def test_create_starts_and_stops(self):
        gene = Gene()
        mrna = Mock()

        gene.children = {'mrna':[mrna]}

        gene.create_starts_and_stops('ATGC')

        mrna.create_starts_and_stops.assertCalledWith('ATGC')
    def test_get_cds_length(self):
        gene = Gene()
        mrna = Mock()
        cds = Mock()
        cds.length = Mock(return_value=42)
        mrna.get_cds = Mock(return_value=cds)
        gene.children = {'mrna':[mrna]}

        self.assertEquals(gene.get_cds_length(), 42)
    def test_match_cds_and_exon_end(self):
        gene = Gene()
        mrna = Mock()

        gene.children = {'mrna':[mrna]}

        gene.match_cds_and_exon_end()

        mrna.match_cds_and_exon_end.assertCalled()
Exemple #4
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 def process_gene_line(self, line, gene_type):
     """Extracts arguments from a line and instantiates a Gene object."""
     kwargs = self.extract_gene_args(line)
     if not kwargs:
         return
     gene_id = kwargs['identifier']
     gene = Gene(**kwargs)
     if gene_type == 'pseudogene':
         gene.pseudo = True
     self.genes[gene_id] = gene
Exemple #5
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 def process_gene_line(self, line, gene_type):
     """Extracts arguments from a line and instantiates a Gene object."""
     kwargs = self.extract_gene_args(line)
     if not kwargs:
         return
     gene_id = kwargs['identifier']
     gene = Gene(**kwargs)
     if gene_type == 'pseudogene':
         gene.pseudo = True
     self.genes[gene_id] = gene
Exemple #6
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 def test_to_tbl_negative(self):
     gene = Gene("seq1", "maker", [1, 50], "-", "foo_gene_1")
     mrna1 = Mock()
     mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
     mrna2 = Mock()
     mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
     gene.mrnas.append(mrna1)
     gene.mrnas.append(mrna2)
     expected = "50\t1\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
     self.assertEquals(gene.to_tbl(), expected)
Exemple #7
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 def test_to_tbl_negative(self):
     gene = Gene("seq1", "maker", [1, 50], "-", "foo_gene_1")
     mrna1 = Mock()
     mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
     mrna2 = Mock()
     mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
     gene.mrnas.append(mrna1)
     gene.mrnas.append(mrna2)
     expected = "50\t1\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
     self.assertEquals(gene.to_tbl(), expected)
Exemple #8
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    def test_max_intron_length_filter(self):
        intron_length = MaxIntronLengthFilter(30)

        # Create a mock sequence
        seq = Sequence()

        # Give the sequence some genes
        seq.genes = [
            Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo1'),
            Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo2'),
            Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo3')
        ]

        # Give the mock mrnas some exon's
        test_mrna0 = Mock()
        test_mrna0.identifier = 'foo1-RA'
        test_mrna0.death_flagged = False
        test_mrna0.exon = Mock()
        test_mrna0.get_shortest_intron = Mock(return_value=20)
        test_mrna0.get_longest_intron = Mock(return_value=20)

        test_mrna1 = Mock()
        test_mrna1.identifier = 'foo2-RA'
        test_mrna1.death_flagged = False
        test_mrna1.exon = Mock()
        test_mrna1.get_shortest_intron = Mock(return_value=30)
        test_mrna1.get_longest_intron = Mock(return_value=30)

        test_mrna2 = Mock()
        test_mrna2.identifier = 'foo2-RB'
        test_mrna2.death_flagged = False
        test_mrna2.exon = None

        test_mrna3 = Mock()
        test_mrna3.identifier = 'foo3-RA'
        test_mrna3.death_flagged = False
        test_mrna3.exon = Mock()
        test_mrna3.get_shortest_intron = Mock(return_value=40)
        test_mrna3.get_longest_intron = Mock(return_value=40)

        # Give the mock genes some mrnas
        seq.genes[0].mrnas = [test_mrna0]
        seq.genes[0].death_flagged = False
        seq.genes[1].mrnas = [test_mrna1, test_mrna2]
        seq.genes[1].death_flagged = False
        seq.genes[2].mrnas = [test_mrna3]
        seq.genes[2].death_flagged = False

        # Apply the filter
        intron_length.apply(seq)

        self.assertEqual(len(seq.genes), 3)
        self.assertEqual(seq.genes[0].mrnas, [test_mrna0])
        self.assertEqual(seq.genes[1].mrnas, [test_mrna1, test_mrna2])
Exemple #9
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 def test_to_tbl_positive_with_name(self):
     gene = Gene(seq_name="seq1", source="maker", indices=[1, 50], strand="+", identifier="foo_gene_1", name="wtfg")
     self.assertFalse(gene.annotations)
     gene.add_annotation('foo', 'dog')
     mrna1 = Mock()
     mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
     mrna2 = Mock()
     mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
     gene.mrnas.append(mrna1)
     gene.mrnas.append(mrna2)
     expected = "1\t50\tgene\n\t\t\tgene\twtfg\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
     self.assertEquals(gene.to_tbl(), expected)
Exemple #10
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    def test_max_cds_length_filter(self):
        cds_length = MaxCDSLengthFilter(100)

        # Create a mock sequence
        seq = Sequence()

        # Give the sequence some genes
        seq.genes = [
            Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo1'),
            Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo2'),
            Gene('foo_seq', 'geib_labs', [1, 2], '+', 'foo3')
        ]

