def assign_taxonomy(self):
"""Assign taxonomy to genomes.
"""
# take user-defined taxIds of input genomes
if self.input_tax:
try:
self.input_tax = dict_from_param(self.input_tax)
except ValueError:
if len(self.data) > 1:
raise ValueError('Invalid input taxonomy format.')
# for single-sample analysis, one can simply enter a taxId
self.input_tax = {max(self.data.keys()): self.input_tax}
print('User-specified TaxIDs of input genomes:')
for sid, tid in sorted(self.input_tax.items()):
if tid not in self.taxdump:
# TODO: read from both temp and master taxdump
raise ValueError('TaxID {} is not present in taxonomy '
'database.'.format(tid))
print(' {}: {} ({}).'.format(sid, tid,
self.taxdump[tid]['name']))
else:
self.input_tax = {}
# auto-infer taxIds of remaining genomes
sids = sorted([x for x in self.data if x not in self.input_tax])
if sids:
print('Auto-inferring plausible taxIds for input genomes based on '
'taxonomy of search results...')
for sid in sids:
try:
tid, cov = self.infer_genome_tax(self.data[sid],
self.taxdump,
self.input_cov)
self.input_tax[sid] = tid
except ValueError:
raise ValueError('Cannot auto-infer taxonomy for {}. '
'Please specify manually.'.format(sid))
print(' {}: {} ({}) (covering {:2g}% best hits).'.format(
sid, tid, self.taxdump[tid]['name'], cov))
# refine taxonomy database
print('Refining taxonomy database...')
refine_taxdump(self.sum_taxids(), self.taxdump)
add_children(self.taxdump)
print('Done. Retained {} taxa.'.format(len(self.taxdump)))
# find lowest common ancestor (LCA) of all genomes
self.lca = find_lca(self.input_tax.values(), self.taxdump)
print('All input genomes belong to {} ({}).'.format(
self.lca, describe_taxon(self.lca, self.taxdump)))
def test_refine_taxdump(self):
taxdump = taxdump_from_text(taxdump_archaea)
tids = ['2', '2157'] # Bacteria and Archaea
obs = set(refine_taxdump(tids, taxdump))
exp = {'1', '131567', '2', '2157'} # plus cellular organisms and root
self.assertSetEqual(obs, exp)