# Path: alfpy/lempelziv.py
# def complexity(s):
# def complexity1(seq):
# def is_reproducible(seq, index, hist_len, last_match=0):
#     def __init__(self, seq_records, disttype='d1_star'):
#     def __precompute_complexity(self):
#     def __get_complexity(self, seq1idx, seq2idx):
#     def pwdist_d(self, seq1idx, seq2idx):
#     def pwdist_d_star(self, seq1idx, seq2idx):
#     def pwdist_d1(self, seq1idx, seq2idx):
#     def pwdist_d1_star(self, seq1idx, seq2idx):
#     def pwdist_d1_star2(self, seq1idx, seq2idx):
#     def set_disttype(self, disttype):
# def main():
# class Distance:
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():
# 
# Path: alfpy/utils/seqrecords.py
# class SeqRecords:
#     def __init__(self, id_list=None, seq_list=None):
#     def add(self, seqid, seq):
#     def fasta(self, wrap=70):
#     def length_list(self):
#     def __iter__(self):
#     def __len__(self):
#     def __repr__(self):
# def read_fasta(handle):
# def main():
# 
# Path: alfpy/version.py



import argparse
import sys
from alfpy import lempelziv
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.version import __version__

    group = parser.add_argument_group('OUTPUT ARGUMENTS')
    group.add_argument('--out', '-o', help="output filename",
                       metavar="FILE")
    group.add_argument('--outfmt', choices=['phylip', 'pairwise'],
                       default='phylip',
                       help='distances output format [DEFAULT: %(default)s]')

    group = parser.add_argument_group("OTHER OPTIONS")
    group.add_argument("-h", "--help", action="help",
                       help="show this help message and exit")
    group.add_argument('--version', action='version',
                       version='%(prog)s {}'.format(__version__))

    if len(sys.argv[1:]) == 0:
        # parser.print_help()
        parser.print_usage()
        parser.exit()
    return parser


def validate_args(parser):
    args = parser.parse_args()
    return args


def main():
    parser = get_parser()
    args = validate_args(parser)


# Path: alfpy/lempelziv.py
# def complexity(s):
# def complexity1(seq):
# def is_reproducible(seq, index, hist_len, last_match=0):
#     def __init__(self, seq_records, disttype='d1_star'):
#     def __precompute_complexity(self):
#     def __get_complexity(self, seq1idx, seq2idx):
#     def pwdist_d(self, seq1idx, seq2idx):
#     def pwdist_d_star(self, seq1idx, seq2idx):
#     def pwdist_d1(self, seq1idx, seq2idx):
#     def pwdist_d1_star(self, seq1idx, seq2idx):
#     def pwdist_d1_star2(self, seq1idx, seq2idx):
#     def set_disttype(self, disttype):
# def main():
# class Distance:
# 
# Path: alfpy/utils/distmatrix.py
# def create(id_list, distance):
# def read_highcharts_matrix(id_list, data):
#     def __init__(self, id_list, data):
#     def normalize(self):
#     def __iter__(self):
#     def writer(self, handle, f, decimal_places):
#     def display(self, f="phylip", decimal_places=7):
#     def write_to_file(self, handle, f="phylip", decimal_places=7):
#     def highcharts(self):
#     def format(self, decimal_places=7):
#     def min(self):
#     def max(self):
#     def is_zero(self):
#     def __repr__(self):
# class Matrix():
# 
# Path: alfpy/utils/seqrecords.py
# class SeqRecords:
#     def __init__(self, id_list=None, seq_list=None):
#     def add(self, seqid, seq):
#     def fasta(self, wrap=70):
#     def length_list(self):
#     def __iter__(self):
#     def __len__(self):
#     def __repr__(self):
# def read_fasta(handle):
# def main():
# 
# Path: alfpy/version.py



# Path: bin/calc_lempelziv.py
import argparse
import sys
from alfpy import lempelziv
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.version import __version__


    group = parser.add_argument_group('OUTPUT ARGUMENTS')
    group.add_argument('--out', '-o', help="output filename",
                       metavar="FILE")
    group.add_argument('--outfmt', choices=['phylip', 'pairwise'],
                       default='phylip',
                       help='distances output format [DEFAULT: %(default)s]')

    group = parser.add_argument_group("OTHER OPTIONS")
    group.add_argument("-h", "--help", action="help",
                       help="show this help message and exit")
    group.add_argument('--version', action='version',
                       version='%(prog)s {}'.format(__version__))

    if len(sys.argv[1:]) == 0:
        # parser.print_help()
        parser.print_usage()
        parser.exit()
    return parser


def validate_args(parser):
    args = parser.parse_args()
    return args


def main():
    parser = get_parser()
    args = validate_args(parser)


    seq_records = seqrecords.read_fasta(args.fasta)