def main():
""" main function """
## not in ipython
ip.__interactive__ = 0
## parse params file input (returns to stdout if --help or --version)
args = parse_command_line()
print(HEADER.format(ip.__version__))
## set random seed
np.random.seed(args.rseed)
random.seed(args.rseed)
## debugger----------------------------------------
if os.path.exists(ip.__debugflag__):
os.remove(ip.__debugflag__)
if args.debug:
print("\n ** Enabling debug mode ** ")
ip.debug_on()
atexit.register(ip.debug_off)
## if JSON, load existing Tetrad analysis -----------------------
if args.json:
data = ipa.tetrad.load_json(args.json)
## if force then remove all results
if args.force:
data.refresh()
## else create a new tmp assembly for the seqarray-----------------
else:
## create new Tetrad class Object if it doesn't exist
newjson = os.path.join(args.outdir, args.name+'.tet.json')
if (not os.path.exists(newjson)) or args.force:
data = ipa.tetrad.Tetrad(name=args.name,
wdir=args.outdir,
method=args.method,
seqfile=args.seq,
resolve=args.resolve,
mapfile=args.map,
treefile=args.tree,
nboots=args.boots,
nquartets=args.nquartets)
print(" new Tetrad instance: {}".format(args.name))
else:
raise IPyradWarningExit(QUARTET_EXISTS\
.format(args.name, args.outdir, args.outdir, args.name, args.name))
## boots can be set either for a new object or loaded JSON to continue it
if args.boots:
data.nboots = int(args.boots)
## set CLI ipcluster terms
data._ipcluster["cores"] = args.cores if args.cores else detect_cpus()
## if more ipcluster args from command-line then use those
if args.MPI:
data._ipcluster["engines"] = "MPI"
else:
data._ipcluster["engines"] = "Local"
## launch a NEW ipcluster instance and register "cluster_id"
## for later destruction, and to avoid conflicts between
## simultaneous ipcluster instances. If a user wanted to use
## an ipcluster instance that is already running instead then
## they have to use the API, or to have set args.ipcluster
if args.ipcluster:
data._ipcluster["profile"] = "ipyrad"
#ip.__interactive__ = 1
else:
data = register_ipcluster(data)
## message about whether we are continuing from existing
if data.checkpoint.boots or data.checkpoint.arr:
print(ipa.tetrad.LOADING_MESSAGE.format(data.name,
data.method, data.checkpoint.boots, data.checkpoint.arr))
## run tetrad main function within a wrapper. The wrapper creates an
## ipyclient view and appends to the list of arguments to run 'run'.
data.run(force=args.force)
def main():
""" main function """
## parse params file input (returns to stdout if --help or --version)
args = parse_command_line()
print(HEADER.format(ip.__version__))
## set random seed
np.random.seed(args.rseed)
random.seed(args.rseed)
## debugger----------------------------------------
if os.path.exists(ip.__debugflag__):
os.remove(ip.__debugflag__)
if args.debug:
print("\n ** Enabling debug mode ** ")
ip.debug_on()
atexit.register(ip.debug_off)
## if JSON, load existing Tetrad analysis -----------------------
if args.json:
#data = ipa.tetrad.load_json(args.json)
data = ipa.tetrad(name=args.name, workdir=args.workdir, load=True)
## if force then remove all results
if args.force:
data.refresh()
## else create a new tmp assembly for the seqarray-----------------
else:
## create new Tetrad class Object if it doesn't exist
newjson = os.path.join(args.workdir, args.name + '.tet.json')
if (not os.path.exists(newjson)) or args.force:
## purge any files associated with this name if forced
if args.force:
ipa.tetrad(name=args.name,
workdir=args.workdir,
seqfile=args.seq,
initarr=False,
quiet=True).refresh()
## create new tetrad object
data = ipa.tetrad(
name=args.name,
workdir=args.workdir,
method=args.method,
seqfile=args.seq,
resolve=args.resolve,
mapfile=args.map,
guidetreefile=args.tree,
nboots=args.boots,
nquartets=args.nquartets,
cli=True,
)
