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)
except IndexError:
newnexusname = None
nexus = NexusReader(nexusname)
newnexus = None
if options.number:
if newnexusname is not None:
print_site_values(nexus, newnexusname)
else:
print_site_values(nexus)
elif options.constant:
const = find_constant_sites(nexus)
newnexus = new_nexus_without_sites(nexus, const)
print("Constant Sites: %s" % ",".join([str(i) for i in const]))
elif options.unique:
unique = find_unique_sites(nexus)
newnexus = new_nexus_without_sites(nexus, unique)
print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
elif options.stats:
d = print_character_stats(nexus)
else:
exit()
# check for saving
if newnexus is not None and newnexusname is not None:
newnexus.write_to_file(newnexusname)
print("New nexus written to %s" % newnexusname)
def test_remove_sites_list(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
nexus = new_nexus_without_sites(nexus, [1])
assert len(nexus.data) == 1
newnexusname = args[1]
except IndexError:
newnexusname = None
nexus = NexusReader(nexusname)
newnexus = None
if options.number:
if newnexusname is not None:
print_site_values(nexus, newnexusname)
else:
print_site_values(nexus)
elif options.constant:
const = find_constant_sites(nexus)
newnexus = new_nexus_without_sites(nexus, const)
print("Constant Sites: %s" % ",".join([str(i) for i in const]))
elif options.unique:
unique = find_unique_sites(nexus)
newnexus = new_nexus_without_sites(nexus, unique)
print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
elif options.stats:
d = print_character_stats(nexus)
else:
exit()
# check for saving
if newnexus is not None and newnexusname is not None:
newnexus.write_to_file(newnexusname)
print("New nexus written to %s" % newnexusname)
def test_remove_sites_1(self):
nexus = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
nexus = new_nexus_without_sites(nexus, [1])
assert len(nexus.data) == 1
if options.number:
print_site_values(nexus)
exit()
if options.stats:
print_character_stats(nexus)
exit()
const, unique, zeros, remove = [], [], [], []
if options.constant:
const = find_constant_sites(nexus)
print("Constant Sites: %s" % ",".join([str(i) for i in const]))
if options.unique:
unique = find_unique_sites(nexus)
print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
if options.zeros:
zeros = check_zeros(nexus)
print("Zero Sites: %s" % ",".join([str(i) for i in zeros]))
if options.remove:
remove = [int(i) for i in parse_deltree(options.remove)]
print("Remove: %s" % ",".join([str(i) for i in zeros]))
newnexus = new_nexus_without_sites(nexus, set(const + unique + zeros + remove))
# check for saving
if newnexus is not None and newnexusname is not None:
newnexus.write_to_file(newnexusname)
print("New nexus written to %s" % newnexusname)
newnexus = None
if options.number:
print_site_values(nexus)
exit()
if options.stats:
print_character_stats(nexus)
exit()
const, unique, zeros, remove = [], [], [], []
if options.constant:
const = find_constant_sites(nexus)
print("Constant Sites: %s" % ",".join([str(i) for i in const]))
if options.unique:
unique = find_unique_sites(nexus)
print("Unique Sites: %s" % ",".join([str(i) for i in unique]))
if options.zeros:
zeros = check_zeros(nexus)
print("Zero Sites: %s" % ",".join([str(i) for i in zeros]))
if options.remove:
remove = [int(i) for i in parse_deltree(options.remove)]
print("Remove: %s" % ",".join([str(i) for i in zeros]))
newnexus = new_nexus_without_sites(nexus, set(const + unique + zeros + remove))
# check for saving
if newnexus is not None and newnexusname is not None:
newnexus.write_to_file(newnexusname)
print("New nexus written to %s" % newnexusname)
def test_remove_sites_set(nex):
nexus = new_nexus_without_sites(nex, set([1]))
assert len(nexus.data) == 1
def test_remove_sites_list(nex):
nexus = new_nexus_without_sites(nex, [1])
assert len(nexus.data) == 1