def sequence_book(spectrum, n, m):
if spectrum[0] != 0:
spectrum = [0] + spectrum
bitches = convolutions(spectrum, m)
matches = defaultdict(list)
leader, leader_score = (0, ), 0
leaderboard = [leader]
parent = spectrum[-1]
while leaderboard:
leaderboard = expand(leaderboard, bitches)
next_leaderboard = []
for peptide in leaderboard:
if sum(peptide) == parent:
score = get_score(peptide, spectrum)
if score > leader_score:
leader, leader_score = peptide, score
print ts(peptide), '', score, '', ts(
generate_spec(peptide))
matches[score].append(peptide)
if sum(peptide) < parent:
next_leaderboard.append(peptide)
leaderboard = next_leaderboard
leaderboard = cut_book(leaderboard, spectrum, n)
return leader, leader_score, matches
def brute_forse(spec):
possible_spec_acids = [acid for acid in spec if acid in all_acids]
desired_sum = spec[-1]
max_len = len(possible_spec_acids)
matches = []
def combinate(peptides):
next_peps = set()
for peptide in peptides:
if sum(peptide) == desired_sum:
matches.append(peptide)
if sum(peptide) < desired_sum and len(peptide) <= max_len:
l = len(peptide)
for acid in possible_spec_acids:
next_peps.add(peptide + (acid, ))
if next_peps:
print l, len(next_peps)
combinate(next_peps)
combinate([(a, ) for a in possible_spec_acids])
print '\nMatches:', len(matches)
for peptide in matches:
test_spec = generate_spec(peptide)
if test_spec == spec:
print '-'.join(map(str, peptide)), ' ', \
''.join(map(acid_by_mass.get, peptide)), ' ', \
' '.join(map(str, test_spec))
def sequence_book(spectrum, n, m):
if spectrum[0] != 0:
spectrum = [0] + spectrum
bitches = convolutions(spectrum, m)
matches = defaultdict(list)
leader, leader_score = (0,), 0
leaderboard = [leader]
parent = spectrum[-1]
while leaderboard:
leaderboard = expand(leaderboard, bitches)
next_leaderboard = []
for peptide in leaderboard:
if sum(peptide) == parent:
score = get_score(peptide, spectrum)
if score > leader_score:
leader, leader_score = peptide, score
print ts(peptide), '', score, '', ts(generate_spec(peptide))
matches[score].append(peptide)
if sum(peptide) < parent:
next_leaderboard.append(peptide)
leaderboard = next_leaderboard
leaderboard = cut_book(leaderboard, spectrum, n)
return leader, leader_score, matches
def get_score(peptide, ref_spec):
spectrum = [0] + sorted(generate_spec(peptide))
ref_spec = ref_spec[:]
#print ' '.join(map(str, spectrum))
#print ' '.join(map(str, ref_spec))
score = 0
i, j = 0, 0
while i < len(spectrum) and j < len(ref_spec):
if spectrum[i] == ref_spec[j]:
#print spectrum[i],
score += 1
#print spectrum[i], ref_spec[j], '', score
i += 1
j += 1
elif spectrum[i] < ref_spec[j]:
#print spectrum[i], ' '
i += 1
elif spectrum[i] > ref_spec[j]:
#print ' ', ref_spec[j]
j += 1
#print
return score
def get_score(peptide, ref_spec):
spectrum = [0] + sorted(generate_spec(peptide))
ref_spec = ref_spec[:]
#print ' '.join(map(str, spectrum))
#print ' '.join(map(str, ref_spec))
score = 0
i, j = 0, 0
while i < len(spectrum) and j < len(ref_spec):
if spectrum[i] == ref_spec[j]:
#print spectrum[i],
score += 1
#print spectrum[i], ref_spec[j], '', score
i += 1
j += 1
elif spectrum[i] < ref_spec[j]:
#print spectrum[i], ' '
i += 1
elif spectrum[i] > ref_spec[j]:
#print ' ', ref_spec[j]
j += 1
#print
return score