def test_map_ids_to_taxonomy(self):
"""Mapping sequence ids to taxonomy functions as expected
"""
p = BlastTaxonAssigner({})
id_to_taxonomy_map = {
"AY800210": "Archaea;Euryarchaeota;Halobacteriales;uncultured",
"EU883771":
"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",
"EF503699": "Archaea;Crenarchaeota;uncultured;uncultured",
"DQ260310":
"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
"EF503697": "Archaea;Crenarchaeota;uncultured;uncultured",
}
hits = {
's1': ("AY800210", 1e-99),
's5': ("EU883771", 'weird confidence value'),
's3': ("DQ260310", 42.),
's4': None,
}
expected = {
's1': ("Archaea;Euryarchaeota;Halobacteriales;uncultured", 1e-99,
"AY800210"),
's5':
('Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.',
'weird confidence value', "EU883771"),
's3': ("Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
42., "DQ260310"),
's4': ('No blast hit', None, None),
}
actual = p._map_ids_to_taxonomy(hits, id_to_taxonomy_map)
self.assertEqual(actual, expected)
def test_seqs_to_taxonomy(self):
"""BlastTaxonAssigner._seqs_to_taxonomy: functions as expected
"""
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
# build the id_to_taxonomy_map as this test doesn't execute __call__
id_to_taxonomy_map = {
"AY800210": \
"Archaea;Euryarchaeota;Halobacteriales;uncultured",
"EU883771": \
"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",
"EF503699": \
"Archaea;Crenarchaeota;uncultured;uncultured",
"DQ260310": \
"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
"EF503697": \
"Archaea;Crenarchaeota;uncultured;uncultured",
}
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
# read the input file into (seq_id, seq) pairs
seqs = list(MinimalFastaParser(open(self.input_seqs_fp)))
actual = p._seqs_to_taxonomy(seqs, blast_db, id_to_taxonomy_map)
self.assertEqual(actual, self.expected1)
# passing empty list of seqs functions as expected
actual = p._seqs_to_taxonomy([], blast_db, id_to_taxonomy_map)
self.assertEqual(actual, {})
def test_map_ids_to_taxonomy(self):
"""Mapping sequence ids to taxonomy functions as expected
"""
p = BlastTaxonAssigner({})
id_to_taxonomy_map = {
"AY800210": "Archaea;Euryarchaeota;Halobacteriales;uncultured",
"EU883771": "Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",
"EF503699": "Archaea;Crenarchaeota;uncultured;uncultured",
"DQ260310": "Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
"EF503697": "Archaea;Crenarchaeota;uncultured;uncultured",
}
hits = {
's1': ("AY800210", 1e-99),
's5': ("EU883771", 'weird confidence value'),
's3': ("DQ260310", 42.),
's4': None,
}
expected = {
's1': ("Archaea;Euryarchaeota;Halobacteriales;uncultured", 1e-99, "AY800210"),
's5': ('Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.',
'weird confidence value',"EU883771"),
's3': ("Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium", 42.,"DQ260310"),
's4': ('No blast hit', None, None),
}
actual = p._map_ids_to_taxonomy(hits,id_to_taxonomy_map)
self.assertEqual(actual,expected)
def test_seqs_to_taxonomy(self):
"""BlastTaxonAssigner._seqs_to_taxonomy: functions as expected
"""
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
# build the id_to_taxonomy_map as this test doesn't execute __call__
id_to_taxonomy_map = {
"AY800210": \
"Archaea;Euryarchaeota;Halobacteriales;uncultured",
"EU883771": \
"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",
"EF503699": \
"Archaea;Crenarchaeota;uncultured;uncultured",
"DQ260310": \
"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",
"EF503697": \
"Archaea;Crenarchaeota;uncultured;uncultured",
}
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
# read the input file into (seq_id, seq) pairs
seqs = list(MinimalFastaParser(open(self.input_seqs_fp)))
actual = p._seqs_to_taxonomy(seqs,blast_db,id_to_taxonomy_map)
self.assertEqual(actual,self.expected1)
# passing empty list of seqs functions as expected
actual = p._seqs_to_taxonomy([],blast_db,id_to_taxonomy_map)
self.assertEqual(actual,{})
def test_parse_id_to_taxonomy_file(self):
"""Parsing taxonomy files functions as expected
"""
lines = id_to_taxonomy_string.splitlines()
p = BlastTaxonAssigner({})
expected = {\
"AY800210":"Archaea;Euryarchaeota;Halobacteriales;uncultured",\
"EU883771":"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",\
"EF503699":"Archaea;Crenarchaeota;uncultured;uncultured",\
"DQ260310":"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",\
"EF503697":"Archaea;Crenarchaeota;uncultured;uncultured"}
