def test_mrna_contains_internal_stop(self):
helper = SeqHelper("gattacaTAGgattaca") # TAG = stop codon
mrna = Mock()
mrna.strand = '+'
mrna.cds = Mock()
mrna.cds.indices = [[2, 4], [8, 14]]
# verify that the internal stop is in the sequence ...
self.assertEquals("attTAGgatt", helper.get_sequence_from_indices('+', mrna.cds.indices))
# make sure the method catches it
self.assertTrue(helper.mrna_contains_internal_stop(mrna))
def test_mrna_contains_internal_stop(self):
helper = SeqHelper("gattacaTAGgattaca") # TAG = stop codon
mrna = Mock()
mrna.strand = '+'
mrna.cds = Mock()
mrna.cds.indices = [[2, 4], [8, 14]]
# verify that the internal stop is in the sequence ...
self.assertEquals(
"attTAGgatt",
helper.get_sequence_from_indices('+', mrna.cds.indices))
# make sure the method catches it
self.assertTrue(helper.mrna_contains_internal_stop(mrna))
class TestSeqHelper(unittest.TestCase):
def setUp(self):
self.helper = SeqHelper("nnnGATTACAnnnnnNNNNNgattacaNNN")
def test_initialize(self):
self.assertEquals("nnnGATTACAnnnnnNNNNNgattacaNNN",
self.helper.full_sequence)
def test_mrna_to_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '+'
expected = ">foo_mrna\nGATTACAgattaca\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_fasta_reverse_strand(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_cds_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna CDS\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_cds_fasta(mrna))
def test_mrna_to_protein_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.cds.get_phase.return_value = 0
mrna.strand = '+'
expected = ">foo_mrna protein\nDYRL\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_phase1(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.cds.get_phase.return_value = 1
mrna.strand = '+'
expected = ">foo_mrna protein\nITDY\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.cds.get_phase.return_value = 0
mrna.strand = '-'
expected = ">foo_mrna protein\nCNL*\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_reverse_phase1(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.cds.get_phase.return_value = 1
mrna.strand = '-'
expected = ">foo_mrna protein\nVICN\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_get_sequence_from_indices(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '+'
expected = 'gattacaGATTACA'
calculated = self.helper.get_sequence_from_indices(
mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_get_sequence_from_indices_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '-'
expected = 'TGTAATCtgtaatc'
calculated = self.helper.get_sequence_from_indices(
mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_mrna_contains_internal_stop(self):
helper = SeqHelper("gattacaTAGgattaca") # TAG = stop codon
mrna = Mock()
mrna.strand = '+'
mrna.cds = Mock()
mrna.cds.indices = [[2, 4], [8, 14]]
# verify that the internal stop is in the sequence ...
self.assertEquals(
"attTAGgatt",
helper.get_sequence_from_indices('+', mrna.cds.indices))
# make sure the method catches it
self.assertTrue(helper.mrna_contains_internal_stop(mrna))
class TestSeqHelper(unittest.TestCase):
def setUp(self):
self.helper = SeqHelper("nnnGATTACAnnnnnNNNNNgattacaNNN")
def test_initialize(self):
self.assertEquals("nnnGATTACAnnnnnNNNNNgattacaNNN", self.helper.full_sequence)
def test_mrna_to_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '+'
expected = ">foo_mrna\nGATTACAgattaca\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_fasta_reverse_strand(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.exon = Mock()
mrna.exon.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_fasta(mrna))
def test_mrna_to_cds_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.strand = '-'
expected = ">foo_mrna CDS\ntgtaatcTGTAATC\n"
self.assertEquals(expected, self.helper.mrna_to_cds_fasta(mrna))
def test_mrna_to_protein_fasta(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.cds.get_phase.return_value = 0
mrna.strand = '+'
expected = ">foo_mrna protein\nDYRL\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_phase1(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[4, 10], [21, 27]]
mrna.cds.get_phase.return_value = 1
mrna.strand = '+'
expected = ">foo_mrna protein\nITDY\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.cds.get_phase.return_value = 0
mrna.strand = '-'
expected = ">foo_mrna protein\nCNL*\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_mrna_to_protein_fasta_reverse_phase1(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.cds.get_phase.return_value = 1
mrna.strand = '-'
expected = ">foo_mrna protein\nVICN\n"
self.assertEquals(expected, self.helper.mrna_to_protein_fasta(mrna))
def test_get_sequence_from_indices(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '+'
expected = 'gattacaGATTACA'
calculated = self.helper.get_sequence_from_indices(mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_get_sequence_from_indices_reverse(self):
mrna = Mock()
mrna.identifier = "foo_mrna"
mrna.cds = Mock()
mrna.cds.indices = [[21, 27], [4, 10]]
mrna.strand = '-'
expected = 'TGTAATCtgtaatc'
calculated = self.helper.get_sequence_from_indices(mrna.strand, mrna.cds.indices)
self.assertEquals(expected, calculated)
def test_mrna_contains_internal_stop(self):
helper = SeqHelper("gattacaTAGgattaca") # TAG = stop codon
mrna = Mock()
mrna.strand = '+'
mrna.cds = Mock()
mrna.cds.indices = [[2, 4], [8, 14]]
# verify that the internal stop is in the sequence ...
self.assertEquals("attTAGgatt", helper.get_sequence_from_indices('+', mrna.cds.indices))
# make sure the method catches it
self.assertTrue(helper.mrna_contains_internal_stop(mrna))