def run(args):
nexus = get_reader(args)
if args.number:
print_site_values(nexus)
return 0
if args.stats:
print_character_stats(nexus)
return 0
const, unique, zeros, remove = [], [], [], []
if args.constant:
const = list(iter_constant_sites(nexus))
if const:
args.log.info("Constant Sites: %s" %
",".join([str(i + 1) for i in const]))
if args.unique:
unique = list(iter_unique_sites(nexus))
if unique:
args.log.info("Unique Sites: %s" %
",".join([str(i + 1) for i in unique]))
if args.zeros:
zeros = check_zeros(nexus)
if zeros:
args.log.info("Zero Sites: %s" %
",".join([str(i + 1) for i in zeros]))
if args.remove:
args.log.info("Remove: %s" % ",".join([str(i) for i in args.remove]))
remove = [i - 1
for i in args.remove] # translate to zero-based indices.
write_output(
new_nexus_without_sites(nexus, set(const + unique + zeros + remove)),
args)
def run(args):
nexus_obj = get_reader(args, required_blocks=['data'])
print(nexus_obj.filename)
with Table(args, 'Taxon', 'Characters') as t:
for taxon in sorted(nexus_obj.data.matrix):
tally = collections.Counter()
for site in nexus_obj.data.matrix[taxon]:
tally.update([site])
t.append([
taxon,
", ".join(['%s x %s' % (k, tally[k]) for k in sorted(tally)])
])
def run(args):
checkers = CHECKERS['base']
if args.extra:
checkers.extend(CHECKERS['extra'])
if args.ascertainment:
checkers.extend(CHECKERS['ascertainment'])
with warnings.catch_warnings(record=True) as warned:
warnings.simplefilter("always")
nex = get_reader(args)
if len(warned):
print("Warnings encountered in reading nexus:")
for w in warned:
print("\t%s" % w)
for checker in checkers:
checker(nex).status()
def run(args):
nexus = get_reader(args, required_blocks=['trees'])
args.log.info("{0} trees found with {1} translated taxa".format(
nexus.trees.ntrees, len(nexus.trees.translators)))
if args.deltree:
nexus = delete_trees(nexus, args.deltree, log=args.log)
if args.resample:
nexus = sample_trees(nexus, every_nth=args.resample, log=args.log)
if args.random:
nexus = sample_trees(nexus, num_trees=args.random, log=args.log)
if args.removecomments:
nexus = strip_comments_in_trees(nexus, log=args.log)
if args.detranslate:
nexus.trees.detranslate()
write_output(nexus, args)
def test_get_reader(monkeypatch):
monkeypatch.setattr(
'sys.stdin', io.StringIO('#NEXUS\n\nbegin trees;\ntree t = ();\nend;'))
with pytest.raises(ParserError):
get_reader(argparse.Namespace(filename=None), required_blocks=['data'])
def run(args):
write_output(shufflenexus(get_reader(args), args.numchars or False), args)
def run(args):
print_character_stats(get_reader(args, required_blocks=['data']), args.site_index)
def run(args):
printer = print_binary if args.type == 'binary' else print_tally
printer(TALLY_TYPES[args.type](get_reader(args)))
def run(args):
write_output(binarise(get_reader(args)), args)
def run(args):
write_output(combine_nexuses(get_reader(args, many=True)), args)
def run(args):
write_output(get_reader(args), args)
def run(args):
nexuslist = [
multistatise.multistatise(n) for n in get_reader(args, many=True)
]
write_output(combine_nexuses(nexuslist), args)