        # Give the mock mrnas some cds's
        test_mrna0 = Mock()
        test_mrna0.identifier = 'foo1-RA'
        test_mrna0.death_flagged = False
        test_mrna0.cds = Mock()
        test_mrna0.cds.length = Mock(return_value=90)

        test_mrna1 = Mock()
        test_mrna1.identifier = 'foo2-RA'
        test_mrna1.death_flagged = False
        test_mrna1.cds = None

        test_mrna2 = Mock()
        test_mrna2.identifier = 'foo2-RB'
        test_mrna2.death_flagged = False
        test_mrna2.cds = Mock()
        test_mrna2.cds.length = Mock(return_value=100)

        test_mrna3 = Mock()
        test_mrna3.identifier = 'foo3-RA'
        test_mrna3.death_flagged = False
        test_mrna3.cds = Mock()
        test_mrna3.cds.length = Mock(return_value=110)

        # Give the mock genes some mrnas
        seq.genes[0].mrnas = [test_mrna0]
        seq.genes[0].death_flagged = False
        seq.genes[1].mrnas = [test_mrna1, test_mrna2]
        seq.genes[1].death_flagged = False
        seq.genes[2].mrnas = [test_mrna3]
        seq.genes[2].death_flagged = False

        # Apply the filter
        cds_length.apply(seq)

        self.assertEqual(len(seq.genes), 3)
        self.assertEqual(seq.genes[0].mrnas, [test_mrna0])
        self.assertEqual(seq.genes[1].mrnas, [test_mrna1, test_mrna2])
Exemple #11
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 def setUp(self):
     self.test_gene0 = Gene(seq_name="sctg_0080_0020", source="maker", indices=[3734, 7436], strand='+', identifier=1)
     self.test_gene1 = Gene(seq_name="sctg_0080_0020", source="maker", indices=[3734, 7436], strand='+', identifier=1)
     
     self.fake_mrna1 = Mock()
     self.fake_mrna1.identifier = "fake_mrna1"
     self.fake_mrna1.death_flagged = False
     
     self.fake_mrna2 = Mock()
     self.fake_mrna2.identifier = "fake_mrna2"
     self.fake_mrna2.death_flagged = False
     
     self.test_gene1.mrnas.append(self.fake_mrna1)
     self.test_gene1.mrnas.append(self.fake_mrna2)
    def test_make_positive(self):
        seq_len = 8

        gene = Gene(start=1, end=7, strand='-')

        mrna = Mock()
        mrna.type = 'mrna'
        mrna.make_positive = Mock()
        gene.add_child(mrna)

        gene.make_positive(seq_len)

        self.assertEqual(gene.start, 2)
        self.assertEqual(gene.end, 8)
        self.assertEqual(gene.strand, '+')
        mrna.make_positive.assertCalledWith(seq_len)
def build_transcript_dictionary(seqs, genes):
    transcripts = {}

    for gene in genes:
        gene = Gene.from_gff_feature(gene)
        if gene == None:
            print("Could not convert GFFFeature to Gene, skipping")
            continue

        new_mrnas = []
        for mrna in gene['mrna']:
            mrna = Mrna.from_gff_feature(mrna)
            if mrna == None:
                print("Could not convert GFFFeature to Mrna, skipping")
                continue
            new_mrnas.append(mrna)
        gene.children['mrna'] = new_mrnas

        if gene.seqid in transcripts:
            transcripts[gene.seqid].genes.append(gene)
        else:
            if gene.seqid in seqs:
                transcripts[gene.seqid] = Transcript([gene], seqs[gene.seqid])
            else:
                print("Gene "+gene.attributes["ID"]+" is on sequence "+gene.seqid+" which does not exist. Skipping...")

    return transcripts
Exemple #14
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 def test_to_tbl_positive(self):
     gene = Gene(seq_name="seq1",
                 source="maker",
                 indices=[1, 50],
                 strand="+",
                 identifier="foo_gene_1")
     self.assertFalse(gene.annotations)
     gene.add_annotation('foo', 'dog')
     mrna1 = Mock()
     mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
     mrna2 = Mock()
     mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
     gene.mrnas.append(mrna1)
     gene.mrnas.append(mrna2)
     expected = "1\t50\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
     self.assertEquals(gene.to_tbl(), expected)
Exemple #15
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 def process_gene_line(self, line):
     """Extracts arguments from a line and instantiates a Gene object."""
     kwargs = self.extract_gene_args(line)
     if not kwargs:
         return
     gene_id = kwargs['identifier']
     self.genes[gene_id] = Gene(**kwargs)
Exemple #16
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 def test_gene_initialized_without_annotations(self):
     newgene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1")
     self.assertFalse(newgene.annotations)
     self.assertEquals(0, len(newgene.annotations.keys()))
Exemple #17
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 def __init__(self, population_size, filename_of_genes, max_weight, logger):
     self.population_size = population_size
     self.genes = Gene(filename_of_genes, logger)
     self.max_weight = max_weight
     self.max_score_for_run = None
     self.logger = logger
     self.best_chromosome = np.array([0, 0])
     return
Exemple #18
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 def test_gene_initialized_with_annotations(self):
     newgene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1",
                    annotations={"bar": ["cat"]})
     self.assertTrue(newgene.annotations)
     self.assertEquals(1, len(newgene.annotations.keys()))
Exemple #19
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    def setUp(self):
        self.test_gene0 = Gene(seq_name="sctg_0080_0020",
                               source="maker",
                               indices=[3734, 7436],
                               strand='+',
                               identifier=1)
        self.test_gene1 = Gene(seq_name="sctg_0080_0020",
                               source="maker",
                               indices=[3734, 7436],
                               strand='+',
                               identifier=1)

        self.fake_mrna1 = Mock()
        self.fake_mrna1.identifier = "fake_mrna1"
        self.fake_mrna1.death_flagged = False

        self.fake_mrna2 = Mock()
        self.fake_mrna2.identifier = "fake_mrna2"
        self.fake_mrna2.death_flagged = False

