def setUp(self):
self.test_mrna0 = MRNA(identifier="bdor_foo", indices=[3734, 7436], strand="-", parent_id=1)
self.test_mrna1 = MRNA(identifier=2, indices=[3734, 7436], parent_id=1)
self.fake_exon = Mock()
self.fake_cds = Mock()
self.fake_start_codon = Mock()
self.test_mrna1.exon = self.fake_exon
self.test_mrna1.cds = self.fake_cds
self.test_mrna1.add_other_feature(self.fake_start_codon)
def setUp(self):
self.test_mrna0 = MRNA(identifier='bdor_foo',
indices=[3734, 7436],
strand='-',
parent_id=1)
self.test_mrna1 = MRNA(identifier=2, indices=[3734, 7436], parent_id=1)
self.fake_exon = Mock()
self.fake_cds = Mock()
self.fake_start_codon = Mock()
self.test_mrna1.exon = self.fake_exon
self.test_mrna1.cds = self.fake_cds
self.test_mrna1.add_other_feature(self.fake_start_codon)
def process_mrna_line(self, line):
"""Extracts arguments from a line and instantiates an MRNA object."""
kwargs = self.extract_mrna_args(line)
if not kwargs:
return
mrna_id = kwargs['identifier']
self.mrnas[mrna_id] = MRNA(**kwargs)
class TestMRNA(unittest.TestCase):
def setUp(self):
self.test_mrna0 = MRNA(identifier="bdor_foo", indices=[3734, 7436], strand="-", parent_id=1)
self.test_mrna1 = MRNA(identifier=2, indices=[3734, 7436], parent_id=1)
self.fake_exon = Mock()
self.fake_cds = Mock()
self.fake_start_codon = Mock()
self.test_mrna1.exon = self.fake_exon
self.test_mrna1.cds = self.fake_cds
self.test_mrna1.add_other_feature(self.fake_start_codon)
def test_constructor(self):
self.assertEquals("MRNA", self.test_mrna0.__class__.__name__)
self.assertEquals("-", self.test_mrna0.strand)
def test_constructor_takes_annotations(self):
self.assertTrue(MRNA(identifier="foo", indices=[1, 10], parent_id="bar", annotations=[["Dbxref", "pfam:foo"]]))
def test_length(self):
self.assertEqual(3703, self.test_mrna0.length())
def test_number_of_gagflags(self):
self.fake_cds.gagflagged.return_value = False
self.fake_exon.gagflagged.return_value = True
self.assertEquals(1, self.test_mrna1.number_of_gagflags())
def test_add_other_feature(self):
self.assertEquals(0, len(self.test_mrna0.other_features))
self.test_mrna0.add_other_feature(self.fake_start_codon)
self.assertEquals(1, len(self.test_mrna0.other_features))
def test_add_start_codon(self):
self.assertFalse(self.test_mrna0.has_start())
self.test_mrna0.add_start_codon([4000, 4002])
self.assertTrue(self.test_mrna0.has_start())
self.assertEquals([[4000, 4002]], self.test_mrna0.other_features[0].indices)
def test_add_stop_codon(self):
self.assertFalse(self.test_mrna0.has_stop())
self.test_mrna0.add_stop_codon([7000, 7002])
self.assertTrue(self.test_mrna0.has_stop())
def test_adjust_indices(self):
self.test_mrna1.adjust_indices(32)
self.assertEqual(7468, self.test_mrna1.indices[1])
self.fake_cds.adjust_indices.assert_called_with(32, 1)
self.fake_exon.adjust_indices.assert_called_with(32, 1)
self.fake_start_codon.adjust_indices.assert_called_with(32, 1)
# adjust 'em back
self.test_mrna1.adjust_indices(-32)
self.assertEqual(3734, self.test_mrna1.indices[0])
self.fake_cds.adjust_indices.assert_called_with(-32, 1)
self.fake_exon.adjust_indices.assert_called_with(-32, 1)
self.fake_start_codon.adjust_indices.assert_called_with(-32, 1)
def test_adjust_indices_after_start_index(self):
self.test_mrna1.adjust_indices(32, 8000)
self.assertEqual(3734, self.test_mrna1.indices[0])
self.test_mrna1.adjust_indices(32, 3000)
self.assertEqual(3766, self.test_mrna1.indices[0])