## if not quiet...
print("tetrad instance: {}".format(args.name))
else:
raise SystemExit(QUARTET_EXISTS\
.format(args.name, args.workdir, args.workdir, args.name, args.name))
## boots can be set either for a new object or loaded JSON to continue it
if args.boots:
data.nboots = int(args.boots)
## set CLI ipcluster terms
data._ipcluster["cores"] = args.cores if args.cores else detect_cpus()
## if more ipcluster args from command-line then use those
if args.MPI:
data._ipcluster["engines"] = "MPI"
if not args.cores:
raise IPyradWarningExit("must provide -c argument with --MPI")
else:
data._ipcluster["engines"] = "Local"
## launch a NEW ipcluster instance and register "cluster_id"
## for later destruction, and to avoid conflicts between
## simultaneous ipcluster instances. If a user wanted to use
## an ipcluster instance that is already running instead then
## they have to use the API, or to have set args.ipcluster
if args.ipcluster:
data._ipcluster["cluster_id"] = ""
else:
data = register_ipcluster(data)
## message about whether we are continuing from existing
if data.checkpoint.boots or data.checkpoint.arr:
print(
ipa.tetrad.LOADING_MESSAGE.format(data.name, data.method,
data.checkpoint.boots,
data.checkpoint.arr))
## run tetrad main function within a wrapper. The wrapper creates an
## ipyclient view and appends to the list of arguments to run 'run'.
data.run(force=args.force)
def main():
""" main function """
## turn off traceback for the CLI
ip.__interactive__ = 0
## parse params file input (returns to stdout if --help or --version)
args = parse_command_line()
## Turn the debug output written to ipyrad_log.txt up to 11!
## Clean up the old one first, it's cleaner to do this here than
## at the end (exceptions, etc)
if os.path.exists(ip.__debugflag__):
os.remove(ip.__debugflag__)
if args.debug:
print("\n ** Enabling debug mode ** ")
ip.debug_on()
atexit.register(ip.debug_off)
## create new paramsfile if -n
if args.new:
## Create a tmp assembly and call write_params to write out
## default params.txt file
try:
tmpassembly = ip.Assembly(args.new, quiet=True)
tmpassembly.write_params("params-{}.txt".format(args.new),
force=args.force)
except Exception as inst:
print(inst)
sys.exit(2)
print("\n New file 'params-{}.txt' created in {}\n".\
format(args.new, os.path.realpath(os.path.curdir)))
sys.exit(2)
## if params then must provide action argument with it
if args.params:
if not any([args.branch, args.results, args.steps]):
print("""
Must provide action argument along with -p argument for params file.
e.g., ipyrad -p params-test.txt -r ## shows results
e.g., ipyrad -p params-test.txt -s 12 ## runs steps 1 & 2
e.g., ipyrad -p params-test.txt -b newbranch ## branch this assembly
""")
sys.exit(2)
if not args.params:
if any([args.branch, args.results, args.steps]):
print("""
Must provide params file for branching, doing steps, or getting results.
e.g., ipyrad -p params-test.txt -r ## shows results
e.g., ipyrad -p params-test.txt -s 12 ## runs steps 1 & 2
e.g., ipyrad -p params-test.txt -b newbranch ## branch this assembly
""")
## if branching, or merging do not allow steps in same command
## print spacer
if any([args.branch, args.merge]):
args.steps = ""
print("")
## always print the header when doing steps
header = \
"\n -------------------------------------------------------------"+\
"\n ipyrad [v.{}]".format(ip.__version__)+\
"\n Interactive assembly and analysis of RAD-seq data"+\
"\n -------------------------------------------------------------"
## if merging just do the merge and exit
if args.merge:
print(header)
merge_assemblies(args)
sys.exit(1)
## create new Assembly or load existing Assembly, quit if args.results
elif args.params:
parsedict = parse_params(args)
if args.branch:
branch_assembly(args, parsedict)
elif args.steps:
## print header
print(header)
## run Assembly steps
## launch or load assembly with custom profile/pid
data = getassembly(args, parsedict)
## set CLI ipcluster terms
data._ipcluster["cores"] = args.cores if args.cores else detect_cpus()
data._ipcluster["threads"] = args.threads
## if more ipcluster args from command-line then use those
if args.MPI:
data._ipcluster["engines"] = "MPI"
else:
data._ipcluster["engines"] = "Local"
## launch a NEW ipcluster instance and register "cluster_id"
## for later destruction, and to avoid conflicts between
## simultaneous ipcluster instances. If a user wanted to use
## an ipcluster instance that is already running instead then
## they have to use the API, or to have set args.ipcluster
if args.ipcluster:
data._ipcluster["profile"] = "ipyrad"
#ip.__interactive__ = 1
else:
data = register_ipcluster(data)
## set to print headers
data._headers = 1
## run assembly steps
steps = list(args.steps)
data.run(steps=steps, force=args.force, preview=args.preview, show_cluster=1)
if args.results:
showstats(parsedict)
def main():
""" main function """
## turn off traceback for the CLI
ip.__interactive__ = 0
## Check for a new version on anaconda
_check_version()
## parse params file input (returns to stdout if --help or --version)
args = parse_command_line()