        self.test_gene1.mrnas.append(self.fake_mrna1)
        self.test_gene1.mrnas.append(self.fake_mrna2)
    def setUp(self):
        self.gene1 = Gene()
        self.mrna1 = Mock()
        self.cds1 = Mock()
        self.exon1 = Mock()
        self.gene1.get_mrna = Mock(return_value=self.mrna1)
        self.mrna1.get_cds = Mock(return_value=self.cds1)
        self.mrna1.get_exon = Mock(return_value=self.exon1)

        self.gene1.start = 1
        self.gene1.end = 100
        self.gene1.attributes = {'ID':'foo_gene'}

        self.mrna1.start = 1
        self.mrna1.end = 100
        self.mrna1.attributes = {'ID':'m.foo'}

        self.cds1.start = 1
        self.cds1.end = 100
        self.cds1.phase = 0

        self.exon1.start = 1
        self.exon1.end = 100
Exemple #21
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class TestGene(unittest.TestCase):

    def setUp(self):
        self.test_gene0 = Gene(seq_name="sctg_0080_0020", source="maker", indices=[3734, 7436], strand='+', identifier=1)
        self.test_gene1 = Gene(seq_name="sctg_0080_0020", source="maker", indices=[3734, 7436], strand='+', identifier=1)
        
        self.fake_mrna1 = Mock()
        self.fake_mrna1.identifier = "fake_mrna1"
        self.fake_mrna1.death_flagged = False
        
        self.fake_mrna2 = Mock()
        self.fake_mrna2.identifier = "fake_mrna2"
        self.fake_mrna2.death_flagged = False
        
        self.test_gene1.mrnas.append(self.fake_mrna1)
        self.test_gene1.mrnas.append(self.fake_mrna2)

    def test_constructor(self):
        self.assertEqual('Gene', self.test_gene0.__class__.__name__)

    def test_length(self):
        self.assertEqual(3703, self.test_gene0.length())

    def test_gagflagged(self):
        self.assertFalse(self.test_gene0.gagflagged())
        self.test_gene0.annotations = [["gag_flag", "nice gene"]]
        self.assertTrue(self.test_gene0.gagflagged())

    def test_number_of_gagflags(self):
        self.fake_mrna1.number_of_gagflags.return_value = 2
        self.fake_mrna2.number_of_gagflags.return_value = 1
        self.test_gene1.annotations = [["gag_flag", "nice gene"]]
        self.assertEquals(4, self.test_gene1.number_of_gagflags())

    def test_get_mrna_ids(self):
        expected = ["fake_mrna1", "fake_mrna2"]
        self.assertEquals(self.test_gene1.get_mrna_ids(), expected)
    
    def test_remove_mrna(self):
        self.assertEquals(self.test_gene1.mrnas, [self.fake_mrna1, self.fake_mrna2])
        self.assertEquals(len(self.test_gene1.removed_mrnas), 0)
        self.test_gene1.remove_mrna('fake_mrna1')
        self.assertEquals(self.test_gene1.mrnas, [self.fake_mrna2])
        self.assertEquals(self.test_gene1.removed_mrnas, [self.fake_mrna1])

    def test_get_longest_exon(self):
        self.fake_mrna1.get_longest_exon.return_value = 10
        self.fake_mrna2.get_longest_exon.return_value = 20
        self.assertEquals(20, self.test_gene1.get_longest_exon())

    def test_get_shortest_exon(self):
        self.fake_mrna1.get_shortest_exon.return_value = 5
        self.fake_mrna2.get_shortest_exon.return_value = 8
        self.assertEquals(5, self.test_gene1.get_shortest_exon())

    def test_get_total_exon_length(self):
        self.fake_mrna1.get_total_exon_length.return_value = 15
        self.fake_mrna2.get_total_exon_length.return_value = 25
        self.assertEquals(40, self.test_gene1.get_total_exon_length())

    def test_get_num_exons(self):
        self.fake_mrna1.get_num_exons.return_value = 5
        self.fake_mrna2.get_num_exons.return_value = 4
        self.assertEquals(9, self.test_gene1.get_num_exons())

    def test_get_longest_intron(self):
        self.fake_mrna1.get_longest_intron.return_value = 8
        self.fake_mrna2.get_longest_intron.return_value = 10
        self.assertEquals(10, self.test_gene1.get_longest_intron())

    def test_get_shortest_intron(self):
        self.fake_mrna1.get_shortest_intron.return_value = 5
        self.fake_mrna2.get_shortest_intron.return_value = 8
        self.assertEquals(5, self.test_gene1.get_shortest_intron())

    def test_get_total_intron_length(self):
        self.fake_mrna1.get_total_intron_length.return_value = 15
        self.fake_mrna2.get_total_intron_length.return_value = 25
        self.assertEquals(40, self.test_gene1.get_total_intron_length())

    def test_get_num_introns(self):
        self.fake_mrna1.get_num_introns.return_value = 3
        self.fake_mrna2.get_num_introns.return_value = 2
        self.assertEquals(5, self.test_gene1.get_num_introns())

    def test_get_partial_info(self):
        self.fake_mrna1.has_stop.return_value = True
        self.fake_mrna1.has_start.return_value = True
        self.fake_mrna2.has_stop.return_value = False
        self.fake_mrna2.has_start.return_value = True
        results = self.test_gene1.get_partial_info()
        self.assertEquals(1, results["complete"])

    def test_adjust_indices(self):
        self.test_gene1.adjust_indices(16)
        self.fake_mrna1.adjust_indices.assert_called_with(16, 1)
        self.assertEquals(3750, self.test_gene1.indices[0])
        # adjust them back
        self.test_gene1.adjust_indices(-16)
        self.fake_mrna1.adjust_indices.assert_called_with(-16, 1)
        self.assertEquals(3734, self.test_gene1.indices[0])

