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))