## Turn the debug output written to ipyrad_log.txt up to 11!
## Clean up the old one first, it's cleaner to do this here than
## at the end (exceptions, etc)
if os.path.exists(ip.__debugflag__):
os.remove(ip.__debugflag__)
if args.debug:
print("\n ** Enabling debug mode ** ")
ip._debug_on()
atexit.register(ip._debug_off)
## create new paramsfile if -n
if args.new:
## Create a tmp assembly, call write_params to make default params.txt
try:
tmpassembly = ip.Assembly(args.new, quiet=True, cli=True)
tmpassembly.write_params("params-{}.txt".format(args.new),
force=args.force)
except Exception as inst:
print(inst)
sys.exit(2)
print("\n New file 'params-{}.txt' created in {}\n".\
format(args.new, os.path.realpath(os.path.curdir)))
sys.exit(2)
## if params then must provide action argument with it
if args.params:
if not any([args.branch, args.results, args.steps]):
print("""
Must provide action argument along with -p argument for params file.
e.g., ipyrad -p params-test.txt -r ## shows results
e.g., ipyrad -p params-test.txt -s 12 ## runs steps 1 & 2
e.g., ipyrad -p params-test.txt -b newbranch ## branch this assembly
""")
sys.exit(2)
if not args.params:
if any([args.branch, args.results, args.steps]):
print("""
Must provide params file for branching, doing steps, or getting results.
e.g., ipyrad -p params-test.txt -r ## shows results
e.g., ipyrad -p params-test.txt -s 12 ## runs steps 1 & 2
e.g., ipyrad -p params-test.txt -b newbranch ## branch this assembly
""")
## if branching, or merging do not allow steps in same command
## print spacer
if any([args.branch, args.merge]):
args.steps = ""
print("")
## always print the header when doing steps
header = \
"\n -------------------------------------------------------------"+\
"\n ipyrad [v.{}]".format(ip.__version__)+\
"\n Interactive assembly and analysis of RAD-seq data"+\
"\n -------------------------------------------------------------"
## Log the current version. End run around the LOGGER
## so it'll always print regardless of log level.
with open(ip.__debugfile__, 'a') as logfile:
logfile.write(header)
logfile.write("\n Begin run: {}".format(time.strftime("%Y-%m-%d %H:%M")))
logfile.write("\n Using args {}".format(vars(args)))
logfile.write("\n Platform info: {}".format(os.uname()))
## if merging just do the merge and exit
if args.merge:
print(header)
merge_assemblies(args)
sys.exit(1)
## if download data do it and then exit. Runs single core in CLI.
if args.download:
if len(args.download) == 1:
downloaddir = "sra-fastqs"
else:
downloaddir = args.download[1]
sratools_download(args.download[0], workdir=downloaddir, force=args.force)
sys.exit(1)
## create new Assembly or load existing Assembly, quit if args.results
elif args.params:
parsedict = parse_params(args)
if args.branch:
branch_assembly(args, parsedict)
elif args.steps:
## print header
print(header)