    def test_remove_mrnas_with_internal_stops(self):
        helper = Mock()
        helper.mrna_contains_internal_stop.return_value = True
        self.assertEquals(2, len(self.test_gene1.mrnas))
        self.test_gene1.remove_mrnas_with_internal_stops(helper)
        self.assertEquals(0, len(self.test_gene1.mrnas))

    def test_contains_mrna(self):
        self.fake_mrna1.identifier = "foo_mrna"
        self.fake_mrna2.identifier = "bar_mrna"
        self.assertTrue(self.test_gene1.contains_mrna("foo_mrna"))
        self.assertFalse(self.test_gene1.contains_mrna("zub_mrna"))

    def test_cds_to_gff(self):
        self.fake_mrna1.identifier = "foo_mrna"
        foo = self.test_gene1.cds_to_gff("foo_seq", "foo_mrna")
        self.fake_mrna1.cds_to_gff.assert_called_with("foo_seq", "maker")

    def test_cds_to_gff_no_such_mrna(self):
        self.fake_mrna1.identifier = "foo_mrna"
        foo = self.test_gene1.cds_to_gff("foo_seq", "bar_mrna")
        self.assertFalse(foo)

    def test_cds_to_tbl(self):
        self.fake_mrna1.identifier = "foo_mrna"
        foo = self.test_gene1.cds_to_tbl("foo_mrna")
        self.fake_mrna1.cds_to_tbl.assert_called_with()

    def test_to_mrna_fasta(self):
        helper = Mock()
        helper.mrna_to_fasta.return_value = "mrna_to_fasta\n"
        expected = "mrna_to_fasta\nmrna_to_fasta\n"
        self.assertEquals(expected, self.test_gene1.to_mrna_fasta(helper))

    def test_to_cds_fasta(self):
        helper = Mock()
        helper.mrna_to_cds_fasta.return_value = "mrna_to_CDS_fasta\n"
        expected = "mrna_to_CDS_fasta\nmrna_to_CDS_fasta\n"
        self.assertEquals(expected, self.test_gene1.to_cds_fasta(helper))

    def test_to_protein_fasta(self):
        helper = Mock()
        helper.mrna_to_protein_fasta.return_value = "mrna_to_protein_fasta\n"
        expected = "mrna_to_protein_fasta\nmrna_to_protein_fasta\n"
        self.assertEquals(expected, self.test_gene1.to_protein_fasta(helper))

    def test_to_gff(self):
        self.fake_mrna1.to_gff.return_value = "fake mrna1 to gff here:)\n"
        self.fake_mrna2.to_gff.return_value = "fake mrna2 to gff here:)\n"
        expected = "sctg_0080_0020\tmaker\tgene\t3734\t7436\t.\t+\t."
        expected += "\tID=1;foo=dog\n"
        expected += "fake mrna1 to gff here:)\n"
        expected += "fake mrna2 to gff here:)\n"
        self.test_gene1.add_annotation('foo', 'dog')
        self.assertEquals(expected, self.test_gene1.to_gff())

    def test_to_gff_with_name(self):
        self.fake_mrna1.to_gff.return_value = "fake mrna1 to gff here:)\n"
        self.fake_mrna2.to_gff.return_value = "fake mrna2 to gff here:)\n"
        expected = "sctg_0080_0020\tmaker\tgene\t3734\t7436\t.\t+\t."
        expected += "\tID=1;Name=foo_gene;foo=dog\n"
        expected += "fake mrna1 to gff here:)\n"
        expected += "fake mrna2 to gff here:)\n"
        self.test_gene1.add_annotation('foo', 'dog')
        self.test_gene1.name = "foo_gene"
        self.assertEquals(expected, self.test_gene1.to_gff())

    def test_str(self):
        expected = "Gene (ID=1, seq_name=sctg_0080_0020) containing 2 mrnas"
        self.assertEquals(expected, str(self.test_gene1))

    def test_create_starts_and_stops(self):
        mrna1 = Mock()
        mrna2 = Mock()
        self.test_gene0.mrnas = [mrna1, mrna2]
        seq_object = Mock()
        self.test_gene0.create_starts_and_stops(seq_object)
        mrna1.create_start_and_stop_if_necessary.assert_called_with(seq_object, '+')
        mrna2.create_start_and_stop_if_necessary.assert_called_with(seq_object, '+')

    def test_to_tbl_positive(self):
        gene = Gene(seq_name="seq1", source="maker", indices=[1, 50], strand="+", identifier="foo_gene_1")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "1\t50\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_to_tbl_positive_with_name(self):
        gene = Gene(seq_name="seq1", source="maker", indices=[1, 50], strand="+", identifier="foo_gene_1", name="wtfg")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "1\t50\tgene\n\t\t\tgene\twtfg\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_gene_initialized_without_annotations(self):
        newgene = Gene(seq_name="seq1", source="maker", indices=[1, 50], strand="+", identifier="foo_gene_1")
        self.assertFalse(newgene.annotations)
        self.assertEquals(0, len(newgene.annotations))

    def test_gene_initialized_with_annotations(self):
        newgene = Gene(seq_name="seq1", source="maker", indices=[1, 50], strand="+", identifier="foo_gene_1",\
                annotations=[["bar", "cat"]])
        self.assertTrue(newgene.annotations)
        self.assertEquals(1, len(newgene.annotations))

    def test_to_tbl_negative(self):
        gene = Gene("seq1", "maker", [1, 50], "-", "foo_gene_1")
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "50\t1\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)
class TestGene(unittest.TestCase):

