def msgf2seq_file(filepath, fasta_file, msb_psms):
"""
msb_psms: set of spectid_peptidesequence
"""
def parse_spec_pep_row(r):
# get spec_pep from _best file format
parsed = '_'.join(r[0].split('.')[:2] + [r[4]])
#print parsed
return parsed
usedir,fin = os.path.split(filepath)
# Get the sample filename from the first item of the third line
fout = next(it.islice(ut.load_tab_file(filepath),2,3))[0].split('.')[0]
in_gen = ut.load_tab_file(filepath)
in_gen.next(); in_gen.next() # skip 2 lines
p2g = seqs.prots2genes(fasta_file)
g2p = ut.dict_inverse(p2g)
fout = os.path.join(usedir, '.'.join([fout, fin.split('.')[-1] ,
'sequestformat']))
search = searches[filepath.split('.')[-1]]
print "Converting/filtering; Search:", search
output = (msgfbest2sequest_line(r,p2g, g2p, search) for r in in_gen
if parse_spec_pep_row(r) in msb_psms)
print "Writing", fout
ut.write_tab_file(output, fout)
return fout
def ensg_to_ensp_and_park(ppips):
dhpg = seqs.prots2genes('/Users/blakeweb/Dropbox/complex/data/sequences/canon/Hs.fasta')
dhgp = ut.dict_inverse(dhpg)
parkids = ut.load_lol('./orth_similarities/table.Hsapiens/Hsapiens_id.txt')
ppips_ensp = [dhgp[g] for g in ppips]
dg2park = dict([(x[2],x[0]) for x in parkids])
dp2park = dict([(x[1],x[0]) for x in parkids])
park_ppips_most = [dp2park[p] for p in ppips_ensp if p in dp2park]
ppips_ensp_rest = [p for p in ppips_ensp if p not in dp2park]
ppips_ensg_rest = [dhpg[p] for p in ppips_ensp_rest]
park_ppips_rest = [dg2park[p] for p in ppips_ensg_rest if p in dg2park]
park_ppips = park_ppips_most + park_ppips_rest
return park_ppips
def check(fasta, protq, do_convert):
p2g = seqs.prots2genes(fasta)
g2p = ut.dict_inverse(p2g)
fprots = el.load_elution(protq).prots
print "checking", ut.shortname(protq)
print "proteins: %s of %s" % (len([p for p in fprots if p in p2g]),
len(fprots))
ngenesfound = len([p for p in fprots if p in g2p])
print "genes: %s of %s" % (ngenesfound,
len(fprots))
if do_convert and ngenesfound < len(fprots):
print "converting prots to genes:", protq
seqs.elut_p2g(protq, p2g)
def main(options):
if options.initial_point.lower(
) == 'true' and options.qbits_limit.lower() != 'true':
raise Exception(
"Can't use initial_point if the number of required qubits varies from one optimization step to the following. Set also qbits_limit to true."
)
# fixed values
stock_tickers = ['FXD', 'FXR', 'FXL', 'FTXR', 'QTEC']
start_date = date(2017, 1, 1)
computation_date = date(2020, 1, 1)
end_date = date(2021, 1, 1)
#hyperparameters
optim_dict = {
"quantum_instance": 'qasm_simulator',
"shots": 1024,
"print": True,
"logfile": True,
"solver": 'vqe',
"optimizer": SLSQP,
"maxiter": 1000,
"depth": 1,
"alpha": 0.35
}
# etf collector
etfs = {}
# building the quantum etf
quantum_etf = {}
date_ = copy(computation_date)
while date_ < end_date:
# generate main values for the model
prices_, mu_, sigma_ = generate_values(stock_tickers=stock_tickers +
['IFV'],
start_date=start_date,
end_date=date_)
# values for quantum etf
prices = prices_[:-1]
mu = mu_[:-1]
sigma = sigma_[:-1, :-1]
# find budget, best allocation, results
if len(quantum_etf) == 0:
B = copy(options.budget)
else:
previous_month_etf = copy(
quantum_etf[previous_month(date_).strftime('%Y-%m-%d')])
B = previous_month_etf['liquidity'] + np.sum(
np.array(previous_month_etf['allocation']) * prices)
if options.initial_point.lower() == 'true':
print(
"Using best parameters of previous optimization as an initial point"
)
optim_dict['initial_point'] = last_optimal_params
if options.qbits_limit.lower() == 'true':
qbits_dict = {
k0: max(l0)
for k0, l0 in dict_inverse({
j: model_qbits(prices, j, B)
for j in range(1, options.max_k)
}).items()
}
if options.max_qbits in qbits_dict:
k_ = qbits_dict[options.max_qbits]
elif options.max_qbits > max(qbits_dict):
k_ = copy(options.max_k)
warn(
"Number of qbits provided exceeds qbits dictionary. Initialising k as the maximum given."
