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))
def remove_mrnas_with_internal_stops(self):
helper = SeqHelper(self.bases)
for gene in self.genes:
gene.remove_mrnas_with_internal_stops(helper)
if not gene.mrnas:
gene.death_flagged = True
self.genes = [g for g in self.genes if not g.death_flagged]
def to_protein_fasta(self):
helper = SeqHelper(self.bases)
result = ""
for gene in self.genes:
result += gene.to_protein_fasta(helper)
return result
def setUp(self):
self.helper = SeqHelper("nnnGATTACAnnnnnNNNNNgattacaNNN")
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_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 setUp(self):
self.helper = SeqHelper("nnnGATTACAnnnnnNNNNNgattacaNNN")
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_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))