def test_punctuation(self):
s = Strand('CGGATACTAAACCGA')
e = strand_to_enzymes(s)
e_known = [Enzyme([AminoAcid('cop'), AminoAcid('ina'), AminoAcid('rpy'), AminoAcid('off')]),
Enzyme([AminoAcid('cut'), AminoAcid('cop')])]
self.assert_enzymes_eq(e, e_known)
def test_del_gap(self):
"""
delete
v
Secondary: ........CCCC.
Primary: ACGTGGGGGG.GG
^
"""
s = Strand('ACGTGGGGGGGGG')
e = Enzyme([
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('cop'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvl'),
AminoAcid('delete')
])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['ACGTGGGGGG', 'CCCC', 'GG'])
def test_delete(self):
s = Strand('ACGT')
e = Enzyme([AminoAcid('delete')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['CGT'])
def test_swi_swi(self):
"""
v
Secondary: ....
Primary: ACGT
^
Copy mode: False
cop
v
Secondary: ..C.
Primary: ACGT
^
Copy mode: True
swi
v
Secondary: TGCA
Primary: .C..
^
Copy mode: True
swi
v
Secondary: ..C.
Primary: ACGT
^
"""
s = Strand('ACGT')
e = Enzyme([AminoAcid('cop'), AminoAcid('swi'), AminoAcid('swi')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['ACGT', 'C'])
def test_inc_cop(self):
"""
v
Secondary: ....
Primary: ACGT
^
Copy mode: False
cop
v
Secondary: T...
Primary: ACGT
^
Copy mode: True
inc
v
Secondary: TG...
Primary: ACCGT
^
Copy mode: True
['ACCGT', 'GT']
"""
s = Strand('ACGT')
e = Enzyme([AminoAcid('cop'), AminoAcid('inc')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['ACCGT', 'GT'])
def test_apply_enzyme_ACA(self):
s = Strand('ACA')
e = Enzyme([AminoAcid('delete'), AminoAcid('mvr'), AminoAcid('int')])
final_strands = apply_enzyme(s, e)
assert (isinstance(final_strands[0], Strand) == True)
assert (final_strands[0].strand == 'CAT')
def test_cop_mvl(self):
"""
v
Secondary: ....
Primary: ACGT
^
Copy mode: False
mvr
v
Secondary: ....
Primary: ACGT
^
Copy mode: False
cop
v
Secondary: ...A
Primary: ACGT
^
Copy mode: True
mvl
v
Secondary: ..CA
Primary: ACGT
^
Copy mode: True
['AC', 'ACGT']
"""
s = Strand('ACGT')
e = Enzyme([AminoAcid('mvr'), AminoAcid('cop'), AminoAcid('mvl')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['AC', 'ACGT'])
def test_apply_longer_enzyme(self):
s = Strand('CAAAGAGAATCCTCTTTGAT')
e = Enzyme([AminoAcid('rpy'), AminoAcid('cop'), AminoAcid('rpu')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['CAAAGAGAATCCTCTTTGAT', 'CAAAGAGGA'])
def test_strand_to_enzymes(self):
s = Strand('TAGATCCAGTCCACATCGA')
e = strand_to_enzymes(s)
e_known = [Enzyme([AminoAcid('rpy'), AminoAcid('ina'), AminoAcid('rpu'), AminoAcid('mvr'),
AminoAcid('int'), AminoAcid('mvl'), AminoAcid('cut'), AminoAcid('swi'),
AminoAcid('cop')])]
self.assert_enzymes_eq(e, e_known)
def test_ing_cop(self):
"""
v
Secondary: ....
Primary: ACGT
^
Copy mode: False
cop
v
Secondary: T...
Primary: ACGT
^
Copy mode: True
off
v
Secondary: T...
Primary: ACGT
^
Copy mode: False
mvr
v
Secondary: T...
Primary: ACGT
^
Copy mode: False
mvr
v
Secondary: T...
Primary: ACGT
^
Copy mode: False
cop
v
Secondary: T.C.
Primary: ACGT
^
Copy mode: True
ing
v
Secondary: T.CC.
Primary: ACGGT
^
Copy mode: True
['ACGGT', 'CC', 'T']
"""
s = Strand('ACGT')
e = Enzyme([
AminoAcid('cop'),
AminoAcid('off'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('cop'),
AminoAcid('ing')
])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['ACGGT', 'CC', 'T'])
def test_delete_outofbounds(self):
s = Strand('ACGT')
e = Enzyme([
AminoAcid('mvr'),
AminoAcid('delete'),
AminoAcid('delete'),
AminoAcid('delete'),
AminoAcid('inc')
])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['A'])
def test_swi_none(self):
"""
v
Secondary: ....
Primary: ACGT
^
"""
s = Strand('ACGT')
e = Enzyme([AminoAcid('swi')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['ACGT'])
def strand_to_enzymes(strand):
""" Tranlate the strand encoding to enzymes via ribosomes """
def chunk_strand(strand):
for idx in range(len(strand) / 2):
yield strand[idx * 2:idx * 2 + 2]
# translate the chunks to amino acids or punctuation
amino_acids = [AminoAcid(TYPOGENETIC_CODE[chunk]) for chunk in chunk_strand(strand.strand)]
enzymes = []
current_enzyme = []
for amino_acid in amino_acids:
# if there is an AA chunk present, we finish off the current enzyme and start a new one
if amino_acid.op == 'pun':
enzymes.append(Enzyme(current_enzyme))
current_enzyme = []
else:
current_enzyme.append(amino_acid)
enzymes.append(Enzyme(current_enzyme))
return filter(lambda e: len(e.amino_acids), enzymes) # filter out any empty enzyimes
def test_cut(self):
"""
v
Secondary: ....
Primary: ACGT
^
Copy mode: False
cut
v
Secondary: .
Primary: A
^
Copy mode: False
['A', 'CGT']
"""
s = Strand('ACGT')
e = Enzyme([AminoAcid('cut')])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['A', 'CGT'])
def test_book_example(self):
s = Strand('TAGATCCAGTCCATCGA')
e = Enzyme([
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid('mvr'),
AminoAcid(
'mvr'
), # some extra movements to lineup with the known example
AminoAcid('rpu'),
AminoAcid('inc'),
AminoAcid('cop'),
AminoAcid('mvr'),
AminoAcid('mvl'),
AminoAcid('swi'),
AminoAcid('lpu'),
AminoAcid('int')
])
final_strands = apply_enzyme(s, e)
strand_strs = sorted([strand.strand for strand in final_strands])
assert (strand_strs == ['ATG', 'TAGATCCAGTCCACATCGA'])
def test_constructor(self):
Enzyme([AminoAcid('cut'), AminoAcid('delete')])
def test_input_all_amino_acids(self):
with assert_raises_regexp(InvalidEnzyme,
'Must all be of type AminoAcid'):
Enzyme([AminoAcid('cut'), AminoAcid('delete'), 4])
def test_empty_strand(self):
s = Strand('')
e = Enzyme([AminoAcid('delete')])
final_strands = apply_enzyme(s, e)
assert (final_strands[0] == s)
def test_input_not_a_list(self):
with assert_raises_regexp(InvalidEnzyme, 'Input must be a list'):
Enzyme('cut')
def test_apply_empty_enzyme(self):
s = Strand('ACGT')
e = Enzyme([])
final_strands = apply_enzyme(s, e)
assert (final_strands[0].strand == 'ACGT')