def _tax_diff_table(self, tax1, tax2, output_table):
"""Tabulate incongruency of taxonomy strings at each rank."""
fout = open(output_table, 'w')
fout.write('Lineage\tNo. Extent Taxa')
for rank_label in Taxonomy.rank_labels:
fout.write('\t%s (%%)' % rank_label.title())
fout.write('\n')
taxonomy = Taxonomy()
named_lineages_at_rank = taxonomy.named_lineages_at_rank(tax1)
for rank, taxa in named_lineages_at_rank.iteritems():
rank_label = Taxonomy.rank_labels[rank]
if rank_label == 'species':
continue
extant_taxa_for_rank = taxonomy.extant_taxa_for_rank(rank_label, tax1)
for taxon in taxa:
extent_taxa = extant_taxa_for_rank[taxon]
fout.write('%s\t%d' % (taxon, len(extent_taxa)))
row = defaultdict(list)
for genome_id in extent_taxa:
taxa1 = tax1[genome_id]
taxa2 = tax2[genome_id]
for cur_rank, (taxa1, taxa2) in enumerate(zip(taxa1, taxa2)):
row[cur_rank].append(taxa1 == taxa2)
for cur_rank, matches in row.iteritems():
if cur_rank <= rank:
fout.write('\t-')
else:
perc_match = sum(matches) * 100.0 / len(matches)
fout.write('\t%.1f' % (100.0 - perc_match))
fout.write('\n')
fout.close()
def _tax_diff_table(self, tax1, tax2, output_table):
"""Tabulate incongruency of taxonomy strings at each rank."""
fout = open(output_table, 'w')
fout.write('Lineage\tNo. Extent Taxa')
for rank_label in Taxonomy.rank_labels:
fout.write('\t%s (%%)' % rank_label.title())
fout.write('\n')
taxonomy = Taxonomy()
named_lineages_at_rank = taxonomy.named_lineages_at_rank(tax1)
for rank, taxa in named_lineages_at_rank.items():
rank_label = Taxonomy.rank_labels[rank]
if rank_label == 'species':
continue
extant_taxa_for_rank = taxonomy.extant_taxa_for_rank(rank_label, tax1)
for taxon in taxa:
extent_taxa = extant_taxa_for_rank[taxon]
fout.write('%s\t%d' % (taxon, len(extent_taxa)))
row = defaultdict(list)
for genome_id in extent_taxa:
taxa1 = tax1[genome_id]
taxa2 = tax2[genome_id]
for cur_rank, (taxa1, taxa2) in enumerate(list(zip(taxa1, taxa2))):
row[cur_rank].append(taxa1 == taxa2)
for cur_rank, matches in row.items():
if cur_rank <= rank:
fout.write('\t-')
else:
perc_match = sum(matches) * 100.0 / len(matches)
fout.write('\t%.1f' % (100.0 - perc_match))
fout.write('\n')
fout.close()
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.')
