def main():
def check_int_range(value, min_val, max_val, require_odd=False):
ival = int(value)
if ival < min_val or ival > max_val:
raise argparse.ArgumentTypeError("value should be in the "
"range [{0}, {1}]".format(
min_val, max_val))
if require_odd and ival % 2 == 0:
raise argparse.ArgumentTypeError("should be an odd number")
return ival
parser = argparse.ArgumentParser \
(description="Assembly of long reads with repeat graphs",
formatter_class=argparse.RawDescriptionHelpFormatter,
usage=_usage(), epilog=_epilog())
read_group = parser.add_mutually_exclusive_group(required=True)
read_group.add_argument("--pacbio-raw",
dest="pacbio_raw",
default=None,
metavar="path",
nargs="+",
help="PacBio regular CLR reads (<20%% error)")
read_group.add_argument(
"--pacbio-corr",
dest="pacbio_corrected",
default=None,
metavar="path",
nargs="+",
help="PacBio reads that were corrected with other methods (<3%% error)"
)
read_group.add_argument("--pacbio-hifi",
dest="pacbio_hifi",
default=None,
metavar="path",
nargs="+",
help="PacBio HiFi reads (<1%% error)")
read_group.add_argument("--nano-raw",
dest="nano_raw",
nargs="+",
default=None,
metavar="path",
help="ONT regular reads, pre-Guppy5 (<20%% error)")
read_group.add_argument(
"--nano-corr",
dest="nano_corrected",
nargs="+",
default=None,
metavar="path",
help="ONT reads that were corrected with other methods (<3%% error)")
read_group.add_argument(
"--nano-hq",
dest="nano_hq",
nargs="+",
default=None,
metavar="path",
help="ONT high-quality reads: Guppy5+ SUP or Q20 (<5%% error)")
read_group.add_argument("--subassemblies",
dest="subassemblies",
nargs="+",
default=None,
metavar="path",
help="[deprecated] high-quality contigs input")
parser.add_argument("-g",
"--genome-size",
dest="genome_size",
metavar="size",
required=False,
default=None,
help="estimated genome size (for example, 5m or 2.6g)")
parser.add_argument("-o",
"--out-dir",
dest="out_dir",
default=None,
required=True,
metavar="path",
help="Output directory")
parser.add_argument("-t",
"--threads",
dest="threads",
type=lambda v: check_int_range(v, 1, 128),
default=1,
metavar="int",
help="number of parallel threads [1]")
parser.add_argument("-i",
"--iterations",
dest="num_iters",
type=lambda v: check_int_range(v, 0, 10),
default=1,
help="number of polishing iterations [1]",
metavar="int")
parser.add_argument("-m",
"--min-overlap",
dest="min_overlap",
metavar="int",
type=lambda v: check_int_range(v, 1000, 10000),
default=None,
help="minimum overlap between reads [auto]")
parser.add_argument("--asm-coverage",
dest="asm_coverage",
metavar="int",
default=None,
help="reduced coverage for initial "
"disjointig assembly [not set]",
type=int)
parser.add_argument("--hifi-error",
dest="hifi_error",
metavar="float",
default=None,
help="[deprecated] same as --read-error",
type=float)
parser.add_argument(
"--read-error",
dest="read_error",
metavar="float",
default=None,
help=
"adjust parameters for given read error rate (as fraction e.g. 0.03)",
type=float)
parser.add_argument(
"--extra-params",
dest="extra_params",
metavar="extra_params",
required=False,
default=None,
help="extra configuration parameters list (comma-separated)")
parser.add_argument("--plasmids",
action="store_true",
dest="plasmids",
default=False,
help="unused (retained for backward compatibility)")
parser.add_argument("--meta",
action="store_true",
dest="meta",
default=False,
help="metagenome / uneven coverage mode")
parser.add_argument("--keep-haplotypes",
action="store_true",
dest="keep_haplotypes",
default=False,
help="do not collapse alternative haplotypes")
parser.add_argument(
"--no-alt-contigs",
action="store_true",
dest="no_alt_contigs",
default=False,
