def setUp(self):
cfg = EpacTrainerConfig()
cfg.debug = True
testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"testfiles")
tax_fname = os.path.join(testfile_dir, "test.tax")
phy_fname = os.path.join(testfile_dir, "test.phy")
tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname)
seqs = SeqGroup(sequences=phy_fname, format="phylip")
self.inval = InputValidator(cfg, tax, seqs, False)
self.expected_mis_ids = ["Missing1", "Missing2"]
self.expected_dups = ["DupSeq(01)", "DupSeq02"]
self.expected_merges = [
self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups
]
class InputValidatorTests(unittest.TestCase):
def setUp(self):
cfg = EpacTrainerConfig()
cfg.debug = True
testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"testfiles")
tax_fname = os.path.join(testfile_dir, "test.tax")
phy_fname = os.path.join(testfile_dir, "test.phy")
tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname)
seqs = SeqGroup(sequences=phy_fname, format="phylip")
self.inval = InputValidator(cfg, tax, seqs, False)
self.expected_mis_ids = ["Missing1", "Missing2"]
self.expected_dups = ["DupSeq(01)", "DupSeq02"]
self.expected_merges = [
self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups
]
def test_seq_ids(self):
mis_ids = self.inval.check_seq_ids()
self.assertEqual(set(mis_ids), set(self.expected_mis_ids))
def test_identical_seqs(self):
count, dups = self.inval.check_identical_seqs()
self.assertEqual(len(dups), 1)
self.assertEqual(set(dups[0]), set(self.expected_dups))
def test_identical_ranks(self):
merged_ranks = self.inval.check_identical_ranks()
self.assertEqual(len(merged_ranks), 1)
self.assertEqual(set(merged_ranks.popitem()[1]),
set(self.expected_merges))
def test_validate(self):
corr_ranks, corr_seqid, merged_ranks = self.inval.validate()
self.assertEqual(len(merged_ranks), 1)
merged_list = merged_ranks.popitem()[1]
corr_merged_list = [
self.inval.taxonomy.get_uncorr_rank_id(i) for i in merged_list
]
self.assertEqual(set(corr_merged_list), set(self.expected_merges))
def setUp(self):
cfg = EpacTrainerConfig()
cfg.debug=True
testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testfiles")
tax_fname = os.path.join(testfile_dir, "test.tax")
phy_fname = os.path.join(testfile_dir, "test.phy")
tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname)
seqs = SeqGroup(sequences=phy_fname, format = "phylip")
self.inval = InputValidator(cfg, tax, seqs, False)
self.expected_mis_ids = ["Missing1", "Missing2"]
self.expected_dups = ["DupSeq(01)", "DupSeq02"]
self.expected_merges = [self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups]
class InputValidatorTests(unittest.TestCase):
def setUp(self):
cfg = EpacTrainerConfig()
cfg.debug=True
testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "testfiles")
tax_fname = os.path.join(testfile_dir, "test.tax")
phy_fname = os.path.join(testfile_dir, "test.phy")
tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname)
seqs = SeqGroup(sequences=phy_fname, format = "phylip")
self.inval = InputValidator(cfg, tax, seqs, False)
self.expected_mis_ids = ["Missing1", "Missing2"]
self.expected_dups = ["DupSeq(01)", "DupSeq02"]
self.expected_merges = [self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups]
def test_seq_ids(self):
mis_ids = self.inval.check_seq_ids()
self.assertEqual(set(mis_ids), set(self.expected_mis_ids))
def test_identical_seqs(self):
count, dups = self.inval.check_identical_seqs()
self.assertEqual(len(dups), 1)
self.assertEqual(set(dups[0]), set(self.expected_dups))
def test_identical_ranks(self):
merged_ranks = self.inval.check_identical_ranks()
self.assertEqual(len(merged_ranks), 1)
self.assertEqual(set(merged_ranks.popitem()[1]), set(self.expected_merges))
def test_validate(self):
corr_ranks, corr_seqid, merged_ranks = self.inval.validate()
self.assertEqual(len(merged_ranks), 1)
merged_list = merged_ranks.popitem()[1]
corr_merged_list = [self.inval.taxonomy.get_uncorr_rank_id(i) for i in merged_list]
self.assertEqual(set(corr_merged_list), set(self.expected_merges))