def test_dict_from_param(self):
# nothing
self.assertEqual(dict_from_param(None), {})
self.assertEqual(dict_from_param(''), {})
# already dict
self.assertEqual(dict_from_param({'a': 1}), {'a': 1})
# dict string
exp = {'a': '1', 'b': '2', 'c': '3'}
self.assertDictEqual(dict_from_param('a:1,b:2,c:3'), exp)
# invalid dict string
with self.assertRaises(ValueError) as ctx:
dict_from_param('test')
msg = 'Invalid dictionary string: "test".'
self.assertEqual(str(ctx.exception), msg)
# dict file
fp = join(self.tmpdir, 'test.txt')
with open(fp, 'w') as f:
for itm in exp.items():
print('\t'.join(itm), file=f)
obs = dict_from_param(fp)
self.assertDictEqual(obs, exp)
# invalid dict file
with open(fp, 'w') as f:
for itm in exp.items():
print('test', file=f)
with self.assertRaises(ValueError) as ctx:
dict_from_param(fp)
msg = f'Invalid dictionary file: "{fp}".'
self.assertEqual(str(ctx.exception), msg)
remove(fp)
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)))