ipyrad/analysis/__tetrad_cli__.py
def parse_command_line():
    """ Parse CLI args. Only three options now. """

    ## create the parser
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
  * Example command-line usage ---------------------------------------------- 

  * Read in sequence/SNP data file, provide linkage, output name, ambig option. 
     tetrad -s data.snps.phy -n test             ## input phylip and give name
     tetrad -s data.snps.phy -l data.snps.map    ## sample one SNP per locus
     tetrad -s data.snps.phy -n noambigs -r 0    ## do not use hetero sites

  * Load saved/checkpointed analysis from '.tet.json' file, or force restart. 
     tetrad -j test.tet.json -b 100         ## continue 'test' until 100 boots
     tetrad -j test.tet.json -b 100 -f      ## force restart of 'test'

  * Sampling modes: 'equal' uses guide tree to sample quartets more efficiently 
     tetrad -s data.snps.phy -m all                       ## sample all quartets
     tetrad -s data.snps.phy -m random -q 1e6 -x 123      ## sample 1M randomly
     tetrad -s data.snps.phy -m equal -q 1e6 -t guide.tre ## sample 1M across tree

  * Connect to N cores on a computer (default without -c arg is to use all avail.)
     tetrad -s data.snps.phy -c 20

  * Start an MPI cluster to connect to nodes across multiple available hosts.
     tetrad -s data.snps.phy --MPI     

  * Connect to a manually started ipcluster instance with default or named profile
     tetrad -s data.snps.phy --ipcluster        ## connects to default profile
     tetrad -s data.snps.phy --ipcluster pname  ## connects to profile='pname'

  * Further documentation: http://ipyrad.readthedocs.io/analysis.html
    """)


    ## get version from ipyrad 
    ipyversion = str(pkg_resources.get_distribution('ipyrad'))
    parser.add_argument('-v', '--version', action='version', 
        version="tetrad "+ipyversion.split()[1])

    parser.add_argument('-f', "--force", action='store_true',
        help="force overwrite of existing data")

    parser.add_argument('-s', metavar="seq", dest="seq",
        type=str, default=None,
        help="path to input phylip file (only SNPs)")

    parser.add_argument('-j', metavar='json', dest="json",
        type=str, default=None,
        help="load checkpointed/saved analysis from JSON file.")

    parser.add_argument('-m', metavar="method", dest="method",
        type=str, default="all",
        help="method for sampling quartets (all, random, or equal)")

    parser.add_argument('-q', metavar="nquartets", dest="nquartets",
        type=int, default=0,
        help="number of quartets to sample (if not -m all)")

    parser.add_argument('-b', metavar="boots", dest="boots",
        type=int, default=0,
        help="number of non-parametric bootstrap replicates")

    parser.add_argument('-l', metavar="map_file", dest="map",
        type=str, default=None,
        help="map file of snp linkages (e.g., ipyrad .snps.map)")

    parser.add_argument('-r', metavar="resolve", dest='resolve', 
        type=int, default=1, 
        help="randomly resolve heterozygous sites (default=1)")

    parser.add_argument('-n', metavar="name", dest="name",
        type=str, default="test",
        help="output name prefix (default: 'test')")

    parser.add_argument('-o', metavar="workdir", dest="workdir",
        type=str, default="./analysis-tetrad",
        help="output directory (default: creates ./analysis-tetrad)")

    parser.add_argument('-t', metavar="starting_tree", dest="tree",
        type=str, default=None,
        help="newick file starting tree for equal splits sampling")

    parser.add_argument("-c", metavar="CPUs/cores", dest="cores",
        type=int, default=0,
        help="setting -c improves parallel efficiency with --MPI")

    parser.add_argument("-x", metavar="random_seed", dest="rseed",
        type=int, default=None,
        help="random seed for quartet sampling and/or bootstrapping")    

    parser.add_argument('-d', "--debug", action='store_true',
        help="print lots more info to debugger: ipyrad_log.txt.")

    parser.add_argument("--MPI", action='store_true',
        help="connect to parallel CPUs across multiple nodes")

    parser.add_argument("--invariants", action='store_true',
        help="save a (large) database of all invariants")

    parser.add_argument("--ipcluster", metavar="ipcluster", dest="ipcluster",
        type=str, nargs="?", const="default",
        help="connect to ipcluster profile (default: 'default')")