def test_has_start(self):
self.fake_start_codon.feature_type = "start_codon"
self.assertTrue(self.test_mrna1.has_start())
def test_has_stop(self):
self.assertFalse(self.test_mrna1.has_stop())
def test_str(self):
expected = "mRNA (ID=2) containing Exon, CDS and 1 other features"
self.assertEquals(expected, str(self.test_mrna1))
def test_cds_to_gff(self):
foo = self.test_mrna1.cds_to_gff("foo_seq", "maker")
self.fake_cds.to_gff.assert_called_with("foo_seq", "maker")
def test_cds_to_tbl(self):
foo = self.test_mrna1.cds_to_tbl()
self.fake_cds.to_tbl.assert_called_with(False, False)
def test_to_gff(self):
self.fake_exon.to_gff.return_value = "...exon to gff\n"
self.fake_cds.to_gff.return_value = "...cds to gff\n"
self.fake_start_codon.to_gff.return_value = "...start codon to gff\n"
expected = "sctg_0080_0020\tmaker\tmRNA\t"
expected += "3734\t7436\t.\t+\t.\t"
expected += "ID=2;Parent=1;foo=dog\n"
expected += "...exon to gff\n...cds to gff\n"
expected += "...start codon to gff\n"
self.test_mrna1.add_annotation("foo", "dog")
actual = self.test_mrna1.to_gff(seq_name="sctg_0080_0020", source="maker")
self.assertEquals(expected, actual)
self.fake_exon.to_gff.assert_called_with("sctg_0080_0020", "maker")
self.fake_cds.to_gff.assert_called_with("sctg_0080_0020", "maker")
self.fake_start_codon.to_gff.assert_called_with("sctg_0080_0020", "maker")
def test_indices_intersect_mrna_false(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id="foo")
self.assertFalse(mrna.indices_intersect_mrna([5, 9]))
self.assertFalse(mrna.indices_intersect_mrna([21, 25]))
def test_indices_intersect_mrna_true(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id="foo")
self.assertTrue(mrna.indices_intersect_mrna([5, 10]))
self.assertTrue(mrna.indices_intersect_mrna([20, 25]))
self.assertTrue(mrna.indices_intersect_mrna([9, 21]))
def test_create_start_and_stop_if_necessary(self):
seq_object = Mock()
cds = Mock()
cds.extract_sequence.return_value = "atgtag" # startstop
cds.get_start_indices.return_value = 20
cds.get_stop_indices.return_value = 40
self.test_mrna0.cds = cds
seq_name = "seq_foo"
strand = "+"
self.assertFalse(self.test_mrna0.other_features)
self.test_mrna0.create_start_and_stop_if_necessary(seq_object, strand)
self.assertTrue(self.test_mrna0.other_features)
self.assertEquals(2, len(self.test_mrna0.other_features))
def test_create_start_and_stop_when_no_start_or_stop(self):
seq_object = Mock()
cds = Mock()
cds.extract_sequence.return_value = "tagatg" # no start or stop
cds.get_start_indices.return_value = 20
cds.get_stop_indices.return_value = 40
self.test_mrna0.cds = cds
seq_name = "seq_foo"
strand = "+"
self.assertFalse(self.test_mrna0.other_features)
self.test_mrna0.create_start_and_stop_if_necessary(seq_object, strand)
self.assertFalse(self.test_mrna0.other_features)
def test_to_tbl(self):
self.fake_exon.to_tbl.return_value = "fake_exon_to_tbl...\n"
self.fake_cds.to_tbl.return_value = "fake_cds_to_tbl...\n"
expected = "fake_exon_to_tbl...\n"
expected += "\t\t\tproduct\thypothetical protein\n"
expected += "fake_cds_to_tbl...\n"
expected += "\t\t\tproduct\thypothetical protein\n"
self.assertEquals(self.test_mrna1.to_tbl(), expected)
def test_indices_intersect_cds_false(self):
self.fake_cds.indices_intersect_cds.return_value = False
self.assertFalse(self.test_mrna1.indices_intersect_cds([1, 9]))
def test_indices_intersect_cds_true(self):
self.fake_cds.indices_intersect_cds.return_value = True
