def test_consistency_unrooted(self):
"""Test consistency of taxa with a taxa that is only monophyletic in unrooted tree"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {'a': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'b': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'c': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'd': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides acidifaciens'],
'e': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides acidifaciens']}
tree = nl.load_tree(StringIO(u'((a,b),(c,(d,e)));'), tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 0.66666666)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
def test_consistency_missing(self):
"""Test consistency of taxa in tree with missing taxa"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {'a': ['f__Lachnospiraceae', 'g__Bacteroides', None],
'c': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'b': ['f__Lachnospiraceae', 'g__Bacteroides', None], 'e': [None, None, None],
'd': ['f__Lachnospiraceae', 'g__Bacteroides', 's__Bacteroides pectinophilus'],
'g': [None, None, None], 'f': ['f__Lachnospiraceae', 'g__Lachnospira', None],
'h': ['f__Lachnospiraceae', 'g__Lachnospira', 's__Bacteroides pectinophilus']}
tree = nl.load_tree(StringIO(u'(((a,b),(c,d)),((e,f),(g,h)));'), tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
def test_consistency_unrooted(self):
"""Test consistency of taxa with a taxa that is only monophyletic in unrooted tree"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {
'a': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'b': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'c': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'd': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides acidifaciens'
],
'e': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides acidifaciens'
]
}
tree = nl.load_tree('((a,b),(c,(d,e)));', tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 0.66666666)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides acidifaciens'], 1.0)
def test_generate_constrings_valid_input(self):
"""Tests generate_constrings with standard valid input.
Checks that our output mirrors nlevel (tax2tree's interface)."""
exp = test_results
determine_rank_order(test_cons[0].split('\t')[1])
cons_map = load_consensus_map(test_cons, False)
tree = load_tree(test_tree, cons_map)
obs = generate_constrings(tree, cons_map)
self.assertEqual(obs, exp)
def test_generate_constrings_valid_input(self):
"""Tests generate_constrings with standard valid input.
Checks that our output mirrors nlevel (tax2tree's interface)."""
exp = test_results
determine_rank_order(test_cons[0].split('\t')[1])
cons_map = load_consensus_map(test_cons, False)
tree = load_tree(test_tree, cons_map)
obs = generate_constrings(tree, cons_map)
self.assertEqual(obs, exp)
def test_consistency_missing(self):
"""Test consistency of taxa in tree with missing taxa"""
seed_con = 'f__Lachnospiraceae; g__Bacteroides; s__'
nl.determine_rank_order(seed_con)
tipname_map = {
'a': ['f__Lachnospiraceae', 'g__Bacteroides', None],
'c': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'b': ['f__Lachnospiraceae', 'g__Bacteroides', None],
'e': [None, None, None],
'd': [
'f__Lachnospiraceae', 'g__Bacteroides',
's__Bacteroides pectinophilus'
],
'g': [None, None, None],
'f': ['f__Lachnospiraceae', 'g__Lachnospira', None],
'h': [
'f__Lachnospiraceae', 'g__Lachnospira',
's__Bacteroides pectinophilus'
]
}
tree = nl.load_tree('(((a,b),(c,d)),((e,f),(g,h)));', tipname_map)
counts = nl.collect_names_at_ranks_counts(tree)
nl.decorate_ntips_rank(tree)
nl.decorate_name_counts(tree)
# determine taxonomic consistency of rooted tree
#expected_consistency_index
c = Consistency(counts, len(nl.RANK_ORDER))
consistency_index = c.calculate(tree, rooted=True)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
#determine consistency of unrooted tree
consistency_index = c.calculate(tree, rooted=False)
self.assertAlmostEqual(consistency_index[0]['f__Lachnospiraceae'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Bacteroides'], 1.0)
self.assertAlmostEqual(consistency_index[1]['g__Lachnospira'], 1.0)
self.assertAlmostEqual(
consistency_index[2]['s__Bacteroides pectinophilus'], 1.0)
def __call__(self, seq_path=None, result_path=None, log_path=None):
"""Returns a dict mapping {seq_id:(taxonomy, confidence)} for each seq
Keep in mind, "confidence" is only done for consistency and in fact
all assignments will have a score of 0 because a method for determining
confidence is not currently implemented.