    ## if no args then return help message
    if len(sys.argv) == 1:
        parser.print_help()
        sys.exit(1)

    ## parse args
    args = parser.parse_args()

    ## RAISE errors right away for some bad argument combinations:
    if args.method not in ["random", "equal", "all"]:
        raise IPyradWarningExit("  method argument (-m) must be one of"+\
        """ "all", "random", or "equal.\n""")

    ## if 'random' require nquarts argument
    #if args.method == 'random':
    #    if not args.nquartets:
    #        raise IPyradWarningExit(\
    #        "  Number of quartets (-q) is required with method = random\n")

    ## if 'equal' method require starting tree and nquarts
    # if args.method == 'equal':
    #     raise IPyradWarningExit(\
    #         "  The equal sampling method is currently for developers only.\n")
    #     if not args.nquartets:
    #         raise IPyradWarningExit(\
    #         "  Number of quartets (-q) is required with method = equal\n")
    #     if not args.tree:
    #         raise IPyradWarningExit(\
    #         "  Input guide tree (-t) is required with method = equal\n")

    ## required args
    if not any(x in ["seq", "json"] for x in vars(args).keys()):
        print("""
    Bad arguments: tetrad command must include at least one of (-s or -j) 
    """)
        parser.print_help()
        sys.exit(1)

    return args
def parse_command_line():
    """ Parse CLI args. Only three options now. """

    ## create the parser
    parser = argparse.ArgumentParser(
        formatter_class=argparse.RawDescriptionHelpFormatter,
        epilog="""
  * Example command-line usage ---------------------------------------------- 

  * Read in sequence/SNP data file, provide linkage, output name, ambig option. 
     tetrad -s data.snps.phy -n test             ## input phylip and give name
     tetrad -s data.snps.phy -l data.snps.map    ## sample one SNP per locus
     tetrad -s data.snps.phy -n noambigs -r 0    ## do not use hetero sites

  * Load saved/checkpointed analysis from '.tet.json' file, or force restart. 
     tetrad -j test.tet.json -b 100         ## continue 'test' until 100 boots
     tetrad -j test.tet.json -b 100 -f      ## force restart of 'test'

  * Sampling modes: 'equal' uses guide tree to sample quartets more efficiently 
     tetrad -s data.snps.phy -m all                       ## sample all quartets
     tetrad -s data.snps.phy -m random -q 1e6 -x 123      ## sample 1M randomly
     tetrad -s data.snps.phy -m equal -q 1e6 -t guide.tre ## sample 1M across tree

  * Connect to N cores on a computer (default without -c arg is to use all avail.)
     tetrad -s data.snps.phy -c 20

  * Start an MPI cluster to connect to nodes across multiple available hosts.
     tetrad -s data.snps.phy --MPI     

  * Connect to a manually started ipcluster instance with default or named profile
     tetrad -s data.snps.phy --ipcluster        ## connects to default profile
     tetrad -s data.snps.phy --ipcluster pname  ## connects to profile='pname'

  * Further documentation: http://ipyrad.readthedocs.io/analysis.html
    """)


    ## get version from ipyrad 
    ipyversion = str(pkg_resources.get_distribution('ipyrad'))
    parser.add_argument('-v', '--version', action='version', 
        version="tetrad "+ipyversion.split()[1])

    parser.add_argument('-f', "--force", action='store_true',
        help="force overwrite of existing data")

    parser.add_argument('-s', metavar="seq", dest="seq",
        type=str, default=None,
        help="path to input phylip file (only SNPs)")

    parser.add_argument('-j', metavar='json', dest="json",
        type=str, default=None,
        help="load checkpointed/saved analysis from JSON file.")

    parser.add_argument('-m', metavar="method", dest="method",
        type=str, default="all",
        help="method for sampling quartets (all, random, or equal)")

    parser.add_argument('-q', metavar="nquartets", dest="nquartets",
        type=int, default=0,
        help="number of quartets to sample (if not -m all)")

    parser.add_argument('-b', metavar="boots", dest="boots",
        type=int, default=0,
        help="number of non-parametric bootstrap replicates")

    parser.add_argument('-l', metavar="map_file", dest="map",
        type=str, default=None,
        help="map file of snp linkages (e.g., ipyrad .snps.map)")

