Converts character data (e.g., dna) from one format to another using dendropy

convert_characters.py

#!/usr/bin/env python

# convert_characters.py -- by Jonathan Chang (March 2013)

import argparse
import os.path
import multiprocessing
import functools

import dendropy

def get_args():
    parser = argparse.ArgumentParser(description="convert character data from one format to another")

    formats = "nexus phylip fasta".split()
    types = "dna rna protein standard restriction infinite".split()

    parser.add_argument("files", nargs="+", help="list of file(s) to convert")

    required = parser.add_argument_group("required arguments")
    required.add_argument("--input-format", "-i", choices=formats, help="input format", required=True)
    required.add_argument("--output-format", "-o", choices=formats, help="output format. also used as the extension for the output files", required=True)
    required.add_argument("--type", "-t", default="dna", help="data type. ignored for nexus input. (default: dna)", choices=types)

    parser.add_argument("--prefix", default="", help="string to prepend to the output files.")
    parser.add_argument("--basename", action="store_true", help="strips away any leading directory entries. useful when specifying a prefix that is a different directory.")
    parser.add_argument("--quiet", action="store_true", help="don't send messages to stdout")

    return parser.parse_args()

def convert(filename, args):
    parsed = dendropy.CharacterMatrix.get_from_path(filename, args.input_format, data_type=args.type)
    if args.basename:
        filename = os.path.basename(filename)
    # replace extension.
    name, ext = list(os.path.splitext(filename))
    ext = args.output_format
    newname = args.prefix + ".".join([name, ext])
    parsed.write_to_path(newname, args.output_format)
    print newname


def main():
    args = get_args()
    pool = multiprocessing.Pool()
    partial = functools.partial(convert, args=args)
    pool.map(partial, args.files)

if __name__ == "__main__":
    main()