Exemplo n.º 1
0
 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)
Exemplo n.º 2
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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)
Exemplo n.º 3
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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)
Exemplo n.º 4
0
 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)
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')