def test_cleave(self):
self.assertEqual(parser._cleave('PEPTIDEKS', parser.expasy_rules['trypsin']), ['PEPTIDEK', 'S'])
self.assertEqual(parser._cleave('PEPTIDEKS', 'trypsin'), ['PEPTIDEK', 'S'])
for seq in self.simple_sequences:
for elem in parser.cleave(
seq, 'trypsin', int(random.uniform(1, 10))):
self.assertIn(elem, seq)
self.assertTrue(any(elem == seq
for elem in parser.cleave(seq, parser.expasy_rules['trypsin'], len(seq))))
def smart_reverse(prot_seq):
'''
Produces a reverse decoy sequence keeping all K and R aminoacids in the same positions.
'''
return ''.join(
fasta.decoy_sequence(pep, mode='reverse', keep_cterm=True)
for pep in parser._cleave(prot_seq, '[RK]', 0))
def test_cleave_semi(self):
self.assertEqual(
parser._cleave('PEPTIDEKS',
parser.expasy_rules['trypsin'],
semi=True),
[
'PEPTIDEK', 'P', 'PE', 'PEP', 'PEPT', 'PEPTI', 'PEPTID',
'EPTIDEK', 'PTIDEK', 'TIDEK', 'IDEK', 'DEK', 'EK', 'K', 'S'
])
self.assertEqual(
parser.cleave('PEPTIDEKS',
parser.expasy_rules['trypsin'],
semi=True),
{
'PEPTIDEK', 'P', 'PE', 'PEP', 'PEPT', 'PEPTI', 'PEPTID',
'EPTIDEK', 'PTIDEK', 'TIDEK', 'IDEK', 'DEK', 'EK', 'K', 'S'
})