    def setUp(self):
        self.gene1 = Gene()
        self.mrna1 = Mock()
        self.cds1 = Mock()
        self.exon1 = Mock()
        self.gene1.get_mrna = Mock(return_value=self.mrna1)
        self.mrna1.get_cds = Mock(return_value=self.cds1)
        self.mrna1.get_exon = Mock(return_value=self.exon1)

        self.gene1.start = 1
        self.gene1.end = 100
        self.gene1.attributes = {'ID':'foo_gene'}

        self.mrna1.start = 1
        self.mrna1.end = 100
        self.mrna1.attributes = {'ID':'m.foo'}

        self.cds1.start = 1
        self.cds1.end = 100
        self.cds1.phase = 0

        self.exon1.start = 1
        self.exon1.end = 100

    def test_from_gff_feature_success(self):
        gff_gene = Mock()
        gff_gene.type = "gene"
        
        tran_gene = Gene.from_gff_feature(gff_gene)
        self.assertTrue(tran_gene)

    def test_from_gff_features_fails(self):
        gff_gene = Mock()
        gff_gene.type = "asdf"
        
        tran_gene = Gene.from_gff_feature(gff_gene)
        self.assertFalse(tran_gene)

    def test_get_cds_length(self):
        gene = Gene()
        mrna = Mock()
        cds = Mock()
        cds.length = Mock(return_value=42)
        mrna.get_cds = Mock(return_value=cds)
        gene.children = {'mrna':[mrna]}

        self.assertEquals(gene.get_cds_length(), 42)

    def test_remove_contig_from_gene_id(self):
        expected = 'g.123'
        self.gene1.attributes['ID'] = 'contig123|g.123'
        self.gene1.remove_contig_from_gene_id()
        self.assertEquals(expected, self.gene1.attributes['ID'])

    def test_gene_to_tbl_nostart_nostop(self):
        expected = \
        "<1\t>100\tgene\n"\
        "\t\t\tlocus_tag\tfoo_gene\n"\
        "<1\t>100\tCDS\n"\
        "\t\t\tprotein_id\tm.foo\n"\
        "\t\t\tproduct\thypothetical protein\n"

        self.mrna1.__contains__ = no_start_no_stop

        tbl = self.gene1.to_tbl()
        self.assertEquals(tbl, expected)

    def test_gene_to_tbl_start_nostop(self):
        expected = \
        "1\t>100\tgene\n"\
        "\t\t\tlocus_tag\tfoo_gene\n"\
        "1\t>100\tCDS\n"\
        "\t\t\tprotein_id\tm.foo\n"\
        "\t\t\tproduct\thypothetical protein\n"

        self.mrna1.__contains__ = start_no_stop

        tbl = self.gene1.to_tbl()
        self.assertEquals(tbl, expected)

    def test_gene_to_tbl_nostart_stop(self):
        expected = \
        "<1\t100\tgene\n"\
        "\t\t\tlocus_tag\tfoo_gene\n"\
        "<1\t100\tCDS\n"\
        "\t\t\tprotein_id\tm.foo\n"\
        "\t\t\tproduct\thypothetical protein\n"

        self.mrna1.__contains__ = no_start_stop

        tbl = self.gene1.to_tbl()
        self.assertEquals(tbl, expected)

    def test_gene_to_tbl_start_stop(self):
        expected = \
        "1\t100\tgene\n"\
        "\t\t\tlocus_tag\tfoo_gene\n"\
        "1\t100\tCDS\n"\
        "\t\t\tprotein_id\tm.foo\n"\
        "\t\t\tproduct\thypothetical protein\n"

        self.mrna1.__contains__ = start_stop

        tbl = self.gene1.to_tbl()
        self.assertEquals(tbl, expected)

    def test_gene_to_tbl_genename(self):
        expected = \
        "<1\t>100\tgene\n"\
        "\t\t\tgene\tf00x4\n"\
        "\t\t\tlocus_tag\tfoo_gene\n"\
        "<1\t>100\tCDS\n"\
        "\t\t\tprotein_id\tm.foo\n"\
        "\t\t\tproduct\thypothetical protein\n"

        self.gene1.attributes["Name"] = "f00x4"

        self.mrna1.__contains__ = no_start_no_stop

        tbl = self.gene1.to_tbl()
        self.assertEquals(tbl, expected)

    def test_gene_to_tbl_dbxref(self):
        expected = \
        "<1\t>100\tgene\n"\
        "\t\t\tlocus_tag\tfoo_gene\n"\
        "<1\t>100\tCDS\n"\
        "\t\t\tprotein_id\tm.foo\n"\
        "\t\t\tdb_xref\tPfam:foo\n"\
        "\t\t\tdb_xref\tPfam:dog\n"\
        "\t\t\tdb_xref\tPfam:baz\n"\
        "\t\t\tproduct\thypothetical protein\n"\

        self.gene1.get_mrna().attributes["Dbxref"] = "Pfam:foo,Pfam:dog,Pfam:baz"

        self.mrna1.__contains__ = no_start_no_stop

        tbl = self.gene1.to_tbl()
        self.assertEquals(tbl, expected)

