parser.add_argument('--plotcache', action='store_true')
parser.add_argument('--only-print', action='store_true')
parser.add_argument('--check', action='store_true')
parser.add_argument('--dryrun', action='store_true')
parser.add_argument('--label', default='xxx')
parser.add_argument('--ete-path', default='/home/' + os.getenv('USER') + '/anaconda_ete/bin')
args = parser.parse_args()
args.methods = sorted(utils.get_arg_list(args.methods))
args.v_genes = utils.get_arg_list(args.v_genes)
args.n_event_list = utils.get_arg_list(args.n_event_list, intify=True)
if args.print_table and args.action == 'data': # only want to print table for single samples
assert not args.sample_vs_sample and not args.method_vs_method
# ----------------------------------------------------------------------------------------
alfdir = utils.fsdir() + '/partis/allele-finder'
baseoutdir = alfdir
if args.label is not None:
baseoutdir += '/' + args.label
baseoutdir += '/' + args.action
if args.varvals is None:
args.varvals = default_varvals[args.action]
kwargs = {}
if args.action == 'mfreq' or args.action == 'prevalence' or args.action == 'n-leaves' or args.action == 'weibull':
kwargs['floatify'] = True
if args.action == 'nsnp':
kwargs['intify'] = True
if args.action != 'alcluster': # could also do this for data i think, if i remove that line up there ^
args.varvals = utils.get_arg_list(args.varvals, **kwargs)
if args.action == 'multi-nsnp':
parser.add_argument('--indel-positions', help='see --snp-positions (a.t.m. the indel length distributions are hardcoded)')
parser.add_argument('--nindel-list', help='see --nsnp-list')
parser.add_argument('--n-genes-per-region', default=glutils.default_n_genes_per_region, help='see bin/partis --help')
parser.add_argument('--n-sim-alleles-per-gene', default=glutils.default_n_alleles_per_gene, help='see bin/partis --help')
parser.add_argument('--min-allele-prevalence-freq', default=glutils.default_min_allele_prevalence_freq, type=float, help='see bin/partis --help')
parser.add_argument('--allele-prevalence-freqs', help='colon-separated list of allele prevalence frequencies, including newly-generated snpd genes (ordered alphabetically)')
parser.add_argument('--dont-remove-template-genes', action='store_true', help='when generating snps, remove the original gene before simulation') # NOTE template gene removal is the default for glutils.generate_germline_set
parser.add_argument('--mut-mult', type=float, help='see bin/partis --help')
parser.add_argument('--slurm', action='store_true')
parser.add_argument('--overwrite', action='store_true')
parser.add_argument('--dry-run', action='store_true')
parser.add_argument('--allele-cluster', action='store_true', help='see bin/partis --help')
parser.add_argument('--kmeans-allele-cluster', action='store_true', help='see bin/partis --help')
parser.add_argument('--plot-annotation-performance', action='store_true', help='see bin/partis --help')
parser.add_argument('--methods', default='simu:partis', help='colon-separated list of methods to run. By default runs simulation, and then partis inference (igdiscover and tigger, if installed, are the other options)')
parser.add_argument('--outdir', default=utils.fsdir() + '/partis/allele-finder')
parser.add_argument('--inf-glfo-dir', help='default set below')
parser.add_argument('--simfname', help='default set below')
parser.add_argument('--workdir', default=utils.fsdir() + '/_tmp/hmms/' + str(random.randint(0, 999999)))
parser.add_argument('--n-tests', type=int, help='instead of just running once, run <N> independent tests simultaneously')
parser.add_argument('--iteststart', type=int, default=0, help='for use with --n-tests, if you want to add more tests on')
parser.add_argument('--plot-and-fit-absolutely-everything', type=int, help='fit every single position for this <istart> and write every single corresponding plot (slow as hell, and only for debugging/making plots for paper)')
parser.add_argument('--partis-path', default='./bin/partis')
parser.add_argument('--species', default='human', choices=('human', 'macaque'))
parser.add_argument('--locus', default='igh')
args = parser.parse_args()
assert args.locus == 'igh' # would just need to update some things, e.g. propagate through to the various methods
args.dj_genes = utils.get_arg_list(args.dj_genes)
args.sim_v_genes = utils.get_arg_list(args.sim_v_genes)
args.inf_v_genes = utils.get_arg_list(args.inf_v_genes)
action='store_true',
help='see bin/partis --help')
parser.add_argument('--kmeans-allele-cluster',
action='store_true',
help='see bin/partis --help')
parser.add_argument('--plot-annotation-performance',
action='store_true',
help='see bin/partis --help')
parser.add_argument(
'--methods',
default='simu:partis',
help=
'colon-separated list of methods to run. By default runs simulation, and then partis inference (igdiscover and tigger, if installed, are the other options)'
)
parser.add_argument('--outdir',
default=utils.fsdir() + '/partis/allele-finder')
parser.add_argument('--inf-glfo-dir', help='default set below')
parser.add_argument('--simfname', help='default set below')
parser.add_argument('--workdir',
default=utils.fsdir() + '/_tmp/hmms/' +
str(random.randint(0, 999999)))
parser.add_argument(
'--n-tests',
type=int,
help=
'instead of just running once, run <N> independent tests simultaneously')
parser.add_argument(
'--iteststart',
type=int,
default=0,
help='for use with --n-tests, if you want to add more tests on')