help="do not output contigs representing alternative haplotypes")
parser.add_argument(
"--scaffold",
action="store_true",
dest="scaffold",
default=False,
help="enable scaffolding using graph [disabled by default]")
parser.add_argument(
"--trestle",
action="store_true",
dest="trestle",
default=False,
help="[deprecated] enable Trestle [disabled by default]")
parser.add_argument("--polish-target",
dest="polish_target",
metavar="path",
required=False,
help="run polisher on the target sequence")
parser.add_argument("--resume",
action="store_true",
dest="resume",
default=False,
help="resume from the last completed stage")
parser.add_argument("--resume-from",
dest="resume_from",
metavar="stage_name",
default=None,
help="resume from a custom stage")
parser.add_argument("--stop-after",
dest="stop_after",
metavar="stage_name",
default=None,
help="stop after the specified stage completed")
#parser.add_argument("--kmer-size", dest="kmer_size",
# type=lambda v: check_int_range(v, 11, 31, require_odd=True),
# default=None, help="kmer size (default: auto)")
parser.add_argument("--debug",
action="store_true",
dest="debug",
default=False,
help="enable debug output")
parser.add_argument("-v",
"--version",
action="version",
version=_version())
args = parser.parse_args()
if args.asm_coverage and (args.genome_size is None):
parser.error(
"--asm-coverage option requires genome size estimate (--genome-size)"
)
if args.asm_coverage and args.meta:
parser.error("--asm-coverage is incompatible with --meta")
if args.hifi_error and not args.read_error:
args.read_error = args.hifi_error
if args.read_error and (args.pacbio_raw or args.nano_raw):
parser.error("--read-error can only be used with corr/hq/hifi modes")
if args.read_error and args.read_error > 1:
parser.error(
"--read-error expressed as a decimal fraction, e.g. 0.01 or 0.03")
if args.read_error:
hifi_str = "assemble_ovlp_divergence={0},repeat_graph_ovlp_divergence={0}".format(
args.read_error)
if args.extra_params:
args.extra_params += "," + hifi_str
else:
args.extra_params = hifi_str
if args.no_alt_contigs:
alt_params = "remove_alt_edges=1"
if args.extra_params:
args.extra_params += "," + alt_params
else:
args.extra_params = "remove_alt_edges=1"
if args.pacbio_raw:
args.reads = args.pacbio_raw
args.platform = "pacbio"
args.read_type = "raw"
if args.pacbio_corrected:
args.reads = args.pacbio_corrected
args.platform = "pacbio"
args.read_type = "corrected"
if args.pacbio_hifi:
args.reads = args.pacbio_hifi
args.platform = "pacbio"
args.read_type = "hifi"
if args.nano_raw:
args.reads = args.nano_raw
args.platform = "nano"
args.read_type = "raw"
if args.nano_corrected:
args.reads = args.nano_corrected
args.platform = "nano"
args.read_type = "corrected"
if args.nano_hq:
args.reads = args.nano_hq
args.platform = "nano"
args.read_type = "nano_hq"
if args.subassemblies:
args.reads = args.subassemblies
args.platform = "pacbio" #arbitrary
args.read_type = "subasm"
if not os.path.isdir(args.out_dir):
os.mkdir(args.out_dir)
args.out_dir = os.path.abspath(args.out_dir)
args.reads = [os.path.abspath(r) for r in args.reads]
args.log_file = os.path.join(args.out_dir, "flye.log")
_enable_logging(args.log_file, args.debug, overwrite=False)
args.asm_config = os.path.join(cfg.vals["pkg_root"],
cfg.vals["bin_cfg"][args.read_type])
if args.plasmids:
logger.warning(
"--plasmids mode is no longer available. Command line option will be removed in the future versions"
)
if args.trestle:
logger.warning(
"--trestle mode is being deprecated. It will be removed in the future versions."
)
if args.subassemblies:
logger.warning(
"--subassemblies mode is being deprecated. It will be removed in the future versions."
