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
print("%d trees found with %d translated taxa" %
(nexus.trees.ntrees, len(nexus.trees.translators)))
# Delete trees
if options.deltree:
nexus = run_deltree(options.deltree, nexus, options.quiet)
# Resample trees
if options.resample:
nexus = run_resample(options.resample, nexus, options.quiet)
# Randomly sample trees
if options.random:
nexus = run_random(options.random, nexus, options.quiet)
# remove comments
if options.removecomments:
nexus = run_removecomments(nexus, options.quiet)
# detranslate
if options.detranslate:
nexus = run_detranslate(nexus)
if newnexus is not None:
nexus.write_to_file(newnexus)
if not options.quiet:
print("New nexus with %d trees written to %s" %
(nexus.trees.ntrees, newnexus))
else:
print(nexus.write())
sys.exit("No trees found in found %s!" % nexusname)
if options.quiet is False:
print "%d trees found with %d translated taxa" % (nexus.trees.ntrees, len(nexus.trees.translators))
# Delete trees
if options.deltree:
nexus = run_deltree(options.deltree, nexus, options.quiet)
# Resample trees
if options.resample:
nexus = run_resample(options.resample, nexus, options.quiet)
# Randomly sample trees
if options.random:
nexus = run_random(options.random, nexus, options.quiet)
# remove comments
if options.removecomments:
nexus = run_removecomments(nexus, options.quiet)
# detranslate
if options.detranslate:
nexus = run_detranslate(nexus, options.quiet)
if newnexus is not None:
nexus.write_to_file(newnexus)
if options.quiet is False:
print "New nexus with %d trees written to %s" % (nexus.trees.ntrees, newnexus)
else:
print nexus.write()
def hash(salt, taxon):
return hashlib.md5("%s-%s" % (salt, taxon)).hexdigest()
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog fudge.nex output.nex")
options, nexuslist = 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', filename)))
def hash(salt, taxon):
return hashlib.md5("%s-%s" % (salt, taxon)).hexdigest()
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog fudge.nex output.nex")
options, nexuslist = 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', filename))