def test_termination_condition(self):
testMRNA1 = MRNA.MRNA(index=5,
length=300,
geneID=None,
ribosomes={
99: None,
300: None
})
self.assertTrue(expr=testMRNA1.termination_condition())
testMRNA2 = MRNA.MRNA(index=6,
length=330,
geneID=None,
ribosomes={
99: None,
300: None
})
self.assertFalse(expr=testMRNA2.termination_condition())
def test_attach_ribosome_at_start(self):
testMRNA = MRNA.MRNA(index=0,
length=parameters.mRNA_av_length,
geneID=None,
ribosomes={})
testMRNA.attach_ribosome_at_start()
self.assertEqual(testMRNA.ribosomes, {0: None},
msg="test_attach_ribosome_at_start...")
def test_first_position_occupied(self):
testMRNA = MRNA.MRNA(index=2,
length=300,
geneID=None,
ribosomes={3: None})
self.assertTrue(expr=testMRNA.first_position_occupied())
testMRNA.detach_ribosome(pos=3)
self.assertFalse(expr=testMRNA.first_position_occupied())
def test_detach_ribosome(self):
testMRNA = MRNA.MRNA(index=1,
length=parameters.mRNA_av_length,
geneID=None,
ribosomes={})
testMRNA.attach_ribosome_at_start()
testMRNA.detach_ribosome(pos=0)
self.assertEqual(testMRNA.ribosomes, {})
def test_prev_range_free(self):
testMRNA = MRNA.MRNA(index=7,
length=600,
geneID=None,
ribosomes={
100: None,
300: None
})
self.assertTrue(expr=testMRNA.prev_range_free(pos=300, by=20))
self.assertFalse(expr=testMRNA.prev_range_free(pos=300, by=220))
def test_next_range_free(self):
testMRNA = MRNA.MRNA(index=3,
length=600,
geneID=None,
ribosomes={
99: None,
300: None
})
self.assertTrue(expr=testMRNA.next_range_free(pos=12, by=24))
self.assertFalse(expr=testMRNA.next_range_free(pos=90, by=300))
def test_find_max_free_range(self):
testMRNA = MRNA.MRNA(index=4,
length=600,
geneID=None,
ribosomes={
99: None,
300: None
})
self.assertEqual(first=testMRNA.find_max_free_range(pos=420),
second=180)
self.assertEqual(first=testMRNA.find_max_free_range(pos=297), second=3)
def test_translocate_ribosome(self):
testMRNA = MRNA.MRNA(index=7,
length=600,
geneID=None,
ribosomes={
100: None,
300: None
})
testMRNA.translocate_ribosome(pos=100, by=6)
self.assertEqual(first=testMRNA.ribosomes,
second={
106: None,
300: None
})
def test_elongate_one_step(self):
trsl = TRSL.TRSL(nribo=2,
proteome=col.Counter({}),
types_tRNA=2,
n_mRNA=2,
detail=False)
# create mRNAs with unoccupied ribosomes
trsl.mRNAs = [
MRNA.MRNA(index=gene, length=66, ribosomes={3: None})
for gene in [0, 1]
]
# now insert tRNA into one of the mRNAs
_ = trsl.insert_tRNA(mRNA=trsl.mRNAs[0], pos=3, tRNA_type=1)
success1 = trsl.elongate_one_step(trsl.mRNAs[0], current_pos=3)
self.assertTrue(success1)
trsl.mRNAs = [
MRNA.MRNA(index=gene, length=12, ribosomes={3: None})
for gene in [0, 1]
]
# now insert tRNA into one of the mRNAs
_ = trsl.insert_tRNA(mRNA=trsl.mRNAs[0], pos=3, tRNA_type=1)
success2 = trsl.elongate_one_step(trsl.mRNAs[0], current_pos=3)
# False because mRNA is too short
self.assertFalse(success2)
def test_insert_tRNA(self):
trsl = TRSL.TRSL(nribo=2,
proteome=col.Counter({}),
types_tRNA=2,
n_mRNA=2,
detail=False)
# create mRNAs with unoccupied ribosomes
trsl.mRNAs = [
MRNA.MRNA(index=gene, length=9, ribosomes={3: None})
for gene in [0, 1]
]
# now insert tRNA into one of the mRNAs
success = trsl.insert_tRNA(mRNA=trsl.mRNAs[0], pos=3, tRNA_type=1)
# did it work overall
self.assertTrue(success)
# is the tRNA in the right place
self.assertEqual(trsl.mRNAs[0].ribosomes, {3: 1})