Parameters:
seq_path: path to file of sequences. The sequences themselves are
never actually used, but they are needed for their ids.
result_path: path to file of results. If specified, dumps the
result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
# initialize the logger
logger = self._get_logger(log_path)
logger.info(str(self))
with open(seq_path, 'U') as f:
seqs = dict(MinimalFastaParser(f))
consensus_map = tax2tree.prep_consensus(
open(self.Params['id_to_taxonomy_fp']),
seqs.keys())
seed_con = consensus_map[0].strip().split('\t')[1]
determine_rank_order(seed_con)
tipnames_map = load_consensus_map(consensus_map, False)
tree = load_tree(open(self.Params['tree_fp']), tipnames_map)
results = tax2tree.generate_constrings(tree, tipnames_map)
results = tax2tree.clean_output(results, seqs.keys())
if result_path:
# if the user provided a result_path, write the
# results to file
with open(result_path, 'w') as f:
for seq_id, (lineage, confidence) in results.iteritems():
f.write('%s\t%s\t%s\n' % (seq_id, lineage, confidence))
logger.info('Result path: %s' % result_path)
return results
def __call__(self, seq_path=None, result_path=None, log_path=None):
"""Returns a dict mapping {seq_id:(taxonomy, confidence)} for each seq
Keep in mind, "confidence" is only done for consistency and in fact
all assignments will have a score of 0 because a method for determining
confidence is not currently implemented.
Parameters:
seq_path: path to file of sequences. The sequences themselves are
never actually used, but they are needed for their ids.
result_path: path to file of results. If specified, dumps the
result to the desired path instead of returning it.
log_path: path to log, which should include dump of params.
"""
# initialize the logger
logger = self._get_logger(log_path)
logger.info(str(self))
with open(seq_path, 'U') as f:
seqs = dict(parse_fasta(f))
consensus_map = tax2tree.prep_consensus(
open(self.Params['id_to_taxonomy_fp']),
seqs.keys())
seed_con = consensus_map[0].strip().split('\t')[1]
determine_rank_order(seed_con)
tipnames_map = load_consensus_map(consensus_map, False)
tree = load_tree(open(self.Params['tree_fp']), tipnames_map)
results = tax2tree.generate_constrings(tree, tipnames_map)
results = tax2tree.clean_output(results, seqs.keys())
if result_path:
# if the user provided a result_path, write the
# results to file
with open(result_path, 'w') as f:
for seq_id, (lineage, confidence) in results.iteritems():
f.write('%s\t%s\t%s\n' % (seq_id, lineage, confidence))
logger.info('Result path: %s' % result_path)
return results
def flat_errors(tax_lines):
"""Flat file errors"""
inc_prefix = 'Incorrect prefixes'
inc_nlevel = 'Incorrect number of levels'
inc_gap = 'Gaps in taxonomy'
seed_con = tax_lines[0].strip().split('\t')[1]
rank_order = determine_rank_order(seed_con)
nlevels = len(rank_order)
errors = defaultdict(list)
errors_seen = defaultdict(set)
for line in tax_lines:
id_, parsed = check_parse(line)
if not check_prefixes(parsed, rank_order):
if parsed not in errors_seen[inc_prefix]:
errors_seen[inc_prefix].add(parsed)
errors[inc_prefix].append(id_)
if not check_n_levels(parsed, nlevels):
if parsed not in errors_seen[inc_nlevel]:
errors_seen[inc_nlevel].add(parsed)
errors[inc_nlevel].append(id_)
if not check_gap(parsed):
gap_idx = find_gap(parsed)
taxon_following_gap = gap_idx + 1
# another +1 as the slice is exclusive
if parsed[:taxon_following_gap + 1] not in errors_seen[inc_gap]:
errors_seen[inc_gap].add(parsed[:taxon_following_gap + 1])
errors['Gaps in taxonomy'].append(id_)
return errors
def flat_errors(tax_lines):
"""Flat file errors"""
inc_prefix = 'Incorrect prefixes'
inc_nlevel = 'Incorrect number of levels'
inc_gap = 'Gaps in taxonomy'
seed_con = tax_lines[0].strip().split('\t')[1]
rank_order = determine_rank_order(seed_con)
nlevels = len(rank_order)
errors = defaultdict(list)
errors_seen = defaultdict(set)
for line in tax_lines:
id_, parsed = check_parse(line)
if not check_prefixes(parsed, rank_order):
if parsed not in errors_seen[inc_prefix]:
errors_seen[inc_prefix].add(parsed)
errors[inc_prefix].append(id_)
if not check_n_levels(parsed, nlevels):
if parsed not in errors_seen[inc_nlevel]:
errors_seen[inc_nlevel].add(parsed)
errors[inc_nlevel].append(id_)
if not check_gap(parsed):
gap_idx = find_gap(parsed)
taxon_following_gap = gap_idx + 1
# another +1 as the slice is exclusive
if parsed[:taxon_following_gap + 1] not in errors_seen[inc_gap]:
errors_seen[inc_gap].add(parsed[:taxon_following_gap + 1])
errors['Gaps in taxonomy'].append(id_)
return errors
