'retained', taxon, taxon))
taxon2_accounted_for[rank].add(taxon)
continue
# check if name was simply corrected by changing suffix
old_taxon = self._change_suffix(taxon, rank, taxa_at_rank2)
if old_taxon:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'corrected', taxon, old_taxon))
taxon2_accounted_for[rank].add(old_taxon)
continue
# check if taxon has been moved up or down in rank
old_taxon, old_rank = self._renamed(taxon, rank, taxa_at_rank2)
if old_taxon:
if rank < old_rank:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'more general', taxon, old_taxon))
elif rank == old_rank:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'corrected', taxon, old_taxon))
else:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'more specific', taxon, old_taxon))
taxon2_accounted_for[old_rank].add(old_taxon)
continue
# otherwise, the taxon appears to be new
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'new', taxon, 'NA'))
# report deprecated taxa
for rank, rank_label in enumerate(Taxonomy.rank_labels[0:-1]):
for taxon in taxa_at_rank2[rank]:
if taxon not in taxon2_accounted_for[rank]:
fout.write('%s\t%s\t%s\t%s\n' % (rank_label, 'deprecated', 'NA', taxon))
fout.close()
# tabulate congruence of taxonomy strings
output_table = os.path.join(output_dir, '%s.perc_diff.tsv' % tax_file_name)
self._tax_diff_table(tax1, tax2, output_table)