)
else:
warn(
'Number of qbits given not found among possible models.Choosing k equal to given value'
)
k_ = copy(options.k)
else:
k_ = copy(options.k)
mdl, grouping = qcmodel(prices, k_, B, mu, sigma, options.q)
optim_dict["docplex_mod"] = mdl
for i in range(options.n_trials):
results = aggregator('optimizer', optim_dict)
if results['is_qp_feasible']:
break
# Integer results (amount of groups of stocks): x
x_val = [
results['result'].variables_dict[f'x{i}']
for i in range(len(prices))
]
# Amount of individual stock
best_allocation = grouping * np.array(x_val)
budget_spent = np.sum(best_allocation * prices)
# Saves optimal parameters as initial point for next iteration
last_optimal_params = results['solver_info']['optimal_params']
#printing tmp_results
tmp_results = {
'computational_time': float(results['computational_time']),
'optimal_function_value': float(results['result'].fval),
'status': str(results['result'].status).split('.')[-1],
'is_qp_feasible': results['is_qp_feasible']
}
# generate etf datapoint
if budget_spent > B: # if budget spent is bigger than current liquidity
tmp_results['wrong_results'] = {
'best_allocation_found': [int(i) for i in best_allocation],
'budget_spent': float(budget_spent)
}
if len(quantum_etf
) == 0: # at step 0, etf does not spend any budget
quantum_etf[date_.strftime('%Y-%m-%d')] = {
'allocation': [0] * len(prices),
'prices': [float(p) for p in prices],
'liquidity': B,
'portfolio_value': 0.,
'results': tmp_results,
'k': k_
}
else: # at step k (any k), etf keeps previous allocation and updates its values with current prices
quantum_etf[date_.strftime('%Y-%m-%d')] = {
'allocation':
previous_month_etf['allocation'],
'prices': [float(p) for p in prices],
'liquidity':
previous_month_etf['liquidity'],
'portfolio_value':
float(
np.sum(
np.array(previous_month_etf['allocation']) *
prices)),
'results':
tmp_results,
'k':
k_
}
else: # if budget spent < B
tmp_results['wrong_results'] = None
quantum_etf[date_.strftime('%Y-%m-%d')] = {
'allocation': [int(i) for i in best_allocation],
'prices': [float(p) for p in prices],
'liquidity': float(B - budget_spent),
'portfolio_value': float(budget_spent),
'results': copy(tmp_results),
'k': k_
}
if not os.path.exists(options.savepath):
os.makedirs(options.savepath)
fs = os.path.join(options.savepath, f'quantum_etf_results.json')
with open(fs, 'wt') as qf:
json.dump(quantum_etf, qf)
# next datapoint
date_ = next_month(date_)
# building the optimum and real etf
# steps separated for clarity only
opt_etf = {}
real_etf = {}
date_ = copy(computation_date)
while date_ < end_date:
# generate main values for the model
prices_, mu_, sigma_ = generate_values(stock_tickers=stock_tickers +
['IFV'],
start_date=start_date,
end_date=date_)
# values for quantum etf
prices = prices_[:-1]
mu = mu_[:-1]
sigma = sigma_[:-1, :-1]
# price of real etf
ifv_price = prices_[-1]
# find budget, best allocation, results
if len(opt_etf) == 0:
B = copy(options.budget)
