from argparse import ArgumentParser parser = ArgumentParser() parser.add_argument("fasta_filename") parser.add_argument("-k", "--kmer_size", default=30, help="K-mer size (default: 30)") parser.add_argument("-s", "--sketch_size", default=1000, help="Sketch size (default: 1000)") parser.add_argument("-d", "--min_dist", default=0.95, help="Minimum distance (default: 0.95)") parser.add_argument("--chunk_size", default=1000, type=int, help="Chunk size") parser.add_argument("--cpus", default=1, type=int, help="# of CPUs (default: 1)") parser.add_argument('--version', action='version', version='%(prog)s ' + str(get_version())) args = parser.parse_args() main(args.fasta_filename, args.kmer_size, args.sketch_size, args.min_dist, args.chunk_size, args.cpus)
# combine the dist files with open(o, 'w') as f: for file in outputs: for line in open(file): f.write(line) # clean up the split files for file in inputs: os.remove(file) for file in files: os.remove(file) for file in outputs: os.remove(file) print >> sys.stderr, "Output written to:", os.path.join(dirname, o) os.chdir(olddir) return os.path.join(dirname, o) if __name__ == "__main__": from argparse import ArgumentParser parser = ArgumentParser() parser.add_argument("fasta_filename") parser.add_argument("-k", "--kmer_size", default=30, help="K-mer size (default: 30)") parser.add_argument("-s", "--sketch_size", default=1000, help="Sketch size (default: 1000)") parser.add_argument("-d", "--min_dist", default=0.95, help="Minimum distance (default: 0.95)") parser.add_argument("--chunk_size", default=1000, type=int, help="Chunk size") parser.add_argument("--cpus", default=1, type=int, help="# of CPUs (default: 1)") parser.add_argument('--version', action='version', version='%(prog)s ' + str(get_version())) args = parser.parse_args() main(args.fasta_filename, args.kmer_size, args.sketch_size, args.min_dist, args.chunk_size, args.cpus)
cleanup_gmap('cogent') if os.path.exists('cogent2') and os.path.isdir('cogent2'): cleanup_gmap('cogent2') if __name__ == "__main__": from argparse import ArgumentParser parser = ArgumentParser() parser.add_argument("dirname") parser.add_argument("-e", "--expected_error_rate", type=int, default=1, help="Expected error rate (default: 1%)") parser.add_argument("--nx_cycle_detection", default=False, action="store_true", help="Cycle detection using networkx (default: off), will increase run-time. Recommend for debugging failed cases only.") parser.add_argument("-k", "--kmer_size", type=int, default=30, help="kmer size (default: 30)") parser.add_argument("-D", "--gmap_db_path", help="GMAP database location (optional)") parser.add_argument("-d", "--gmap_species", help="GMAP species name (optional)") parser.add_argument("--small_genome", action="store_true", default=False, help="Genome size is smaller than 3GB (use gmap instead of gmapl)") parser.add_argument('--version', action='version', version='%(prog)s ' + str(get_version())) parser.add_argument("--debug", action="store_true", default=False) args = parser.parse_args() cc_settings.KMER_SIZE = args.kmer_size assert sp.cc_settings.KMER_SIZE == args.kmer_size cc_settings.EXPECTED_ERR_RATE = args.expected_error_rate cc_settings.NX_CYCLE_DETECTION = args.nx_cycle_detection if not args.small_genome: sanity_check_gmapl_exists()
parser.add_argument( "--nx_cycle_detection", default=False, action="store_true", help="Cycle detection using networkx (default: off), will increase run-time. Recommend for debugging failed cases only.", ) parser.add_argument("-k", "--kmer_size", type=int, default=30, help="kmer size (default: 30)") parser.add_argument("-D", "--gmap_db_path", help="GMAP database location (optional)") parser.add_argument("-d", "--gmap_species", help="GMAP species name (optional)") parser.add_argument( "--small_genome", action="store_true", default=False, help="Genome size is smaller than 3GB (use gmap instead of gmapl)", ) parser.add_argument("--version", action="version", version="%(prog)s " + str(get_version())) parser.add_argument("--debug", action="store_true", default=False) args = parser.parse_args() cc_settings.KMER_SIZE = args.kmer_size assert sp.cc_settings.KMER_SIZE == args.kmer_size cc_settings.EXPECTED_ERR_RATE = args.expected_error_rate cc_settings.NX_CYCLE_DETECTION = args.nx_cycle_detection if not args.small_genome: sanity_check_gmapl_exists() log = logging.getLogger("Cogent") if args.debug: