def main():
'''Function that will parse the given file and convert the tree to the
format specified'''
argParser = ArgumentParser(description='tree structured data converter')
argParser.add_argument('--file',
type=FileType('r'),
action='store',
dest='file',
required=True,
help='file to parse')
argParser.add_argument('--format',
type=str,
action='store',
default='string',
dest='format',
help='format to convert to, default = string')
options = argParser.parse_args()
tree_str = '\n'.join(options.file.readlines())
options.file.close()
node_parser = NewickParser()
tree = node_parser.parse(tree_str)
if options.format == 'xml':
writer = XmlNewickWriter()
elif options.format == 'relational':
writer = RelationalNewickWriter()
else:
writer = IndentedStringNewickWriter()
print(writer.write(tree))
def main():
arg_parser = ArgumentParser(description="Determine leaf branch " "lengths for Newick tree.")
arg_parser.add_argument(
"--file", type=FileType("r"), action="store", dest="file", required=True, help="Newick file to parse"
)
options = arg_parser.parse_args()
tree_str = "\n".join(options.file.readlines())
options.file.close()
node_parser = NewickParser()
tree = node_parser.parse(tree_str)
branch_lengths = compute_branch_lengths(tree)
for taxa, length in list(branch_lengths.items()):
print("{taxa}: {length}".format(taxa=taxa, length=length))
def main():
arg_parser = ArgumentParser(description='Determine leaf branch '
'lengths for Newick tree.')
arg_parser.add_argument('--file',
type=FileType('r'),
action='store',
dest='file',
required=True,
help='Newick file to parse')
options = arg_parser.parse_args()
tree_str = '\n'.join(options.file.readlines())
options.file.close()
node_parser = NewickParser()
tree = node_parser.parse(tree_str)
branch_lengths = compute_branch_lengths(tree)
for taxa, length in list(branch_lengths.items()):
print('{taxa}: {length}'.format(taxa=taxa, length=length))
def main():
'''Function that will parse the given file and convert the tree to the
format specified'''
argParser = ArgumentParser(description='tree structured data converter')
argParser.add_argument('--file', type=FileType('r'), action='store',
dest='file', required=True,
help='file to parse')
argParser.add_argument('--format', type=str, action='store',
default='string', dest='format',
help='format to convert to, default = string')
options = argParser.parse_args()
tree_str = '\n'.join(options.file.readlines())
options.file.close()
node_parser = NewickParser()
tree = node_parser.parse(tree_str)
if options.format == 'xml':
writer = XmlNewickWriter()
elif options.format == 'relational':
writer = RelationalNewickWriter()
else:
writer = IndentedStringNewickWriter()
print(writer.write(tree))
