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: