def compute_leaderboard(n, spectrum, table):
leaderboard = ['']
leader_peptide = ''
leader_score = score(leader_peptide, spectrum, table)
parent_mass = spectrum[-1]
while len(leaderboard) > 0:
new_leaderboard = []
map(lambda x: new_leaderboard.extend([peptide + x for peptide in leaderboard]), LETTERS)
leaderboard = new_leaderboard
stuff_to_remove = []
for peptide in leaderboard:
if weight(peptide, table) == parent_mass:
if score(peptide, spectrum, table) > leader_score:
leader_peptide = peptide
leader_score = score(peptide, spectrum, table)
elif weight(peptide, table) > parent_mass:
stuff_to_remove.append(peptide)
[leaderboard.remove(x) for x in stuff_to_remove]
def trim(leaderboard, spectrum, N):
temp = []
for peptide in leaderboard:
temp.append((peptide, score(peptide, spectrum, table)))
temp.sort(key=lambda x: x[1])
return [x[0] for x in temp[-N:]]
leaderboard = trim(leaderboard, spectrum, n)
return leader_peptide
def compute_leaderboard(n, spectrum, table):
leaderboard = ['']
leader_peptide = ''
leader_score = score(leader_peptide, spectrum, table)
parent_mass = spectrum[-1]
while len(leaderboard) > 0:
new_leaderboard = []
map(
lambda x: new_leaderboard.extend(
[peptide + x for peptide in leaderboard]), LETTERS)
leaderboard = new_leaderboard
stuff_to_remove = []
for peptide in leaderboard:
if weight(peptide, table) == parent_mass:
if score(peptide, spectrum, table) > leader_score:
leader_peptide = peptide
leader_score = score(peptide, spectrum, table)
elif weight(peptide, table) > parent_mass:
stuff_to_remove.append(peptide)
[leaderboard.remove(x) for x in stuff_to_remove]
def trim(leaderboard, spectrum, N):
temp = []
for peptide in leaderboard:
temp.append((peptide, score(peptide, spectrum, table)))
temp.sort(key=lambda x: x[1])
return [x[0] for x in temp[-N:]]
leaderboard = trim(leaderboard, spectrum, n)
return leader_peptide
def compute_leaderboard(n, spectrum, table):
leaderboard = ['']
leader_peptides = ['']
leader_score = score(leader_peptides[0], spectrum, table)
parent_mass = spectrum[-1]
peptides_83 = []
while len(leaderboard) > 0:
new_leaderboard = []
map(
lambda x: new_leaderboard.extend(
[peptide + x for peptide in leaderboard]), LETTERS)
leaderboard = new_leaderboard
stuff_to_remove = []
for peptide in leaderboard:
if weight(peptide, table) == parent_mass:
if score(peptide, spectrum, table) == 83:
peptides_83.append(peptide)
if score(peptide, spectrum, table) > leader_score:
leader_peptides = [peptide]
leader_score = score(peptide, spectrum, table)
elif score(peptide, spectrum, table) == leader_score:
leader_peptides.append(peptide)
elif weight(peptide, table) > parent_mass:
stuff_to_remove.append(peptide)
[leaderboard.remove(x) for x in stuff_to_remove]
def trim(leaderboard, spectrum, N):
if (len(leaderboard) < N):
return leaderboard
temp = []
for peptide in leaderboard:
temp.append((peptide, score(peptide, spectrum, table)))
temp.sort(key=lambda x: x[1], reverse=True)
edge_score = temp[N - 1][1]
assert temp[0][1] >= temp[-1][1]
result = [x[0] for x in temp if x[1] >= edge_score]
print 'Trimmed length %s against given N=%s' % (len(result), N)
return result
leaderboard = trim(leaderboard, spectrum, n)
print leader_score
return leader_peptides
def compute_leaderboard(n, spectrum, table):
leaderboard = ['']
leader_peptides = ['']
leader_score = score(leader_peptides[0], spectrum, table)
parent_mass = spectrum[-1]
peptides_83 = []
while len(leaderboard) > 0:
new_leaderboard = []
map(lambda x: new_leaderboard.extend([peptide + x for peptide in leaderboard]), LETTERS)
leaderboard = new_leaderboard
stuff_to_remove = []
for peptide in leaderboard:
if weight(peptide, table) == parent_mass:
if score(peptide, spectrum, table) == 83:
peptides_83.append(peptide)
if score(peptide, spectrum, table) > leader_score:
leader_peptides = [peptide]
leader_score = score(peptide, spectrum, table)
elif score(peptide, spectrum, table) == leader_score:
leader_peptides.append(peptide)
elif weight(peptide, table) > parent_mass:
stuff_to_remove.append(peptide)
[leaderboard.remove(x) for x in stuff_to_remove]
def trim(leaderboard, spectrum, N):
if (len(leaderboard) < N):
return leaderboard
temp = []
for peptide in leaderboard:
temp.append((peptide, score(peptide, spectrum, table)))
temp.sort(key=lambda x: x[1], reverse=True)
edge_score = temp[N - 1][1]
assert temp[0][1] >= temp[-1][1]
result = [x[0] for x in temp if x[1] >= edge_score]
print 'Trimmed length %s against given N=%s' % (len(result), N)
return result
leaderboard = trim(leaderboard, spectrum, n)
print leader_score
return leader_peptides
def cyclo_sequence(spectrum, table):
leaderboard = ['']
leader_peptides = ['']
parent_mass = spectrum[-1]
while len(leaderboard) > 0:
new_leaderboard = []
map(lambda x: new_leaderboard.extend([peptide + x for peptide in leaderboard]), LETTERS)
leaderboard = new_leaderboard
stuff_to_remove = []
for peptide in leaderboard:
if weight(peptide, table) == parent_mass:
if generate_cyclo_spectrum(peptide, table) == spectrum:
leader_peptides.append(peptide)
stuff_to_remove.append(peptide)
elif not is_spectrum_consistent(generate_linear_spectrum(peptide, table), perfect_spectrum):
stuff_to_remove.append(peptide)
[leaderboard.remove(x) for x in stuff_to_remove]
return leader_peptides