예제 #1
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    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
        ]
예제 #2
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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))
예제 #3
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    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]
예제 #4
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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))