def test_combine_with_character_labels(self):
n1 = NexusReader()
n1.read_string(
"""
BEGIN DATA;
DIMENSIONS NTAX=3 NCHAR=3;
FORMAT DATATYPE=STANDARD MISSING=0 GAP=- SYMBOLS="123";
CHARSTATELABELS
1 char1,
2 char2,
3 char3
;
MATRIX
Tax1 123
Tax2 123
Tax3 123
;
"""
)
n2 = NexusReader()
n2.read_string(
"""
BEGIN DATA;
DIMENSIONS NTAX=3 NCHAR=3;
FORMAT DATATYPE=STANDARD MISSING=0 GAP=- SYMBOLS="456";
CHARSTATELABELS
1 char1,
2 char2,
3 char3
;
MATRIX
Tax1 456
Tax2 456
Tax3 456
;
"""
)
newnex = combine_nexuses([n1, n2])
assert re.search(r"""\bNTAX=3\b""", newnex.write())
assert re.search(r"""\bNCHAR=6\b""", newnex.write())
assert re.search(r'\sSYMBOLS="123456"[\s;]', newnex.write())
for tax in [1,2,3]:
assert re.search(r"""\bTax%d\s+123456\b""" % tax, newnex.write())
counter = 1
for nex_id in [1,2]:
for char_id in [1,2,3]:
assert re.search(
r"""\b%d\s+%d.char%d\b""" % (counter, nex_id, char_id),
newnex.write(charblock=True)
)
counter += 1
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(
usage="usage: %prog [-o output.nex] nex1.nex nex2.nex ... nexN.nex"
)
parser.add_option("-o", "--output", dest="output",
action="store", default=None, type="string",
help="output nexus file")
options, nexuslist = parser.parse_args()
if len(nexuslist) < 1:
print(__doc__)
parser.print_help()
sys.exit()
if options.output is not None:
outfile = options.output
else:
outfile = 'multistate.nex'
nexuslist2 = []
for nfile in nexuslist:
n = NexusReader(nfile)
n = multistatise(n)
nexuslist2.append(n)
out = combine_nexuses(nexuslist2)
out.write_to_file(outfile, charblock=True, interleave=False)
print("Written to %s" % outfile)
parser = OptionParser(
usage="usage: %prog [-o output.nex] nex1.nex nex2.nex ... nexN.nex")
parser.add_option("-o",
"--output",
dest="output",
action="store",
default=None,
type="string",
help="output nexus file")
options, nexuslist = parser.parse_args()
if len(nexuslist) < 1:
print __doc__
parser.print_help()
sys.exit()
if options.output is not None:
outfile = options.output
else:
outfile = 'multistate.nex'
nexuslist2 = []
for nfile in nexuslist:
n = NexusReader(nfile)
n = multistatise(n)
nexuslist2.append(n)
out = combine_nexuses(nexuslist2)
out.write_to_file(outfile, charblock=True, interleave=False)
print("Written to %s" % outfile)
def run(args):
write_output(combine_nexuses(get_reader(args, many=True)), args)
def test_combine_missing_generated_formatline(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert re.search(r"""\bNTAX=4\b""", newnex.write())
assert re.search(r"""\bNCHAR=2\b""", newnex.write())
assert re.search(r'\sSYMBOLS="12345"[\s;]', newnex.write())
def test_combine_missing_generated_matrix(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert re.search(r"""\bSimon\s+25\b""", newnex.write())
assert re.search(r"""\bHarry\s+1\\?\b""", newnex.write())
assert re.search(r"""\bBetty\s+\?3\b""", newnex.write())
assert re.search(r"""\bBoris\s+\?4\b""", newnex.write())
def test_combine_missing(self):
newnex = combine_nexuses([self.nex1, self.nex3])
assert newnex.data['1.1']['Harry'] == '1'
assert newnex.data['1.1']['Simon'] == '2'
assert newnex.data['2.1']['Betty'] == '3'
assert newnex.data['2.1']['Boris'] == '4'
def test_combine_simple_generated_matrix(self):
newnex = combine_nexuses([self.nex1, self.nex2])
assert re.search(r"""\bSimon\s+24\b""", newnex.write())
assert re.search(r"""\bHarry\s+13\b""", newnex.write())
def test_combine_simple(self):
newnex = combine_nexuses([self.nex1, self.nex2])
assert newnex.data['1.1']['Harry'] == '1'
assert newnex.data['1.1']['Simon'] == '2'
assert newnex.data['2.1']['Harry'] == '3'
assert newnex.data['2.1']['Simon'] == '4'
def run(args):
nexuslist = [
multistatise.multistatise(n) for n in get_reader(args, many=True)
]
write_output(combine_nexuses(nexuslist), args)
