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 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 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")