def do_test_job(input_directory, gurobi_log_file):
logging.info(
'Let\'s do comparison test for the GMP-ILP. Input directory is {0}'.
format(input_directory))
for path, name in get_immediate_subdirectories(input_directory):
for subpath, subname in get_immediate_subdirectories(path):
if os.path.isfile(subpath):
continue
logging.info("Working with directory {0}".format(subpath))
ilppath = os.path.join(subpath, "force_ilp")
genome1 = os.path.join(ilppath, "S1.gen")
genome2 = os.path.join(ilppath, "S2.gen")
genome3 = os.path.join(ilppath, "S4.gen")
result_out_file = os.path.join(ilppath, "result.txt")
genome_out_file = os.path.join(ilppath, "median.gen")
medians_without_singletons(
genome_files=[genome1, genome2, genome3],
out_result_file=result_out_file,
out_median_file=genome_out_file,
problem="GMP",
gurobi_log_file=gurobi_log_file,
time_limit=7200)
def do_test_job(input_directory, gurobi_log_file):
logging.info(
'Let\'s do comparison test for the RGGHP-ILP. Input directory is {0}'.
format(input_directory))
for path, name in get_immediate_subdirectories(input_directory):
for subpath, subname in get_immediate_subdirectories(path):
if os.path.isfile(subpath):
continue
logging.info("Working with directory {0}".format(subpath))
ilppath = os.path.join(subpath, "rgghp_ilp")
ordinary_genome_file = os.path.join(ilppath, "B.gen")
all_dupl_genome_file = os.path.join(ilppath, "A.gen")
result_out_file = os.path.join(ilppath, "result.txt")
genome_out_file = os.path.join(ilppath, "pre_dup.gen")
# TODO
halvings_without_singletons(
ordinary_genome_file=ordinary_genome_file,
all_dupl_genome_file=all_dupl_genome_file,
out_result_file=result_out_file,
out_predup_file=genome_out_file,
problem="RGGHP",
gurobi_log_file=gurobi_log_file,
time_limit=7200)
def do_test_job(input_directory, gurobi_log_file):
logging.info(
'Let\'s do comparison test for the IGMP-ILP. Input directory is {0}'.
format(input_directory))
for path, name in get_immediate_subdirectories(input_directory):
for subpath, subname in get_immediate_subdirectories(path):
if os.path.isfile(subpath):
continue
logging.info("Working with directory {0}".format(subpath))
ilppath = os.path.join(subpath, "igmp_ilp")
genome1 = os.path.join(ilppath, "S1.gen")
genome2 = os.path.join(ilppath, "S2.gen")
genome3 = os.path.join(ilppath, "S4.gen")
result_out_file = os.path.join(ilppath, "result.txt")
genome_out_file = os.path.join(ilppath, "median.gen")
solve_restricted_median_problem(
genome_files=[genome1, genome2, genome3],
out_result_file=result_out_file,
out_median_file=genome_out_file,
gurobi_log_file=gurobi_log_file)
def do_test_job(input_directory, gurobi_log_file, ilp_type):
logging.info(
'Let\'s do comparison test for the DDP-ILP. Input directory is {0}'.
format(input_directory))
for path, name in get_immediate_subdirectories(input_directory):
for subpath, subname in get_immediate_subdirectories(path):
if os.path.isfile(subpath):
continue
logging.info("Working with directory {0}".format(subpath))
ilppath = os.path.join(subpath, "ilp")
ordinary_genome = os.path.join(ilppath, "target_genome.gen")
all_dupl_genome = os.path.join(ilppath, "a.gen")
out_file = os.path.join(ilppath, "result.txt")
solve_double_distance_problem(ord_genome_file=ordinary_genome,
all_dupl_genome_file=all_dupl_genome,
out_result_file=out_file,
gurobi_log_file=gurobi_log_file,
ilp_type=ilp_type)
def do_job_tannier_dataset(name_directory, gurobi_log_file):
logging.info('Let\'s do the CGGHP-ILP calculations for Tannier\'s dataset. Input directory is {0}')
for path, name in get_immediate_subdirectories(name_directory):
if os.path.isfile(path):
continue
logging.info("Working with directory {0}".format(path))
ilppath = os.path.join(path, "heur_ilp")
ordinary_genome_file = os.path.join(ilppath, "B.gen")
all_dupl_genome_file = os.path.join(ilppath, "A.gen")
result_out_file = os.path.join(ilppath, "result.txt")
genome_out_file = os.path.join(ilppath, "pre_dup.gen")
halvings_without_singletons(ordinary_genome_file=ordinary_genome_file,
all_dupl_genome_file=all_dupl_genome_file,
out_result_file=result_out_file,
out_predup_file=genome_out_file,
problem="CGGHP",
gurobi_log_file=gurobi_log_file,
time_limit=7200
)
