def test_run():
parser = argparse.ArgumentParser(description="ILP solver for the Restricted Guided Genome Halving Problem (RGGHP)",
formatter_class=argparse.RawDescriptionHelpFormatter, epilog=epilog())
parser.add_argument("-pt", "--paper_test", dest="paper_test",
default=None, metavar="PATH",
help="The directory with data from the paper. Please use only "
"for reproducibility of the paper results")
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.paper_test):
parser.error("The directory must exist and have correct structure")
args.paper_test = os.path.abspath(args.paper_test)
args.log_file = os.path.join(args.paper_test, "rgghp.log")
args.gurobi_log_file = os.path.join(args.paper_test, "gurobi_rgghp.log")
enable_logging(args.log_file, overwrite=False)
do_test_job(args.paper_test, args.gurobi_log_file)
def main():
parser = argparse.ArgumentParser(
description="ILP solver for the Double Distance Problem (DDP)",
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, "double_distance.log")
args.gurobi_log_file = os.path.join(args.out_dir,
"gurobi_double_distance.log")
enable_logging(args.log_file, overwrite=False)
path_to_ord_genome = os.path.abspath(args.ordinary)
path_to_dupl_genome = os.path.abspath(args.duplicated)
result_out_file = os.path.join(args.out_dir, "result.txt")
solve_double_distance_problem(ord_genome_file=path_to_ord_genome,
all_dupl_genome_file=path_to_dupl_genome,
out_result_file=result_out_file,
gurobi_log_file=args.gurobi_log_file,
time_limit=args.time_limit)
def main():
parser = argparse.ArgumentParser(
description="ILP solver for the Genome Median Problem (GMP)",
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=epilog())
parser.add_argument("-f",
"--files",
dest="files",
default=None,
metavar="PATH",
nargs=3,
help="Three files 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, "gmp.log")
args.gurobi_log_file = os.path.join(args.out_dir, "gurobi_gmp.log")
enable_logging(args.log_file, overwrite=False)
path_to_genomes = [os.path.abspath(f) for f in args.files]
result_out_file = os.path.join(args.out_dir, "result.txt")
genome_out_file = os.path.join(args.out_dir, "median.gen")
medians_without_singletons(genome_files=path_to_genomes,
out_result_file=result_out_file,
out_median_file=genome_out_file,
problem="GMP",
gurobi_log_file=args.gurobi_log_file,
time_limit=args.time_limit)
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)