)
try:
aln.check_binaries()
pol.check_binaries()
asm.check_binaries()
repeat.check_binaries()
if not args.polish_target:
_run(args)
else:
_run_polisher_only(args)
except (AlignmentException, pol.PolishException, asm.AssembleException,
repeat.RepeatException, ResumeException, fp.FastaError,
ConfigException) as e:
logger.error(e)
logger.error("Pipeline aborted")
return 1
return 0
def main():
def check_int_range(value, min_val, max_val, require_odd=False):
ival = int(value)
if ival < min_val or ival > max_val:
raise argparse.ArgumentTypeError("value should be in the "
"range [{0}, {1}]".format(
min_val, max_val))
if require_odd and ival % 2 == 0:
raise argparse.ArgumentTypeError("should be an odd number")
return ival
parser = argparse.ArgumentParser \
(description="Assembly of long reads with repeat graphs",
formatter_class=argparse.RawDescriptionHelpFormatter,
usage=_usage(), epilog=_epilog())
read_group = parser.add_mutually_exclusive_group(required=True)
read_group.add_argument("--pacbio-raw",
dest="pacbio_raw",
default=None,
metavar="path",
nargs="+",
help="PacBio raw reads")
read_group.add_argument("--pacbio-corr",
dest="pacbio_corrected",
default=None,
metavar="path",
nargs="+",
help="PacBio corrected reads")
read_group.add_argument("--pacbio-hifi",
dest="pacbio_hifi",
default=None,
metavar="path",
nargs="+",
help="PacBio HiFi reads")
read_group.add_argument("--nano-raw",
dest="nano_raw",
nargs="+",
default=None,
metavar="path",
help="ONT raw reads")
read_group.add_argument("--nano-corr",
dest="nano_corrected",
nargs="+",
default=None,
metavar="path",
help="ONT corrected reads")
read_group.add_argument("--subassemblies",
dest="subassemblies",
nargs="+",
default=None,
metavar="path",
help="high-quality contigs input")
parser.add_argument("-g",
"--genome-size",
dest="genome_size",
metavar="size",
required=False,
default=None,
help="estimated genome size (for example, 5m or 2.6g)")
parser.add_argument("-o",
"--out-dir",
dest="out_dir",
default=None,
required=True,
metavar="path",
help="Output directory")
parser.add_argument("-t",
"--threads",
dest="threads",
type=lambda v: check_int_range(v, 1, 128),
default=1,
metavar="int",
help="number of parallel threads [1]")
parser.add_argument("-i",
"--iterations",
dest="num_iters",
type=lambda v: check_int_range(v, 0, 10),
default=1,
help="number of polishing iterations [1]",
metavar="int")
parser.add_argument("-m",
"--min-overlap",
dest="min_overlap",
metavar="int",
type=lambda v: check_int_range(v, 1000, 10000),
default=None,
help="minimum overlap between reads [auto]")
parser.add_argument("--asm-coverage",
dest="asm_coverage",
metavar="int",
default=None,
help="reduced coverage for initial "
"disjointig assembly [not set]",
type=int)
parser.add_argument("--plasmids",
action="store_true",
dest="plasmids",
default=False,
help="rescue short unassembled plasmids")
parser.add_argument("--meta",
action="store_true",
dest="meta",
default=False,
help="metagenome / uneven coverage mode")
parser.add_argument("--keep-haplotypes",
action="store_true",
dest="keep_haplotypes",
default=False,
help="do not collapse alternative haplotypes")
parser.add_argument("--trestle",
action="store_true",
dest="trestle",
default=False,
help="enable Trestle [disabled]")
parser.add_argument("--polish-target",
dest="polish_target",
metavar="path",
required=False,
help="run polisher on the target sequence")
parser.add_argument("--resume",
action="store_true",
dest="resume",
default=False,
help="resume from the last completed stage")
parser.add_argument("--resume-from",
dest="resume_from",
metavar="stage_name",
default=None,
help="resume from a custom stage")
parser.add_argument("--stop-after",
dest="stop_after",
metavar="stage_name",
default=None,
help="stop after the specified stage completed")
#parser.add_argument("--kmer-size", dest="kmer_size",
# type=lambda v: check_int_range(v, 11, 31, require_odd=True),
# default=None, help="kmer size (default: auto)")
parser.add_argument("--debug",
action="store_true",
dest="debug",
default=False,
help="enable debug output")
parser.add_argument("-v",
"--version",
action="version",
version=_version())
args = parser.parse_args()
if args.asm_coverage and (args.genome_size is None):
parser.error(
"--asm-coverage option requires genome size estimate (--genome-size)"
)
if args.asm_coverage and args.meta:
parser.error("--asm-coverage is incompatible with --meta")
#if not args.genome_size and not args.polish_target:
# parser.error("Genome size argument (-g/--genome-size) "
# "is required for assembly")
if args.pacbio_raw:
args.reads = args.pacbio_raw
args.platform = "pacbio"
args.read_type = "raw"
if args.pacbio_corrected:
args.reads = args.pacbio_corrected
args.platform = "pacbio"
args.read_type = "corrected"
if args.pacbio_hifi:
args.reads = args.pacbio_hifi
