def testTotalCreation(self):
"""Enzyme is created with all possible commands"""
commands = [
'cut', 'dlt', 'swi', 'mvr', 'mvl', 'cop', 'off', 'ina', 'inc',
'ing', 'itt', 'rpy', 'rpu', 'lpy', 'lpu'
]
e = enzyme.Enzyme(commands, 'A')
self.assertEquals(e.commands, commands)
def testASimpleTranslation(self):
string = 'TAGATCCAGTCCATCGA'
s = strand.Strand(string)
e = enzyme.Enzyme(['rpu', 'inc'], 'G')
locus = 1
e.attach(s, locus)
self.assertEquals(e.locus, 8)
result = next(e.translate())
self.assertEquals(result, [list('TAGATCCAGTCCACTCGA')])
def testASimplestTranslation(self):
"""Strand is translated by enzyme to produce set of new strands"""
string = 'ACA'
s = strand.Strand(string)
e = enzyme.Enzyme(['dlt', 'mvr', 'itt'], 'A')
locus = 0
e.attach(s, locus)
result = next(e.translate())
self.assertEquals(result, [list('CAT')])
def testIncorrectRun(self):
"""Invalid attachment should raise exception"""
string = 'TAGATCCATCCATCA' # Only one 'G'
s = strand.Strand(string)
binding = 'G'
e = enzyme.Enzyme(['itt'], binding)
d = utility.string_chars_indices(string)
locus = 1 # Sets index of unit to bind to; second 'G' assumed
self.assertRaises(enzyme.InvalidLocus, e.attach, s, locus)
def testASimpleCopyingTranslation(self):
string = 'ACGT'
s = strand.Strand(string)
e = enzyme.Enzyme([
'cop', 'rpy', 'rpy', 'mvl', 'mvl', 'mvl', 'off', 'ina'],
'A')
locus = 0
e.attach(s, locus)
result = next(e.translate())
self.assertEquals(result, [list('AACGT'), list('T GCA')])
def testCorrectRun(self):
"""Successfull attachment should set strand and locus"""
string = 'TAGATCCAGTCCATGCA'
s = strand.Strand(string)
binding = 'G'
e = enzyme.Enzyme(['itt'], binding)
d = utility.string_chars_indices(string)
locus = 1 # Sets index of unit to bind to
e.attach(s, locus)
self.assertEquals(e.locus, d[binding][locus])
self.assertEquals(e.strand, s)
self.assertEquals(e.status, 'attached')
def testCorrectTranslation(self):
"""Strand is translated by enzyme to produce set of new strands"""
string = 'TAGATCCAGTCCATCGA'
s = strand.Strand(string)
e = enzyme.Enzyme([
'rpu', 'inc', 'cop', 'mvr', 'mvl', 'swi', 'lpu', 'itt'],
'G')
locus = 1
e.attach(s, locus)
self.assertEquals(e.locus, 8)
result = next(e.translate())
self.assertEquals(result,
[list('AGCTACACCTGACCTAGAT'), list(' ATG ')])
def testNotAttachedTranslation(self):
"""When enzyme isn't attached, it can't translate"""
e = enzyme.Enzyme(['rpu'], 'A')
i = e.translate()
self.assertRaises(enzyme.NotAttached, next, i)
def testCorrectCreation(self):
"""Enzyme is created from an iterable with commands"""
commands = ['cut', 'dlt', 'swi']
e = enzyme.Enzyme(commands, 'A')
self.assertEquals(e.commands, commands)