def solve_ddp_brute(ord_genome_file,
all_dupl_genome_file,
out_result_file=None,
tl=50,
mult=2):
ord_genome = parse_genome_in_grimm_file(ord_genome_file)
all_dupl_genome = parse_genome_in_grimm_file(all_dupl_genome_file)
ord_genome = remove_singletons_in_ord_wrt_two_dupl(ord_genome,
all_dupl_genome)
all_dupl_genome = remove_singletons_dupl_wrt_gene_set(
all_dupl_genome, set(ord_genome.get_gene_multiset().keys()))
config = DoubleDistConf(ordinary_genome=ord_genome,
duplicated_genome=all_dupl_genome,
name="DDP",
log_file="brute_double_dist.log",
tl=tl,
mult=mult)
start_time = datetime.now()
answer = solve(config)
end_time = datetime.now()
logging.info(answer)
if out_result_file:
write_answer(answer, out_result_file, end_time - start_time)
return answer
def solve_restricted_halving_problem(ordinary_genome_file,
all_dupl_genome_file, out_result_file,
out_predup_file, gurobi_log_file,
time_limit):
logging.info(
'Start to solve RGGHP problem with time limit equals {0}'.format(
time_limit))
ord_genomes = [parse_genome_in_grimm_file(ordinary_genome_file)]
all_dupl_genome = parse_genome_in_grimm_file(all_dupl_genome_file)
logging.info('Create ILP config')
cfg = RestrictedHalvingConf(duplicated_genome=all_dupl_genome,
ordinary_genomes=ord_genomes,
name="RGGHP",
log_file=gurobi_log_file,
tl=time_limit,
mult=2)
answer = create_ilp_formulation_for_restricted_phalving(cfg)
if answer is not None:
logging.info('Save results.')
answer.write_stats_file(out_result_file)
answer.write_genome_file(out_predup_file)
else:
logging.info('There are no answers. Please, check log file.')
def halvings_without_singletons(ordinary_genome_file, all_dupl_genome_file,
out_result_file, out_predup_file, problem,
gurobi_log_file, time_limit):
logging.info(
'Start to solve {0} (excluding singletons) with time limit equals {1}'.
format(problem, time_limit))
ord_genomes = [parse_genome_in_grimm_file(ordinary_genome_file)]
all_dupl_genome = parse_genome_in_grimm_file(all_dupl_genome_file)
logging.info('Create ILP config')
if problem == "CGGHP":
cfg = ConservedHalving(duplicated_genome=all_dupl_genome,
ordinary_genomes=ord_genomes,
name="CGGHP",
log_file=gurobi_log_file,
tl=time_limit,
mult=2)
else:
cfg = ClassicHalving(duplicated_genome=all_dupl_genome,
ordinary_genomes=ord_genomes,
name="GGHP",
log_file=gurobi_log_file,
tl=time_limit,
mult=2)
answer = create_ilp_formulation_for_halvings_without_singletons(cfg)
if answer is not None:
logging.info('Save results.')
answer.write_stats_file(out_result_file)
answer.write_genome_file(out_predup_file)
else:
logging.info('There are no answers. Please, check log file.')
def solve_double_distance_problem(ord_genome_file,
all_dupl_genome_file,
out_result_file,
gurobi_log_file,
mult=2,
time_limit=7200,
ilp_type='improved'):
logging.info(
'Start to solve DDP problem with time limit equals {0} and solver type "{1}"'
.format(time_limit, ilp_type))
ord_genome = parse_genome_in_grimm_file(ord_genome_file)
all_dupl_genome = parse_genome_in_grimm_file(all_dupl_genome_file)
ord_genome = remove_singletons_in_ord_wrt_two_dupl(ord_genome,
all_dupl_genome)
all_dupl_genome = remove_singletons_dupl_wrt_gene_set(
all_dupl_genome, set(ord_genome.get_gene_multiset().keys()))
logging.info('Create ILP config')
config = DoubleDistConf(ordinary_genome=ord_genome,
duplicated_genome=all_dupl_genome,
name="DDP_" + ilp_type,
log_file=gurobi_log_file,
tl=time_limit,
mult=mult)
answer = create_ilp_formulation_for_ddp(config=config, ilp_type=ilp_type)
if answer is not None:
logging.info('Save results.')
answer.write_stats_file(out_result_file)
return answer.obj_val, answer.score
else:
logging.info('There are no answers. Please, check log file.')
return None
def medians_without_singletons(genome_files, out_result_file, out_median_file,
problem, gurobi_log_file, time_limit):
logging.info(
'Start to solve {0} (excluding singletons) with time limit equals {1}'.
format(problem, time_limit))
genomes = [
parse_genome_in_grimm_file(genome_file) for genome_file in genome_files
]
logging.info('Create ILP config')
if problem == "CGMP":
cfg = ConservedMedian(genomes=genomes,
name="CGMP",
log_file=gurobi_log_file,
tl=time_limit)
else:
cfg = ClassicMedian(genomes=genomes,
name="GMP",
log_file=gurobi_log_file,
tl=time_limit)
answer = create_ilp_formulation_for_medians_without_singletons(cfg)
if answer is not None:
logging.info('Save results.')
answer.write_stats_file(out_result_file)
answer.write_genome_file(out_median_file)
else:
logging.info('There are no answers. Please, check log file.')
def solve_restricted_median_problem(genome_files,
out_result_file,
out_median_file,
gurobi_log_file,
time_limit=7200):
logging.info(
'Start to solve IGMP problem with time limit equals {0}'.format(
time_limit))
genomes = [
parse_genome_in_grimm_file(genome_file) for genome_file in genome_files
]
logging.info('Create ILP config')
cfg = RestrictedMedianConf(genomes=genomes,
name="IGMP",
log_file=gurobi_log_file,
tl=time_limit)
answer = create_ilp_formulation_for_restricted_median(cfg)
if answer is not None:
logging.info('Save results.')
answer.write_stats_file(out_result_file)
answer.write_genome_file(out_median_file)
else:
logging.info('There are no answers. Please, check log file.')
def medians_with_singletons(genome_files, out_result_file, out_median_file,
problem, gurobi_log_file, time_limit):
"""Creates and calculates the ILP instance for GMP or CGMP with assumption of singleton existance in the
ancestral genome.
Args:
TBA
"""
logging.info(
'Start to solve {0} (including singletons) with time limit equals {1}'.
format(problem, time_limit))
genomes = [
parse_genome_in_grimm_file(genome_file) for genome_file in genome_files
]
genomes, numb_of_singletons = remove_known_singletons(genomes)
logging.info('Create ILP config')
if problem == "CGMP":
cfg = ConservedMedian(genomes=genomes,
name="CGMP",
log_file=gurobi_log_file,
tl=time_limit)
else:
cfg = ClassicMedian(genomes=genomes,
name="GMP",
log_file=gurobi_log_file,
tl=time_limit)
answer = create_ilp_formulation_for_medians_with_singletons(cfg)
if answer is not None:
answer.update_score_by_singletons(numb_of_singletons)
logging.info('Save results.')
answer.write_stats_file(out_result_file)
answer.write_genome_file(out_median_file)
else:
logging.info('Solution was not found. Please, check log file.')