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_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_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_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')