    parser.add_argument('-r', metavar="resolve", dest='resolve', 
        type=int, default=1, 
        help="randomly resolve heterozygous sites (default=1)")

    parser.add_argument('-n', metavar="name", dest="name",
        type=str, default="test",
        help="output name prefix (default: 'test')")

    parser.add_argument('-o', metavar="workdir", dest="workdir",
        type=str, default="./analysis-tetrad",
        help="output directory (default: creates ./analysis-tetrad)")

    parser.add_argument('-t', metavar="starting_tree", dest="tree",
        type=str, default=None,
        help="newick file starting tree for equal splits sampling")

    parser.add_argument("-c", metavar="CPUs/cores", dest="cores",
        type=int, default=0,
        help="setting -c improves parallel efficiency with --MPI")

    parser.add_argument("-x", metavar="random_seed", dest="rseed",
        type=int, default=None,
        help="random seed for quartet sampling and/or bootstrapping")    

    parser.add_argument('-d', "--debug", action='store_true',
        help="print lots more info to debugger: ipyrad_log.txt.")

    parser.add_argument("--MPI", action='store_true',
        help="connect to parallel CPUs across multiple nodes")

    parser.add_argument("--invariants", action='store_true',
        help="save a (large) database of all invariants")

    parser.add_argument("--ipcluster", metavar="ipcluster", dest="ipcluster",
        type=str, nargs="?", const="default",
        help="connect to ipcluster profile (default: 'default')")

    ## if no args then return help message
    if len(sys.argv) == 1:
        parser.print_help()
        sys.exit(1)

    ## parse args
    args = parser.parse_args()

    ## RAISE errors right away for some bad argument combinations:
    if args.method not in ["random", "equal", "all"]:
        raise IPyradWarningExit("  method argument (-m) must be one of"+\
        """ "all", "random", or "equal.\n""")

    ## if 'random' require nquarts argument
    #if args.method == 'random':
    #    if not args.nquartets:
    #        raise IPyradWarningExit(\
    #        "  Number of quartets (-q) is required with method = random\n")

    ## if 'equal' method require starting tree and nquarts
    # if args.method == 'equal':
    #     raise IPyradWarningExit(\
    #         "  The equal sampling method is currently for developers only.\n")
    #     if not args.nquartets:
    #         raise IPyradWarningExit(\
    #         "  Number of quartets (-q) is required with method = equal\n")
    #     if not args.tree:
    #         raise IPyradWarningExit(\
    #         "  Input guide tree (-t) is required with method = equal\n")

    ## required args
    if not any(x in ["seq", "json"] for x in vars(args).keys()):
        print("""
    Bad arguments: tetrad command must include at least one of (-s or -j) 
    """)
        parser.print_help()
        sys.exit(1)

    return args
def parse_command_line ( ) : ## create the parser parser = argparse . ArgumentParser ( formatter_class = argparse . RawDescriptionHelpFormatter , epilog = """
  * Example command-line usage ---------------------------------------------- 

  * Read in sequence/SNP data file, provide linkage, output name, ambig option. 
     tetrad -s data.snps.phy -n test             ## input phylip and give name
     tetrad -s data.snps.phy -l data.snps.map    ## sample one SNP per locus
     tetrad -s data.snps.phy -n noambigs -r 0    ## do not use hetero sites

  * Load saved/checkpointed analysis from '.tet.json' file, or force restart. 
     tetrad -j test.tet.json -b 100         ## continue 'test' until 100 boots
     tetrad -j test.tet.json -b 100 -f      ## force restart of 'test'

  * Sampling modes: 'equal' uses guide tree to sample quartets more efficiently 
     tetrad -s data.snps.phy -m all                       ## sample all quartets
     tetrad -s data.snps.phy -m random -q 1e6 -x 123      ## sample 1M randomly
     tetrad -s data.snps.phy -m equal -q 1e6 -t guide.tre ## sample 1M across tree

  * Connect to N cores on a computer (default without -c arg is to use all avail.)
     tetrad -s data.snps.phy -c 20

  * Start an MPI cluster to connect to nodes across multiple available hosts.
     tetrad -s data.snps.phy --MPI     

  * Connect to a manually started ipcluster instance with default or named profile
     tetrad -s data.snps.phy --ipcluster        ## connects to default profile
     tetrad -s data.snps.phy --ipcluster pname  ## connects to profile='pname'