self.assertTrue(self.test_mrna1.indices_intersect_cds([1, 9]))
## STATS STUFF ##
def set_fake_exon_indices(self):
self.fake_exon.indices = [[1, 5], [11, 16], [21, 27]]
def test_get_longest_exon(self):
self.set_fake_exon_indices()
self.assertEquals(7, self.test_mrna1.get_longest_exon())
def test_get_shortest_exon(self):
self.set_fake_exon_indices()
self.assertEquals(5, self.test_mrna1.get_shortest_exon())
def test_get_total_exon_length(self):
self.set_fake_exon_indices()
self.assertEquals(18, self.test_mrna1.get_total_exon_length())
def test_get_num_exons(self):
self.set_fake_exon_indices()
self.assertEquals(3, self.test_mrna1.get_num_exons())
def test_get_num_exons_if_no_exons(self):
# test_mrna0 has no exon
self.assertEquals(0, self.test_mrna0.get_num_exons())
def test_nothing_fails_if_no_exons(self):
self.assertFalse(self.test_mrna0.get_longest_exon())
self.assertFalse(self.test_mrna0.get_shortest_exon())
self.assertFalse(self.test_mrna0.get_total_exon_length())
self.assertFalse(self.test_mrna0.get_longest_intron())
self.assertFalse(self.test_mrna0.get_shortest_intron())
self.assertFalse(self.test_mrna0.get_total_intron_length())
def test_get_longest_intron(self):
self.set_fake_exon_indices()
self.assertEquals(7, self.test_mrna1.get_longest_intron())
def test_get_shortest_intron(self):
self.set_fake_exon_indices()
self.assertEquals(6, self.test_mrna1.get_shortest_intron())
def test_get_total_intron_length(self):
self.set_fake_exon_indices()
self.assertEquals(13, self.test_mrna1.get_total_intron_length())
def test_get_num_introns(self):
self.set_fake_exon_indices()
self.assertEquals(2, self.test_mrna1.get_num_introns())
def test_indices_intersect_mrna_true(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id="foo")
self.assertTrue(mrna.indices_intersect_mrna([5, 10]))
self.assertTrue(mrna.indices_intersect_mrna([20, 25]))
self.assertTrue(mrna.indices_intersect_mrna([9, 21]))
def test_indices_intersect_mrna_false(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id="foo")
self.assertFalse(mrna.indices_intersect_mrna([5, 9]))
self.assertFalse(mrna.indices_intersect_mrna([21, 25]))
class TestMRNA(unittest.TestCase):
def setUp(self):
self.test_mrna0 = MRNA(identifier='bdor_foo',
indices=[3734, 7436],
strand='-',
parent_id=1)
self.test_mrna1 = MRNA(identifier=2, indices=[3734, 7436], parent_id=1)
self.fake_exon = Mock()
self.fake_cds = Mock()
self.fake_start_codon = Mock()
self.test_mrna1.exon = self.fake_exon
self.test_mrna1.cds = self.fake_cds
self.test_mrna1.add_other_feature(self.fake_start_codon)
def test_constructor(self):
self.assertEquals('MRNA', self.test_mrna0.__class__.__name__)
self.assertEquals('-', self.test_mrna0.strand)
def test_constructor_takes_annotations(self):
self.assertTrue(
MRNA(identifier="foo",
indices=[1, 10],
parent_id="bar",
annotations=[["Dbxref", "pfam:foo"]]))
def test_length(self):
self.assertEqual(3703, self.test_mrna0.length())
def test_number_of_gagflags(self):
self.fake_cds.gagflagged.return_value = False
self.fake_exon.gagflagged.return_value = True
self.assertEquals(1, self.test_mrna1.number_of_gagflags())
def test_add_other_feature(self):
self.assertEquals(0, len(self.test_mrna0.other_features))
self.test_mrna0.add_other_feature(self.fake_start_codon)
self.assertEquals(1, len(self.test_mrna0.other_features))
def test_add_start_codon(self):
self.assertFalse(self.test_mrna0.has_start())
