def test_combinations(self):
comb52 = list(collider.combinations( range(5), 2 ) )
self.assertEqual(comb52, [
(0, 1),
(0, 2),
(0, 3),
(0, 4),
(1, 2),
(1, 3),
(1, 4),
(2, 3),
(2, 4),
(3, 4)
])
comb53 = list(collider.combinations( range(5), 3 ) )
self.assertEqual( comb53, [
(0, 1, 2),
(0, 1, 3),
(0, 1, 4),
(0, 2, 3),
(0, 2, 4),
(0, 3, 4),
(1, 2, 3),
(1, 2, 4),
(1, 3, 4),
(2, 3, 4)
])
# now also test the before 2.6 version
comb52 = list(collider.combinations( range(5), 2, True ) )
self.assertEqual(comb52, [
(0, 1),
(0, 2),
(0, 3),
(0, 4),
(1, 2),
(1, 3),
(1, 4),
(2, 3),
(2, 4),
(3, 4)
])
comb53 = list(collider.combinations( range(5), 3, True ) )
self.assertEqual( comb53, [
(0, 1, 2),
(0, 1, 3),
(0, 1, 4),
(0, 2, 3),
(0, 2, 4),
(0, 3, 4),
(1, 2, 3),
(1, 2, 4),
(1, 3, 4),
(2, 3, 4)
])
def get_all_modifications(this_sequence, to_modify, replace_with, max_nr_modifications):
import re
positions = [m.start() for m in re.finditer(to_modify, this_sequence)]
for i in range(1,min(max_nr_modifications,1+len(positions))):
to_replace = list(collider.combinations( positions, i))
for new_peptide in to_replace:
it = 0
curr_seq = ''
for pos in new_peptide:
curr_seq += this_sequence[it:pos] + replace_with
it = pos+1
curr_seq += this_sequence[it:]
pep = DDB.Peptide()
pep.set_sequence(curr_seq)
pep.modifications = i
yield pep
