def nex():
res = NexusReader.from_string("""
Begin data;
Dimensions ntax=3 nchar=2;
Format datatype=standard symbols="01" gap=-;
Charstatelabels
1 char1, 2 char2;
Matrix
Maori 14
Dutch 25
Latin 36
;""")
return binarise(res)
def setUp(self):
self.nex = NexusReader()
self.nex.read_string("""
Begin data;
Dimensions ntax=3 nchar=2;
Format datatype=standard symbols="01" gap=-;
Charstatelabels
1 char1, 2 char2;
Matrix
Maori 14
Dutch 25
Latin 36
;""")
self.nex = binarise(self.nex)
def setUp(self):
self.nex = NexusReader()
self.nex.read_string("""
Begin data;
Dimensions ntax=3 nchar=2;
Format datatype=standard symbols="01" gap=-;
Charstatelabels
1 char1, 2 char2;
Matrix
Maori 14
Dutch 25
Latin 36
;""")
self.nex = binarise(self.nex)
def test_to_binary_alphabetical():
"""Test Nexus -> Binary: alphabetical states"""
nex = binarise(
NexusReader.from_string("""
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=5 NCHAR=2;
FORMAT MISSING=? GAP=- SYMBOLS="ABCDE";
CHARSTATELABELS
1 ALL,
2 ASHES
;
MATRIX
Mehri AB
Geto AB
Walani A-
Hebrew A(C,D)
Soqotri BC
;
END;
"""))
nexus = nex.make_nexus(charblock=True, interleave=False)
assert re.search(r"\s+NCHAR=5;", nexus)
assert re.search(r"1\s+ALL_A,", nexus)
assert re.search(r"2\s+ALL_B,", nexus)
assert re.search(r"3\s+ASHES_B,", nexus)
assert re.search(r"4\s+ASHES_C,", nexus)
assert re.search(r"5\s+ASHES_D", nexus)
assert re.search(r"Geto\s+10100", nexus)
assert re.search(r"Hebrew\s+10011", nexus)
assert re.search(r"Mehri\s+10100", nexus)
assert re.search(r"Soqotri\s+01010", nexus)
assert re.search(r"Walani\s+10000", nexus)
#!/usr/bin/env python
import sys
from nexus import NexusReader, VERSION
from nexus.tools.binarise import binarise
__author__ = 'Simon Greenhill <*****@*****.**>'
__doc__ = """nexus_multistate2binary - python-nexus tools v%(version)s
Converts multistate nexuses to binary present/absent form.
""" % {
'version': VERSION,
}
if __name__ == '__main__':
#set up command-line options
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog old.nex new.nex")
options, args = parser.parse_args()
try:
nexusname = args[0]
newnexusname = args[1]
except IndexError:
print(__doc__)
print("Author: %s\n" % __author__)
parser.print_help()
sys.exit()
new = binarise(NexusReader(nexusname))
new.write_to_file(newnexusname)
if __name__ == '__main__':
#set up command-line options
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog old.nex new.nex")
parser.add_option("-1", "--onefile", dest="onefile",
action="store_true", default=False,
help="One nexus file for each multistate character")
options, args = parser.parse_args()
try:
nexusname = args[0]
newnexusname = args[1]
except IndexError:
print(__doc__)
print("Author: %s\n" % __author__)
parser.print_help()
sys.exit()
new = binarise(NexusReader(nexusname), one_nexus_per_block=options.onefile)
if isinstance(new, NexusWriter):
new.write_to_file(newnexusname)
elif len(new) > 1:
newnexusname, ext = os.path.splitext(newnexusname)
for nex in new:
nex.write_to_file("%s-%s%s" %
(newnexusname, nex.clean(nex.characters[0]), ext)
)
def run(args):
write_output(binarise(get_reader(args)), args)
