for w in wrapper.wrap(s):
print w
print
return
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog [taxa/sites] nexus.nex")
options, commands = parser.parse_args()
if len(commands) != 2:
print __doc__
parser.print_help()
quit()
command, nex = commands
try:
nex = NexusReader(nex)
except IOError:
raise IOError("Unable to read %s" % nex)
if command in ('taxa', 't'):
tally = tally_by_taxon(nex)
elif command in ('site', 's'):
tally = tally_by_site(nex)
else:
quit("Invalid tally command. Only 'taxa' and 'site' are valid.")
print_tally(tally)
for i in sorted(tally):
print("%d\t%d" % (i, tally[i]))
return
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog [taxa/sites/binary] nexus.nex")
options, commands = parser.parse_args()
if len(commands) != 2:
print(__doc__)
print("Author: %s\n" % __author__)
parser.print_help()
quit()
command, nex = commands
try:
nex = NexusReader(nex)
except IOError:
raise IOError("Unable to read %s" % nex)
if command in ('taxa', 't'):
print_tally(tally_by_taxon(nex))
elif command in ('site', 's'):
print_tally(tally_by_site(nex))
elif command in ('binary', 'b'):
print_binary(count_binary_set_size(nex))
else:
quit("Invalid tally command. Only 'taxa' and 'site' are valid.")
for w in wrapper.wrap(s):
print w
print
return
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog [taxa/sites] nexus.nex")
options, commands = parser.parse_args()
if len(commands) != 2:
print __doc__
parser.print_help()
quit()
command, nex = commands
try:
nex = NexusReader(nex)
except IOError:
raise IOError("Unable to read %s" % nex)
if command in ('taxa', 't'):
tally = tally_by_taxon(nex)
elif command in ('site', 's'):
tally = tally_by_site(nex)
else:
quit("Invalid tally command. Only 'taxa' and 'site' are valid.")
print_tally(tally)
print("%d\t%d" % (i, tally[i]))
return
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog [taxa/sites/binary] nexus.nex")
options, commands = parser.parse_args()
if len(commands) != 2:
print(__doc__)
print("Author: %s\n" % __author__)
parser.print_help()
quit()
command, nex = commands
try:
nex = NexusReader(nex)
except IOError:
raise IOError("Unable to read %s" % nex)
if command in ('taxa', 't'):
print_tally(tally_by_taxon(nex))
elif command in ('site', 's'):
print_tally(tally_by_site(nex))
elif command in ('binary', 'b'):
print_binary(count_binary_set_size(nex))
else:
quit("Invalid tally command. Only 'taxa' and 'site' are valid.")