## Only blank the log file if we're actually going to run a new
## assembly. This used to be in __init__, but had the side effect
## of occasionally blanking the log file in an undesirable fashion
## for instance if you run a long assembly and it crashes and
## then you run `-r` and it blanks the log, it's crazymaking.
if os.path.exists(ip.__debugfile__):
if os.path.getsize(ip.__debugfile__) > 50000000:
with open(ip.__debugfile__, 'w') as clear:
clear.write("file reset")
## run Assembly steps
## launch or load assembly with custom profile/pid
data = getassembly(args, parsedict)
## set CLI ipcluster terms
data._ipcluster["threads"] = args.threads
## if ipyclient is running (and matched profile) then use that one
if args.ipcluster:
ipyclient = ipp.Client(profile=args.ipcluster)
data._ipcluster["cores"] = len(ipyclient)
## if not then we need to register and launch an ipcluster instance
else:
## set CLI ipcluster terms
ipyclient = None
data._ipcluster["cores"] = args.cores if args.cores else detect_cpus()
data._ipcluster["engines"] = "Local"
if args.MPI:
data._ipcluster["engines"] = "MPI"
if not args.cores:
raise IPyradWarningExit("must provide -c argument with --MPI")
## register to have a cluster-id with "ip- name"
data = register_ipcluster(data)
## set to print headers
data._headers = 1
## run assembly steps
steps = list(args.steps)
data.run(
steps=steps,
force=args.force,
preview=args.preview,
show_cluster=1,
ipyclient=ipyclient)
if args.results:
showstats(parsedict)
def main():
""" main function """
## parse params file input (returns to stdout if --help or --version)
args = parse_command_line()
print(HEADER.format(ip.__version__))
## set random seed
np.random.seed(args.rseed)
# ## debugger----------------------------------------
# if os.path.exists(ip.__debugflag__):
# os.remove(ip.__debugflag__)
# if args.debug:
# print("\n ** Enabling debug mode ** ")
# ip._debug_on()
## if JSON, load existing Tetrad analysis -----------------------
if args.json:
data = ipa.tetrad(name=args.name, workdir=args.workdir, load=True)
## if force then remove all results
if args.force:
data._refresh()
## else create a new tmp assembly for the seqarray-----------------
else:
## create new Tetrad class Object if it doesn't exist
newjson = os.path.join(args.workdir, args.name + '.tet.json')
## if not quiet...
print("tetrad instance: {}".format(args.name))
if (not os.path.exists(newjson)) or args.force:
## purge any files associated with this name if forced
if args.force:
## init an object in the correct location just to refresh
ipa.tetrad(name=args.name,
workdir=args.workdir,
data=args.seq,
initarr=False,
save_invariants=args.invariants,
cli=True,
quiet=True)._refresh()
## create new tetrad object
data = ipa.tetrad(
name=args.name,
workdir=args.workdir,
method=args.method,
data=args.seq,
resolve=args.resolve,
mapfile=args.map,
guidetree=args.tree,
nboots=args.boots,
nquartets=args.nquartets,
cli=True,
save_invariants=args.invariants,
)
else:
raise SystemExit(
QUARTET_EXISTS.format(args.name, args.workdir, args.workdir,
args.name, args.name))
## boots can be set either for a new object or loaded JSON to continue it
if args.boots:
data.params.nboots = int(args.boots)
## if ipyclient is running (and matched profile) then use that one
if args.ipcluster:
ipyclient = ipp.Client(profile=args.ipcluster)
data.ipcluster["cores"] = len(ipyclient)
## if not then we need to register and launch an ipcluster instance
else:
## set CLI ipcluster terms
ipyclient = None
data.ipcluster["cores"] = args.cores if args.cores else detect_cpus()
data.ipcluster["engines"] = "Local"
if args.MPI:
data.ipcluster["engines"] = "MPI"
if not args.cores:
raise IPyradWarningExit("must provide -c argument with --MPI")
## register to have a cluster-id with "ip- name"
data = register_ipcluster(data)
## message about whether we are continuing from existing
if data.checkpoint.boots:
print(
LOADING_MESSAGE.format(data.name, data.params.method,
data.checkpoint.boots))
## run tetrad main function within a wrapper. The wrapper creates an
## ipyclient view and appends to the list of arguments to run 'run'.
data.run(force=args.force, ipyclient=ipyclient)