    ### FIX PHASE TESTS ###

    def test_fix_phase(self):
        self.gene1.start = 2
        self.mrna1.start = 2
        self.mrna1.__contains__ = no_start_stop
        self.cds1.start = 2
        self.cds1.phase = 0
        self.assertEqual(self.cds1.phase, 0)
        self.gene1.fix_phase("ATGC")
        self.assertEqual(self.cds1.phase, 1)
        
    def test_fix_phase_to_two(self):
        self.gene1.start = 3
        self.mrna1.start = 3
        self.mrna1.__contains__ = no_start_stop
        self.cds1.start = 3
        self.cds1.phase = 0
        self.assertEqual(self.cds1.phase, 0)
        self.gene1.fix_phase("ATGC")
        self.assertEqual(self.cds1.phase, 2)
        
    def test_fix_phase_does_nothing_when_indices_too_large(self):
        self.gene1.start = 4
        self.mrna1.start = 4
        self.mrna1.__contains__ = start_stop
        self.cds1.start = 4
        self.cds1.phase = 0
        self.assertEqual(self.cds1.phase, 0)
        self.gene1.fix_phase("ATGC")
        self.assertEqual(self.cds1.phase, 0)

    def test_fix_phase_works_on_cds_only(self):
        self.gene1.start = 1
        self.mrna1.start = 1
        self.mrna1.__contains__ = no_start_stop
        self.cds1.start = 3
        self.cds1.phase = 0
        self.assertEqual(self.cds1.phase, 0)
        self.assertEqual(self.cds1.start, 3)
        self.gene1.fix_phase("ATGC")
        self.assertEqual(self.cds1.phase, 2)
        self.assertEqual(self.cds1.start, 1)

    def test_fix_phase_does_nothing_when_not_partial(self):
        self.gene1.start = 2
        self.mrna1.start = 2
        self.mrna1.__contains__ = start_stop
        self.cds1.start = 2
        self.cds1.phase = 0
        self.assertEqual(self.cds1.phase, 0)
        self.gene1.fix_phase("ATGC")
        self.assertEqual(self.cds1.phase, 0)

    def test_fix_phase_adjusts_end_on_3prime_partial(self):
        self.gene1.start = 2
        self.mrna1.start = 2
        self.mrna1.__contains__ = start_no_stop
        self.cds1.start = 2
        self.gene1.end = 2
        self.mrna1.end = 2
        self.cds1.end = 2
        self.assertEqual(self.cds1.end, 2)
        self.gene1.fix_phase("ATGC")
        self.assertEqual(self.cds1.end, 4)

    #### MAKE POSITIVE TESTS ####

    def test_make_positive(self):
        seq_len = 8

        gene = Gene(start=1, end=7, strand='-')

        mrna = Mock()
        mrna.type = 'mrna'
        mrna.make_positive = Mock()
        gene.add_child(mrna)

        gene.make_positive(seq_len)

        self.assertEqual(gene.start, 2)
        self.assertEqual(gene.end, 8)
        self.assertEqual(gene.strand, '+')
        mrna.make_positive.assertCalledWith(seq_len)

    #### MATCH CDS AND EXON END TESTS ####

    def test_match_cds_and_exon_end(self):
        gene = Gene()
        mrna = Mock()

        gene.children = {'mrna':[mrna]}

        gene.match_cds_and_exon_end()

        mrna.match_cds_and_exon_end.assertCalled()

    #### STARTS AND STOPS TESTS ####
    
    def test_create_starts_and_stops(self):
        gene = Gene()
        mrna = Mock()

        gene.children = {'mrna':[mrna]}

        gene.create_starts_and_stops('ATGC')

        mrna.create_starts_and_stops.assertCalledWith('ATGC')
Exemple #23
0
class TestGene(unittest.TestCase):
    def setUp(self):
        self.test_gene0 = Gene(seq_name="sctg_0080_0020",
                               source="maker",
                               indices=[3734, 7436],
                               strand='+',
                               identifier=1)
        self.test_gene1 = Gene(seq_name="sctg_0080_0020",
                               source="maker",
                               indices=[3734, 7436],
                               strand='+',
                               identifier=1)

        self.fake_mrna1 = Mock()
        self.fake_mrna1.identifier = "fake_mrna1"
        self.fake_mrna1.death_flagged = False

        self.fake_mrna2 = Mock()
        self.fake_mrna2.identifier = "fake_mrna2"
        self.fake_mrna2.death_flagged = False

        self.test_gene1.mrnas.append(self.fake_mrna1)
        self.test_gene1.mrnas.append(self.fake_mrna2)

    def test_constructor(self):
        self.assertEqual('Gene', self.test_gene0.__class__.__name__)

    def test_length(self):
        self.assertEqual(3703, self.test_gene0.length())

    def test_gagflagged(self):
        self.assertFalse(self.test_gene0.gagflagged())
        self.test_gene0.annotations = {"gag_flag": ["nice gene"]}
        self.assertTrue(self.test_gene0.gagflagged())

    def test_number_of_gagflags(self):
        self.fake_mrna1.number_of_gagflags.return_value = 2
        self.fake_mrna2.number_of_gagflags.return_value = 1
        self.test_gene1.annotations = {"gag_flag": ["nice gene"]}
        self.assertEquals(4, self.test_gene1.number_of_gagflags())

    def test_get_mrna_ids(self):
        expected = ["fake_mrna1", "fake_mrna2"]
        self.assertEquals(self.test_gene1.get_mrna_ids(), expected)

    def test_remove_mrna(self):
        self.assertEquals(self.test_gene1.mrnas,
                          [self.fake_mrna1, self.fake_mrna2])
        self.assertEquals(len(self.test_gene1.removed_mrnas), 0)
        self.test_gene1.remove_mrna('fake_mrna1')
        self.assertEquals(self.test_gene1.mrnas, [self.fake_mrna2])
        self.assertEquals(self.test_gene1.removed_mrnas, [self.fake_mrna1])

    def test_remove_mrnas_from_list(self):
        self.fake_mrna3 = Mock()
        self.fake_mrna3.identifier = "fake_mrna3"
        self.fake_mrna3.death_flagged = False
        self.test_gene1.mrnas.append(self.fake_mrna3)
        bad_mrnas = ["fake_mrna3", "fake_mrna1"]
        self.assertEquals(3, len(self.test_gene1.mrnas))
        self.assertEquals(0, len(self.test_gene1.removed_mrnas))
        removed_mrnas = self.test_gene1.remove_mrnas_from_list(bad_mrnas)
        self.assertEquals(2, len(removed_mrnas))
        self.assertEquals(1, len(self.test_gene1.mrnas))
        self.assertEquals(2, len(self.test_gene1.removed_mrnas))