  * Further documentation: http://ipyrad.readthedocs.io/analysis.html
    """ ) ## get version from ipyrad  ipyversion = str ( pkg_resources . get_distribution ( 'ipyrad' ) ) parser . add_argument ( '-v' , '--version' , action = 'version' , version = "tetrad " + ipyversion . split ( ) [ 1 ] ) parser . add_argument ( '-f' , "--force" , action = 'store_true' , help = "force overwrite of existing data" ) parser . add_argument ( '-s' , metavar = "seq" , dest = "seq" , type = str , default = None , help = "path to input phylip file (only SNPs)" ) parser . add_argument ( '-j' , metavar = 'json' , dest = "json" , type = str , default = None , help = "load checkpointed/saved analysis from JSON file." ) parser . add_argument ( '-m' , metavar = "method" , dest = "method" , type = str , default = "all" , help = "method for sampling quartets (all, random, or equal)" ) parser . add_argument ( '-q' , metavar = "nquartets" , dest = "nquartets" , type = int , default = 0 , help = "number of quartets to sample (if not -m all)" ) parser . add_argument ( '-b' , metavar = "boots" , dest = "boots" , type = int , default = 0 , help = "number of non-parametric bootstrap replicates" ) parser . add_argument ( '-l' , metavar = "map_file" , dest = "map" , type = str , default = None , help = "map file of snp linkages (e.g., ipyrad .snps.map)" ) parser . add_argument ( '-r' , metavar = "resolve" , dest = 'resolve' , type = int , default = 1 , help = "randomly resolve heterozygous sites (default=1)" ) parser . add_argument ( '-n' , metavar = "name" , dest = "name" , type = str , default = "test" , help = "output name prefix (default: 'test')" ) parser . add_argument ( '-o' , metavar = "workdir" , dest = "workdir" , type = str , default = "./analysis-tetrad" , help = "output directory (default: creates ./analysis-tetrad)" ) parser . add_argument ( '-t' , metavar = "starting_tree" , dest = "tree" , type = str , default = None , help = "newick file starting tree for equal splits sampling" ) parser . add_argument ( "-c" , metavar = "CPUs/cores" , dest = "cores" , type = int , default = 0 , help = "setting -c improves parallel efficiency with --MPI" ) parser . add_argument ( "-x" , metavar = "random_seed" , dest = "rseed" , type = int , default = None , help = "random seed for quartet sampling and/or bootstrapping" ) parser . add_argument ( '-d' , "--debug" , action = 'store_true' , help = "print lots more info to debugger: ipyrad_log.txt." ) parser . add_argument ( "--MPI" , action = 'store_true' , help = "connect to parallel CPUs across multiple nodes" ) parser . add_argument ( "--invariants" , action = 'store_true' , help = "save a (large) database of all invariants" ) parser . add_argument ( "--ipcluster" , metavar = "ipcluster" , dest = "ipcluster" , type = str , nargs = "?" , const = "default" , help = "connect to ipcluster profile (default: 'default')" ) ## if no args then return help message if len ( sys . argv ) == 1 : parser . print_help ( ) sys . exit ( 1 ) ## parse args args = parser . parse_args ( ) ## RAISE errors right away for some bad argument combinations: if args . method not in [ "random" , "equal" , "all" ] : raise IPyradWarningExit ( "  method argument (-m) must be one of" + """ "all", "random", or "equal.\n""" ) ## if 'random' require nquarts argument #if args.method == 'random': #    if not args.nquartets: #        raise IPyradWarningExit(\ #        "  Number of quartets (-q) is required with method = random\n") ## if 'equal' method require starting tree and nquarts # if args.method == 'equal': #     raise IPyradWarningExit(\ #         "  The equal sampling method is currently for developers only.\n") #     if not args.nquartets: #         raise IPyradWarningExit(\ #         "  Number of quartets (-q) is required with method = equal\n") #     if not args.tree: #         raise IPyradWarningExit(\ #         "  Input guide tree (-t) is required with method = equal\n") ## required args if not any ( x in [ "seq" , "json" ] for x in vars ( args ) . keys ( ) ) : print ( """
    Bad arguments: tetrad command must include at least one of (-s or -j) 
    """ ) parser . print_help ( ) sys . exit ( 1 ) return args
Parse CLI args. Only three options now.
Parse CLI args . Only three options now .