self.test_mrna0.add_start_codon([4000, 4002])
self.assertTrue(self.test_mrna0.has_start())
self.assertEquals([[4000, 4002]],
self.test_mrna0.other_features[0].indices)
def test_add_stop_codon(self):
self.assertFalse(self.test_mrna0.has_stop())
self.test_mrna0.add_stop_codon([7000, 7002])
self.assertTrue(self.test_mrna0.has_stop())
def test_adjust_indices(self):
self.test_mrna1.adjust_indices(32)
self.assertEqual(7468, self.test_mrna1.indices[1])
self.fake_cds.adjust_indices.assert_called_with(32, 1)
self.fake_exon.adjust_indices.assert_called_with(32, 1)
self.fake_start_codon.adjust_indices.assert_called_with(32, 1)
# adjust 'em back
self.test_mrna1.adjust_indices(-32)
self.assertEqual(3734, self.test_mrna1.indices[0])
self.fake_cds.adjust_indices.assert_called_with(-32, 1)
self.fake_exon.adjust_indices.assert_called_with(-32, 1)
self.fake_start_codon.adjust_indices.assert_called_with(-32, 1)
def test_adjust_indices_after_start_index(self):
self.test_mrna1.adjust_indices(32, 8000)
self.assertEqual(3734, self.test_mrna1.indices[0])
self.test_mrna1.adjust_indices(32, 3000)
self.assertEqual(3766, self.test_mrna1.indices[0])
def test_has_start(self):
self.fake_start_codon.feature_type = 'start_codon'
self.assertTrue(self.test_mrna1.has_start())
def test_has_stop(self):
self.assertFalse(self.test_mrna1.has_stop())
def test_str(self):
expected = "mRNA (ID=2) containing Exon, CDS and 1 other features"
self.assertEquals(expected, str(self.test_mrna1))
def test_cds_to_gff(self):
foo = self.test_mrna1.cds_to_gff("foo_seq", "maker")
self.fake_cds.to_gff.assert_called_with("foo_seq", "maker")
def test_cds_to_tbl(self):
foo = self.test_mrna1.cds_to_tbl()
self.fake_cds.to_tbl.assert_called_with(False, False)
def test_to_gff(self):
self.fake_exon.to_gff.return_value = "...exon to gff\n"
self.fake_cds.to_gff.return_value = "...cds to gff\n"
self.fake_start_codon.to_gff.return_value = "...start codon to gff\n"
expected = "sctg_0080_0020\tmaker\tmRNA\t"
expected += "3734\t7436\t.\t+\t.\t"
expected += "ID=2;Parent=1;foo=dog\n"
expected += "...exon to gff\n...cds to gff\n"
expected += "...start codon to gff\n"
self.test_mrna1.add_annotation('foo', 'dog')
actual = self.test_mrna1.to_gff(seq_name="sctg_0080_0020",
source="maker")
self.assertEquals(expected, actual)
self.fake_exon.to_gff.assert_called_with("sctg_0080_0020", "maker")
self.fake_cds.to_gff.assert_called_with("sctg_0080_0020", "maker")
self.fake_start_codon.to_gff.assert_called_with(
"sctg_0080_0020", "maker")
def test_indices_intersect_mrna_false(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id='foo')
self.assertFalse(mrna.indices_intersect_mrna([5, 9]))
self.assertFalse(mrna.indices_intersect_mrna([21, 25]))
def test_indices_intersect_mrna_true(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id='foo')
self.assertTrue(mrna.indices_intersect_mrna([5, 10]))
self.assertTrue(mrna.indices_intersect_mrna([20, 25]))
self.assertTrue(mrna.indices_intersect_mrna([9, 21]))
def test_create_start_and_stop_if_necessary(self):
seq_object = Mock()
cds = Mock()
cds.extract_sequence.return_value = 'atgtag' # startstop
cds.get_start_indices.return_value = 20
cds.get_stop_indices.return_value = 40
self.test_mrna0.cds = cds
seq_name = 'seq_foo'
strand = '+'
self.assertFalse(self.test_mrna0.other_features)
self.test_mrna0.create_start_and_stop_if_necessary(seq_object, strand)
self.assertTrue(self.test_mrna0.other_features)