    def test_remove_empty_mrnas(self):
        self.fake_mrna1.rna_type = "mRNA"
        self.fake_mrna1.cds = Mock()
        self.fake_mrna1.exon = None
        self.fake_mrna2.rna_type = "mRNA"
        self.fake_mrna2.cds = None
        self.fake_mrna2.exon = Mock()
        self.fake_mrna3 = Mock()
        self.fake_mrna3.rna_type = "mRNA"
        self.fake_mrna3.identifier = "fake_mrna3"
        self.fake_mrna3.death_flagged = False
        self.fake_mrna3.cds = Mock()
        self.fake_mrna3.exon = Mock()
        self.test_gene1.mrnas.append(self.fake_mrna3)
        self.assertEquals(3, len(self.test_gene1.mrnas))
        self.assertEquals(0, len(self.test_gene1.removed_mrnas))
        removed_mrnas = self.test_gene1.remove_empty_mrnas()
        self.assertEquals(2, len(removed_mrnas))
        self.assertEquals(1, len(self.test_gene1.mrnas))
        self.assertEquals(2, len(self.test_gene1.removed_mrnas))

    def test_get_longest_exon(self):
        self.fake_mrna1.get_longest_exon.return_value = 10
        self.fake_mrna2.get_longest_exon.return_value = 20
        self.assertEquals(20, self.test_gene1.get_longest_exon())

    def test_get_shortest_exon(self):
        self.fake_mrna1.get_shortest_exon.return_value = 5
        self.fake_mrna2.get_shortest_exon.return_value = 8
        self.assertEquals(5, self.test_gene1.get_shortest_exon())

    def test_get_total_exon_length(self):
        self.fake_mrna1.get_total_exon_length.return_value = 15
        self.fake_mrna2.get_total_exon_length.return_value = 25
        self.assertEquals(40, self.test_gene1.get_total_exon_length())

    def test_get_num_exons(self):
        self.fake_mrna1.get_num_exons.return_value = 5
        self.fake_mrna2.get_num_exons.return_value = 4
        self.assertEquals(9, self.test_gene1.get_num_exons())

    def test_get_longest_intron(self):
        self.fake_mrna1.get_longest_intron.return_value = 8
        self.fake_mrna2.get_longest_intron.return_value = 10
        self.assertEquals(10, self.test_gene1.get_longest_intron())

    def test_get_shortest_intron(self):
        self.fake_mrna1.get_shortest_intron.return_value = 5
        self.fake_mrna2.get_shortest_intron.return_value = 8
        self.assertEquals(5, self.test_gene1.get_shortest_intron())

    def test_get_total_intron_length(self):
        self.fake_mrna1.get_total_intron_length.return_value = 15
        self.fake_mrna2.get_total_intron_length.return_value = 25
        self.assertEquals(40, self.test_gene1.get_total_intron_length())

    def test_get_num_introns(self):
        self.fake_mrna1.get_num_introns.return_value = 3
        self.fake_mrna2.get_num_introns.return_value = 2
        self.assertEquals(5, self.test_gene1.get_num_introns())

    def test_get_partial_info(self):
        self.fake_mrna1.has_stop.return_value = True
        self.fake_mrna1.has_start.return_value = True
        self.fake_mrna2.has_stop.return_value = False
        self.fake_mrna2.has_start.return_value = True
        results = self.test_gene1.get_partial_info()
        self.assertEquals(1, results["complete"])

    def test_adjust_indices(self):
        self.test_gene1.adjust_indices(16)
        self.fake_mrna1.adjust_indices.assert_called_with(16, 1)
        self.assertEquals(3750, self.test_gene1.indices[0])
        # adjust them back
        self.test_gene1.adjust_indices(-16)
        self.fake_mrna1.adjust_indices.assert_called_with(-16, 1)
        self.assertEquals(3734, self.test_gene1.indices[0])

    def test_remove_mrnas_with_internal_stops(self):
        helper = Mock()
        helper.mrna_contains_internal_stop.return_value = True
        self.assertEquals(2, len(self.test_gene1.mrnas))
        self.test_gene1.remove_mrnas_with_internal_stops(helper)
        self.assertEquals(0, len(self.test_gene1.mrnas))

    def test_contains_mrna(self):
        self.fake_mrna1.identifier = "foo_mrna"
        self.fake_mrna2.identifier = "bar_mrna"
        self.assertTrue(self.test_gene1.contains_mrna("foo_mrna"))
        self.assertFalse(self.test_gene1.contains_mrna("zub_mrna"))

    def test_cds_to_gff(self):
        self.fake_mrna1.identifier = "foo_mrna"
        foo = self.test_gene1.cds_to_gff("foo_seq", "foo_mrna")
        self.fake_mrna1.cds_to_gff.assert_called_with("foo_seq", "maker")

    def test_cds_to_gff_no_such_mrna(self):
        self.fake_mrna1.identifier = "foo_mrna"
        foo = self.test_gene1.cds_to_gff("foo_seq", "bar_mrna")
        self.assertFalse(foo)

    def test_cds_to_tbl(self):
        self.fake_mrna1.identifier = "foo_mrna"
        foo = self.test_gene1.cds_to_tbl("foo_mrna")
        self.fake_mrna1.cds_to_tbl.assert_called_with()

    def test_to_mrna_fasta(self):
        helper = Mock()
        helper.mrna_to_fasta.return_value = "mrna_to_fasta\n"
        expected = "mrna_to_fasta\nmrna_to_fasta\n"
        self.assertEquals(expected, self.test_gene1.to_mrna_fasta(helper))

