def do_test_job(input_directory, gurobi_log_file):
logging.info(
'Let\'s do comparison test for the CGGHP-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, "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)
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)
def main():
parser = argparse.ArgumentParser(description="ILP solver for the Conserved Guided Genome Halving Problem (CGGHP)",
formatter_class=argparse.RawDescriptionHelpFormatter, epilog=epilog())
parser.add_argument("-r", "--ordinary", dest="ordinary",
default=None, metavar="PATH", help="Ordinary genome in GRIMM format")
parser.add_argument("-t", "--two_dupl", dest="duplicated",
default=None, metavar="PATH", help="2-duplicated genome in GRIMM format")
parser.add_argument("-o", "--out-dir", dest="out_dir",
default=None, required=True,
metavar="PATH", help="Output directory")
parser.add_argument("-tl", "--time_limit", dest="time_limit",
default=7200, required=False,
type=int, metavar="NUMBER",
help="Time limit for Gurobi solver")
parser.add_argument("-v", "--version", action="version", version=version())
args = parser.parse_args()
if not os.path.isdir(args.out_dir):
os.mkdir(args.out_dir)
args.out_dir = os.path.abspath(args.out_dir)
args.log_file = os.path.join(args.out_dir, "cgghp.log")
args.gurobi_log_file = os.path.join(args.out_dir, "gurobi_cgghp.log")
enable_logging(args.log_file, overwrite=False)
ordinary_genome_file = os.path.abspath(args.ordinary)
all_dupl_genome_file = os.path.abspath(args.duplicated)
result_out_file = os.path.join(args.out_dir, "result.txt")
genome_out_file = os.path.join(args.out_dir, "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=args.gurobi_log_file,
time_limit=args.time_limit)