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, "heur_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="CGMP", 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): 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 do_test_job(input_directory, gurobi_log_file): 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)