def test_generate_training_files(self):
app = RdpTaxonAssigner({
'id_to_taxonomy_fp':
self.id_to_taxonomy_file.name,
'reference_sequences_fp':
self.reference_seqs_file.name,
})
actual_taxonomy_file, actual_training_seqs_file = \
app._generate_training_files()
# see note in test_build_tree()
self.assertEqual(actual_taxonomy_file.read(), rdp_expected_taxonomy)
def test_log(self):
"""RdpTaxonAssigner should write correct message to log file"""
# expected result when no result_path is provided
a = RdpTaxonAssigner({})
a(seq_path=self.tmp_seq_filepath,
result_path=None,
log_path=self.tmp_log_filepath)
# open the actual log file and the expected file, and pass into lists
obs = [l.strip() for l in list(open(self.tmp_log_filepath, 'r'))]
exp = rdp_test1_log_file_contents.split('\n')
# sort the lists as the entries are written from a dict,
# so order may vary
obs.sort()
exp.sort()
self.assertEqual(obs, exp)
def test_train_on_the_fly(self):
"""Training on-the-fly classifies reference sequence correctly with 100% certainty
"""
input_seqs_file = NamedTemporaryFile(prefix='RdpTaxonAssignerTest_',
suffix='.fasta')
input_seqs_file.write(test_seq_coll.toFasta())
input_seqs_file.seek(0)
expected = rdp_trained_test1_expected_dict
app = RdpTaxonAssigner({
'id_to_taxonomy_fp':
self.id_to_taxonomy_file.name,
'reference_sequences_fp':
self.reference_seqs_file.name,
})
actual = app(self.tmp_seq_filepath)
key = 'X67228 some description'
self.assertEqual(actual[key], expected[key])
def setUp(self):
# Temporary input file
self.tmp_seq_filepath = get_tmp_filename(
prefix='RdpTaxonAssignerTest_', suffix='.fasta')
seq_file = open(self.tmp_seq_filepath, 'w')
seq_file.write(rdp_test1_fasta)
seq_file.close()
# Temporary results filename
self.tmp_res_filepath = get_tmp_filename(
prefix='RdpTaxonAssignerTestResult_',
suffix='.tsv',
)
# touch the file so we don't get an error trying to close it
open(self.tmp_res_filepath, 'w').close()
# Temporary log filename
self.tmp_log_filepath = get_tmp_filename(
prefix='RdpTaxonAssignerTestLog_',
suffix='.txt',
)
# touch the file so we don't get an error trying to close it
open(self.tmp_log_filepath, 'w').close()
self._paths_to_clean_up = \
[self.tmp_seq_filepath, self.tmp_res_filepath, self.tmp_log_filepath]
self.id_to_taxonomy_file = NamedTemporaryFile(
prefix='RdpTaxonAssignerTest_', suffix='.txt')
self.id_to_taxonomy_file.write(rdp_id_to_taxonomy)
self.id_to_taxonomy_file.seek(0)
self.reference_seqs_file = NamedTemporaryFile(
prefix='RdpTaxonAssignerTest_', suffix='.fasta')
self.reference_seqs_file.write(rdp_reference_seqs)
self.reference_seqs_file.seek(0)
self.default_app = RdpTaxonAssigner({})
def test_init(self):
"""RdpTaxonAssigner.__init__ should set default attributes and params
"""
a = RdpTaxonAssigner({})
self.assertEqual(a.Name, 'RdpTaxonAssigner')