    def test_to_cds_fasta(self):
        helper = Mock()
        helper.mrna_to_cds_fasta.return_value = "mrna_to_CDS_fasta\n"
        expected = "mrna_to_CDS_fasta\nmrna_to_CDS_fasta\n"
        self.assertEquals(expected, self.test_gene1.to_cds_fasta(helper))

    def test_to_protein_fasta(self):
        helper = Mock()
        helper.mrna_to_protein_fasta.return_value = "mrna_to_protein_fasta\n"
        expected = "mrna_to_protein_fasta\nmrna_to_protein_fasta\n"
        self.assertEquals(expected, self.test_gene1.to_protein_fasta(helper))

    def test_to_gff(self):
        self.fake_mrna1.to_gff.return_value = "fake mrna1 to gff here:)\n"
        self.fake_mrna2.to_gff.return_value = "fake mrna2 to gff here:)\n"
        expected = "sctg_0080_0020\tmaker\tgene\t3734\t7436\t.\t+\t."
        expected += "\tID=1;foo=dog\n"
        expected += "fake mrna1 to gff here:)\n"
        expected += "fake mrna2 to gff here:)\n"
        self.test_gene1.add_annotation('foo', 'dog')
        self.assertEquals(expected, self.test_gene1.to_gff())

    def test_to_gff_with_name(self):
        self.fake_mrna1.to_gff.return_value = "fake mrna1 to gff here:)\n"
        self.fake_mrna2.to_gff.return_value = "fake mrna2 to gff here:)\n"
        expected = "sctg_0080_0020\tmaker\tgene\t3734\t7436\t.\t+\t."
        expected += "\tID=1;Name=foo_gene;foo=dog\n"
        expected += "fake mrna1 to gff here:)\n"
        expected += "fake mrna2 to gff here:)\n"
        self.test_gene1.add_annotation('foo', 'dog')
        self.test_gene1.name = "foo_gene"
        self.assertEquals(expected, self.test_gene1.to_gff())

    def test_str(self):
        expected = "Gene (ID=1, seq_name=sctg_0080_0020) containing 2 mrnas"
        self.assertEquals(expected, str(self.test_gene1))

    def test_create_starts_and_stops(self):
        mrna1 = Mock()
        mrna2 = Mock()
        self.test_gene0.mrnas = [mrna1, mrna2]
        seq_object = Mock()
        self.test_gene0.create_starts_and_stops(seq_object)
        mrna1.create_start_and_stop_if_necessary.assert_called_with(
            seq_object, '+')
        mrna2.create_start_and_stop_if_necessary.assert_called_with(
            seq_object, '+')

    def test_add_mrna_annotation(self):
        mrna = Mock()
        mrna.identifier = "foo_mrna"
        self.test_gene0.mrnas = [mrna]
        self.test_gene0.add_mrna_annotation("foo_mrna", "gag_flag",
                                            "awesome_anno")
        mrna.add_annotation.assert_called_with("gag_flag", "awesome_anno")

    def test_to_tbl_positive(self):
        gene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "1\t50\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_to_tbl_positive_start_nostop(self):
        gene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        mrna2.has_start.return_value = True
        mrna2.has_stop.return_value = False
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "1\t>50\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_to_tbl_positive_nostart_stop(self):
        gene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        mrna2.has_start.return_value = False
        mrna2.has_stop.return_value = True
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "<1\t50\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_to_tbl_positive_nostart_nostop(self):
        gene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        mrna2.has_start.return_value = False
        mrna2.has_stop.return_value = False
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "<1\t>50\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_to_tbl_positive_with_name(self):
        gene = Gene(seq_name="seq1",
                    source="maker",
                    indices=[1, 50],
                    strand="+",
                    identifier="foo_gene_1",
                    name="wtfg")
        self.assertFalse(gene.annotations)
        gene.add_annotation('foo', 'dog')
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "1\t50\tgene\n\t\t\tgene\twtfg\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_to_tbl_negative(self):
        gene = Gene("seq1", "maker", [1, 50], "-", "foo_gene_1")
        mrna1 = Mock()
        mrna1.to_tbl.return_value = "mrna1_to_tbl...\n"
        mrna2 = Mock()
        mrna2.to_tbl.return_value = "mrna2_to_tbl...\n"
        gene.mrnas.append(mrna1)
        gene.mrnas.append(mrna2)
        expected = "50\t1\tgene\n\t\t\tlocus_tag\tfoo_gene_1\nmrna1_to_tbl...\nmrna2_to_tbl...\n"
        self.assertEquals(gene.to_tbl(), expected)

    def test_gene_initialized_without_annotations(self):
        newgene = Gene(seq_name="seq1",
                       source="maker",
                       indices=[1, 50],
                       strand="+",
                       identifier="foo_gene_1")
        self.assertFalse(newgene.annotations)
        self.assertEquals(0, len(newgene.annotations.keys()))

    def test_gene_initialized_with_annotations(self):
        newgene = Gene(seq_name="seq1", source="maker", indices=[1, 50], strand="+", identifier="foo_gene_1",\
                annotations={"bar": ["cat"]})
        self.assertTrue(newgene.annotations)
        self.assertEquals(1, len(newgene.annotations.keys()))
 def test_from_gff_feature_success(self):
     gff_gene = Mock()
     gff_gene.type = "gene"
     
     tran_gene = Gene.from_gff_feature(gff_gene)
     self.assertTrue(tran_gene)
 def test_from_gff_features_fails(self):
     gff_gene = Mock()
     gff_gene.type = "asdf"
     
     tran_gene = Gene.from_gff_feature(gff_gene)
     self.assertFalse(tran_gene)