def test_write_to_file(self):
tmp = NamedTemporaryFile(delete=False, suffix=".nex")
tmp.close()
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
nex.write_to_file(tmp.name)
assert os.path.isfile(tmp.name)
n2 = NexusReader(tmp.name)
assert n2.data.matrix == nex.data.matrix
assert sorted(n2.data.taxa) == sorted(nex.data.taxa)
os.unlink(tmp.name) # cleanup
def hash(salt, value):
return hashlib.md5(("%s-%s" % (salt, value)).encode('ascii')).hexdigest()
if __name__ == '__main__': # pragma: no cover
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog fudge.nex output.nex")
options, args = parser.parse_args()
try:
nexusname = args[0]
except IndexError:
print(__doc__)
print("Author: %s\n" % __author__)
parser.print_help()
sys.exit()
try:
newnexus = args[1]
except IndexError:
newnexus = None
nexus = NexusReader(nexusname)
nexus = anonymise(nexus)
if newnexus is not None:
nexus.write_to_file(newnexus)
print("New nexus written to %s" % newnexus)
else:
print(nexus.write_to_file(hash('filename', nexusname)))