self.assertEqual(p._parse_id_to_taxonomy_file(lines), expected)
def test_get_first_blast_hit_per_seq(self):
"""Extracting the first blast hit for each seq functions as expected
"""
p = BlastTaxonAssigner({})
blast_hits = {'s1':[('blah',0.0)],\
's3':[('dsasd',1e-42),('rrr',1e-12),('qqq',0.001)],\
's2':[]}
expected = {'s1':('blah',0.0),\
's3':('dsasd',1e-42),\
's2':None}
actual = p._get_first_blast_hit_per_seq(blast_hits)
self.assertEqual(actual, expected)
def test_parse_id_to_taxonomy_file(self):
"""Parsing taxonomy files functions as expected
"""
lines = id_to_taxonomy_string.splitlines()
p = BlastTaxonAssigner({})
expected = {\
"AY800210":"Archaea;Euryarchaeota;Halobacteriales;uncultured",\
"EU883771":"Archaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.",\
"EF503699":"Archaea;Crenarchaeota;uncultured;uncultured",\
"DQ260310":"Archaea;Euryarchaeota;Methanobacteriales;Methanobacterium",\
"EF503697":"Archaea;Crenarchaeota;uncultured;uncultured"}
self.assertEqual(p._parse_id_to_taxonomy_file(lines),expected)
def test_get_first_blast_hit_per_seq(self):
"""Extracting the first blast hit for each seq functions as expected
"""
p = BlastTaxonAssigner({})
blast_hits = {'s1':[('blah',0.0)],\
's3':[('dsasd',1e-42),('rrr',1e-12),('qqq',0.001)],\
's2':[]}
expected = {'s1':('blah',0.0),\
's3':('dsasd',1e-42),\
's2':None}
actual = p._get_first_blast_hit_per_seq(blast_hits)
self.assertEqual(actual,expected)
def test_call_output_to_file(self):
"""BlastTaxonAssigner.__call__ functions w output to file
"""
result_path = get_tmp_filename(prefix='BlastTaxonAssignerTests_',
suffix='.fasta')
self._paths_to_clean_up.append(result_path)
p = BlastTaxonAssigner({
'reference_seqs_filepath':
self.reference_seqs_fp,
'id_to_taxonomy_filepath':
self.id_to_taxonomy_fp,
})
actual = p(self.input_seqs_fp, result_path=result_path)
expected_lines = set([
's1\tArchaea;Euryarchaeota;Halobacteriales;uncultured\t0.0\tAY800210\n',
's2\tArchaea;Euryarchaeota;Methanomicrobiales;Methanomicrobium et rel.\t0.0\tEU883771\n',
's3\tArchaea;Crenarchaeota;uncultured;uncultured\t0.0\tEF503699\n',
's4\tArchaea;Euryarchaeota;Methanobacteriales;Methanobacterium\t0.0\tDQ260310\n',
's5\tArchaea;Crenarchaeota;uncultured;uncultured\t0.0\tEF503697\n',
's6\tNo blast hit\tNone\tNone\n',
])
f = open(result_path)
observed_lines = set(f.readlines())
f.close()
self.assertEqual(observed_lines, expected_lines)
# Return value is None when result_path is provided (Not sure
# if this is what we want yet, or if we would want both so
# results could be logged to file...)
self.assertEqual(actual, None)
def test_init(self):
"""BlastTaxonAssigner __init__ should store name, params"""
p = BlastTaxonAssigner({})
self.assertEqual(p.Name, 'BlastTaxonAssigner')
# default parameters correctly initialized
default_params = {'Min percent identity':0.90,\
'Max E value':1e-30,\
'Application':'blastn/megablast'}
self.assertEqual(p.Params, default_params)
def test_call_on_the_fly_blast_db(self):
"""BlastTaxonAssigner.__call__ functions w creating blast db
"""
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
actual = p(self.input_seqs_fp)
self.assertEqual(actual, self.expected1)
def test_call_existing_blast_db(self):
"""BlastTaxonAssigner.__call__ functions w existing db
"""
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({'blast_db':blast_db,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
actual = p(self.input_seqs_fp)
self.assertEqual(actual, self.expected1)
def test_get_blast_hits(self):
"""BlastTaxonAssigner._get_blast_hits functions w existing db
"""
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({})
seq_coll_blast_results = p._get_blast_hits(blast_db, self.test_seqs)
# mapping from identifier in test_seq_coll to the id of the sequence
# in the refseq collection (a silva derivative)
expected_matches = {\
's1':'AY800210',
's2':'EU883771',\
's3':'EF503699',\
's4':'DQ260310',\
's5':'EF503697'}
# no results for s6 (which is a randomly-generated sequence)
s6_blast_results = seq_coll_blast_results['s6']
self.assertEqual(s6_blast_results, [])
# expected results for all other query sequences
for seq_id in expected_matches:
blast_results = seq_coll_blast_results[seq_id]
blast_results_d = dict(blast_results)
# explicitly checks that the result is in the data before
# pulling it out (this is redundant, but allows for a useful
# error message if the data wasn't in there b/c e.g. there
# were no blast results returned)
self.assertTrue(expected_matches[seq_id] in blast_results_d)