# real values
no_real_bought_stocks = floor(B / ifv_price)
real_liquidity = B - no_real_bought_stocks * ifv_price
else:
previous_month_etf = copy(
opt_etf[previous_month(date_).strftime('%Y-%m-%d')])
B = previous_month_etf['liquidity'] + np.sum(
np.array(previous_month_etf['allocation']) * prices)
if options.qbits_limit == 'true':
qbits_dict = {
k0: max(l0)
for k0, l0 in dict_inverse({
j: model_qbits(prices, j, B)
for j in range(1, options.max_k)
}).items()
}
if options.max_qbits in qbits_dict:
k_ = qbits_dict[options.max_qbits]
elif options.max_qbits > max(qbits_dict):
k_ = copy(options.max_k)
warn(
"Number of qbits provided exceeds qbits dictionary. Initialising k as the maximum given."
)
else:
warn(
'Number of qbits given not found among possible models.Choosing k equal to given value'
)
k_ = copy(options.k)
else:
k_ = copy(options.k)
mdl, grouping = qcmodel(prices, k_, B, mu, sigma, options.q)
# solver
mdl.solve()
sols_dict = dict(
zip([f'x{i}' for i in range(len(prices))], [0] * len(prices)))
for j, v in mdl.solution.as_name_dict().items():
sols_dict[j] = int(v)
x_val = list(sols_dict.values())
# Amount of individual stock
best_allocation = grouping * np.array(x_val)
budget_spent = np.sum(best_allocation * prices)
# generate etf datapoint
if budget_spent > B: # if budget spent is bigger than current liquidity
if len(opt_etf) == 0: # at step 0, etf does not spend any budget
opt_etf[date_.strftime('%Y-%m-%d')] = {
'allocation': [0] * len(prices),
'prices': [float(p) for p in prices],
'liquidity': B,
'portfolio_value': 0.,
'objective_value': mdl.solution.get_objective_value()
}
else: # at step k (any k), etf keeps previous allocation and updates its values with current prices
opt_etf[date_.strftime('%Y-%m-%d')] = {
'allocation':
previous_month_etf['allocation'],
'prices': [float(p) for p in prices],
'liquidity':
previous_month_etf['liquidity'],
'portfolio_value':
float(
np.sum(
np.array(previous_month_etf['allocation']) *
prices)),
'objective_value':
mdl.solution.get_objective_value()
}
else: # if budget spent < B
opt_etf[date_.strftime('%Y-%m-%d')] = {
'allocation': [int(i) for i in best_allocation],
'prices': [float(p) for p in prices],
'liquidity': float(B - budget_spent),
'portfolio_value': float(budget_spent),
'objective_value': mdl.solution.get_objective_value()
}
# real etf
real_etf[date_.strftime('%Y-%m-%d')] = {
'liquidity': real_liquidity,
'prices': float(ifv_price),
'portfolio_value': no_real_bought_stocks * ifv_price
}
# etf is saved at every step
fs_real = os.path.join(options.savepath, f'real_etf_results.json')
with open(fs_real, 'wt') as rf:
json.dump(real_etf, rf)
fs_opt = os.path.join(options.savepath, f'opt_etf_results.json')
with open(fs_opt, 'wt') as rf:
json.dump(opt_etf, rf)
# next datapoint
date_ = next_month(date_)
# clearing notebook output
clear_output()
etfs['quantum'] = copy(quantum_etf)
etfs['optimum'] = copy(opt_etf)
etfs['IFV'] = copy(real_etf)
print_etfs(etfs, savepath=options.savepath)
return None