args.platform = "pacbio"
args.read_type = "hifi"
if args.nano_raw:
args.reads = args.nano_raw
args.platform = "nano"
args.read_type = "raw"
if args.nano_corrected:
args.reads = args.nano_corrected
args.platform = "nano"
args.read_type = "corrected"
if args.subassemblies:
args.reads = args.subassemblies
args.platform = "pacbio" #arbitrary
args.read_type = "subasm"
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, "flye.log")
_enable_logging(args.log_file, args.debug, overwrite=False)
args.asm_config = os.path.join(cfg.vals["pkg_root"],
cfg.vals["bin_cfg"][args.read_type])
try:
aln.check_binaries()
pol.check_binaries()
asm.check_binaries()
repeat.check_binaries()
if not args.polish_target:
_run(args)
else:
_run_polisher_only(args)
except (AlignmentException, pol.PolishException, asm.AssembleException,
repeat.RepeatException, ResumeException, fp.FastaError) as e:
logger.error(e)
logger.error("Pipeline aborted")
return 1
return 0
def main():
def check_int_range(value, min_val, max_val, require_odd=False):
ival = int(value)
if ival < min_val or ival > max_val:
raise argparse.ArgumentTypeError("value should be in "
"range [{0}, {1}]".format(
min_val, max_val))
if require_odd and ival % 2 == 0:
raise argparse.ArgumentTypeError("should be an odd number")
return ival
parser = argparse.ArgumentParser \
(description="Assembly of long and error-prone reads",
formatter_class=argparse.RawDescriptionHelpFormatter,
usage=_usage(), epilog=_epilog())
read_group = parser.add_mutually_exclusive_group(required=True)
read_group.add_argument("--pacbio-raw",
dest="pacbio_raw",
default=None,
metavar="path",
nargs="+",
help="PacBio raw reads")
read_group.add_argument("--pacbio-corr",
dest="pacbio_corrected",
default=None,
metavar="path",
nargs="+",
help="PacBio corrected reads")
read_group.add_argument("--nano-raw",
dest="nano_raw",
nargs="+",
default=None,
metavar="path",
help="ONT raw reads")
read_group.add_argument("--nano-corr",
dest="nano_corrected",
nargs="+",
default=None,
metavar="path",
help="ONT corrected reads")
read_group.add_argument("--subassemblies",
dest="subassemblies",
nargs="+",
default=None,
metavar="path",
help="high-quality contigs input")
parser.add_argument("-g",
"--genome-size",
dest="genome_size",
metavar="size",
required=True,
help="estimated genome size (for example, 5m or 2.6g)")
parser.add_argument("-o",
"--out-dir",
dest="out_dir",
default=None,
required=True,
metavar="path",
help="Output directory")
parser.add_argument("-t",
"--threads",
dest="threads",
type=lambda v: check_int_range(v, 1, 128),
default=1,
metavar="int",
help="number of parallel threads [1]")
parser.add_argument("-i",
"--iterations",
dest="num_iters",
type=lambda v: check_int_range(v, 0, 10),
default=1,
help="number of polishing iterations [1]",
metavar="int")
parser.add_argument("-m",
"--min-overlap",
dest="min_overlap",
metavar="int",
type=lambda v: check_int_range(v, 1000, 10000),
default=None,
help="minimum overlap between reads [auto]")
parser.add_argument("--asm-coverage",
dest="asm_coverage",
metavar="int",
default=None,
help="reduced coverage for initial "
"contig assembly [not set]",
type=int)
parser.add_argument("--resume",
action="store_true",
dest="resume",
default=False,
help="resume from the last completed stage")
parser.add_argument("--resume-from",
dest="resume_from",
metavar="stage_name",
default=None,
help="resume from a custom stage")
#parser.add_argument("--kmer-size", dest="kmer_size",
# type=lambda v: check_int_range(v, 11, 31, require_odd=True),
# default=None, help="kmer size (default: auto)")
parser.add_argument("--debug",
action="store_true",
dest="debug",
default=False,
help="enable debug output")
parser.add_argument("-v",
"--version",
action="version",
version=_version())
args = parser.parse_args()
if args.pacbio_raw:
args.reads = args.pacbio_raw
args.platform = "pacbio"
args.read_type = "raw"
if args.pacbio_corrected:
args.reads = args.pacbio_corrected
args.platform = "pacbio"
args.read_type = "corrected"
if args.nano_raw:
args.reads = args.nano_raw
args.platform = "nano"
args.read_type = "raw"
if args.nano_corrected:
args.reads = args.nano_corrected
args.platform = "nano"
args.read_type = "corrected"
if args.subassemblies:
args.reads = args.subassemblies
args.platform = "pacbio" #arbitrary
args.read_type = "subasm"
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, "flye.log")
_enable_logging(args.log_file, args.debug, overwrite=False)
_set_kmer_size(args)
args.asm_config = os.path.join(cfg.vals["pkg_root"],
cfg.vals["bin_cfg"][args.read_type])
try:
aln.check_binaries()
pol.check_binaries()
asm.check_binaries()
repeat.check_binaries()
_run(args)
except (aln.AlignmentException, pol.PolishException, asm.AssembleException,
repeat.RepeatException, ResumeException) as e:
logger.error(e)
return 1
return 0