# now check that the perfect match got a 0.0 e-value as it should
# on this data
self.assertEqual(blast_results_d[expected_matches[seq_id]], 0.0)
def test_get_blast_hits(self):
"""BlastTaxonAssigner._get_blast_hits functions w existing db
"""
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({})
seq_coll_blast_results = p._get_blast_hits(blast_db,self.test_seqs)
# mapping from identifier in test_seq_coll to the id of the sequence
# in the refseq collection (a silva derivative)
expected_matches = {\
's1':'AY800210',
's2':'EU883771',\
's3':'EF503699',\
's4':'DQ260310',\
's5':'EF503697'}
# no results for s6 (which is a randomly-generated sequence)
s6_blast_results = seq_coll_blast_results['s6']
self.assertEqual(s6_blast_results,[])
# expected results for all other query sequences
for seq_id in expected_matches:
blast_results = seq_coll_blast_results[seq_id]
blast_results_d = dict(blast_results)
# explicitly checks that the result is in the data before
# pulling it out (this is redundant, but allows for a useful
# error message if the data wasn't in there b/c e.g. there
# were no blast results returned)
self.assertTrue(expected_matches[seq_id] in blast_results_d)
# now check that the perfect match got a 0.0 e-value as it should
# on this data
self.assertEqual(blast_results_d[expected_matches[seq_id]],0.0)
def __init__(self, params):
"""Return new BlastFragmentsChimeraChecker object with specified params.
"""
_params = {
'max_e_value': 1e-30,
'min_pct_id': 0.90,
'num_fragments': 3,
'taxonomy_depth': 4
}
_params.update(params)
try:
id_to_taxonomy_fp = params['id_to_taxonomy_fp']
except KeyError:
raise ValueError("id_to_taxonomy_filepath must be provided to %s" %
self.Name)
# Create the blast database if it hasn't been provided
if 'blast_db' not in params or params['blast_db'] is None:
try:
reference_seqs_fp = params['reference_seqs_fp']
except KeyError:
raise ValueError(
"refseqs_fp or blast_db must be provided to %s" %
self.Name)
blast_db, self._db_files_to_remove = \
build_blast_db_from_fasta_path(reference_seqs_fp)
else:
blast_db = params['blast_db']
self._db_files_to_remove = []
self._taxon_assigner = BlastTaxonAssigner({
'blast_db':
blast_db,
'id_to_taxonomy_filepath':
id_to_taxonomy_fp,
'Max E value':
_params['max_e_value'],
'Min percent identity':
_params['min_pct_id']
})
ChimeraChecker.__init__(self, _params)
def test_call_alt_input_types(self):
"""BlastTaxonAssigner.__call__ functions w alt input types """
p = BlastTaxonAssigner({\
'reference_seqs_filepath':self.reference_seqs_fp,\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp})
# neither seqs or seq_fp passed results in AssertionError
self.assertRaises(AssertionError, p)
# Functions with a list of (seq_id, seq) pairs
seqs = list(MinimalFastaParser(open(self.input_seqs_fp)))
actual = p(seqs=seqs)
self.assertEqual(actual, self.expected1)
# Functions with input path
actual = p(self.input_seqs_fp)
self.assertEqual(actual, self.expected1)
# same result when passing fp or seqs
self.assertEqual(p(seqs=seqs), p(self.input_seqs_fp))
def test_call_logs_run(self):
"""BlastTaxonAssigner.__call__ logs the run when expected
"""
log_path = get_tmp_filename(\
prefix='BlastTaxonAssignerTests_',suffix='.fasta')
self._paths_to_clean_up.append(log_path)
# build the blast database and keep track of the files to clean up
blast_db, files_to_remove = \
build_blast_db_from_fasta_path(self.reference_seqs_fp)
self._paths_to_clean_up += files_to_remove
p = BlastTaxonAssigner({\
'id_to_taxonomy_filepath':self.id_to_taxonomy_fp,\
'blast_db':blast_db})
actual = p(self.input_seqs_fp, log_path=log_path)
log_file = open(log_path)
log_file_str = log_file.read()
log_file.close()
log_file_exp = [
"BlastTaxonAssigner parameters:",
'Min percent identity:0.9',
'Application:blastn/megablast',
'Max E value:1e-30',
'Result path: None, returned as dict.',
'blast_db:%s' % str(self.reference_seqs_fp)[1:-1],
'id_to_taxonomy_filepath:%s' % self.id_to_taxonomy_fp,
'Number of sequences inspected: 6',
'Number with no blast hits: 1',
'',
]
# compare data in log file to fake expected log file
# NOTE: Since p.params is a dict, the order of lines is not
# guaranteed, so testing is performed to make sure that
# the equal unordered lists of lines is present in actual and expected
self.assertEqualItems(log_file_str.split('\n'), log_file_exp)