self.assertEquals(2, len(self.test_mrna0.other_features))
def test_create_start_and_stop_when_no_start_or_stop(self):
seq_object = Mock()
cds = Mock()
cds.extract_sequence.return_value = 'tagatg' # no start or stop
cds.get_start_indices.return_value = 20
cds.get_stop_indices.return_value = 40
self.test_mrna0.cds = cds
seq_name = 'seq_foo'
strand = '+'
self.assertFalse(self.test_mrna0.other_features)
self.test_mrna0.create_start_and_stop_if_necessary(seq_object, strand)
self.assertFalse(self.test_mrna0.other_features)
def test_to_tbl(self):
self.fake_exon.to_tbl.return_value = "fake_exon_to_tbl...\n"
self.fake_cds.to_tbl.return_value = "fake_cds_to_tbl...\n"
expected = "fake_exon_to_tbl...\n"
expected += "\t\t\tproduct\thypothetical protein\n"
expected += "fake_cds_to_tbl...\n"
expected += "\t\t\tproduct\thypothetical protein\n"
self.assertEquals(self.test_mrna1.to_tbl(), expected)
def test_indices_intersect_cds_false(self):
self.fake_cds.indices_intersect_cds.return_value = False
self.assertFalse(self.test_mrna1.indices_intersect_cds([1, 9]))
def test_indices_intersect_cds_true(self):
self.fake_cds.indices_intersect_cds.return_value = True
self.assertTrue(self.test_mrna1.indices_intersect_cds([1, 9]))
## STATS STUFF ##
def set_fake_exon_indices(self):
self.fake_exon.indices = [[1, 5], [11, 16], [21, 27]]
def test_get_longest_exon(self):
self.set_fake_exon_indices()
self.assertEquals(7, self.test_mrna1.get_longest_exon())
def test_get_shortest_exon(self):
self.set_fake_exon_indices()
self.assertEquals(5, self.test_mrna1.get_shortest_exon())
def test_get_total_exon_length(self):
self.set_fake_exon_indices()
self.assertEquals(18, self.test_mrna1.get_total_exon_length())
def test_get_num_exons(self):
self.set_fake_exon_indices()
self.assertEquals(3, self.test_mrna1.get_num_exons())
def test_get_num_exons_if_no_exons(self):
# test_mrna0 has no exon
self.assertEquals(0, self.test_mrna0.get_num_exons())
def test_nothing_fails_if_no_exons(self):
self.assertFalse(self.test_mrna0.get_longest_exon())
self.assertFalse(self.test_mrna0.get_shortest_exon())
self.assertFalse(self.test_mrna0.get_total_exon_length())
self.assertFalse(self.test_mrna0.get_longest_intron())
self.assertFalse(self.test_mrna0.get_shortest_intron())
self.assertFalse(self.test_mrna0.get_total_intron_length())
def test_get_longest_intron(self):
self.set_fake_exon_indices()
self.assertEquals(7, self.test_mrna1.get_longest_intron())
def test_get_shortest_intron(self):
self.set_fake_exon_indices()
self.assertEquals(6, self.test_mrna1.get_shortest_intron())
def test_get_total_intron_length(self):
self.set_fake_exon_indices()
self.assertEquals(13, self.test_mrna1.get_total_intron_length())
def test_get_num_introns(self):
self.set_fake_exon_indices()
self.assertEquals(2, self.test_mrna1.get_num_introns())
def test_constructor_takes_annotations(self):
self.assertTrue(
MRNA(identifier="foo",
indices=[1, 10],
parent_id="bar",
annotations=[["Dbxref", "pfam:foo"]]))
def test_indices_intersect_mrna_true(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id='foo')
self.assertTrue(mrna.indices_intersect_mrna([5, 10]))
self.assertTrue(mrna.indices_intersect_mrna([20, 25]))
self.assertTrue(mrna.indices_intersect_mrna([9, 21]))
def test_indices_intersect_mrna_false(self):
mrna = MRNA(identifier=1, indices=[10, 20], parent_id='foo')
self.assertFalse(mrna.indices_intersect_mrna([5, 9]))
self.assertFalse(mrna.indices_intersect_mrna([21, 25]))
