# Path: alfpy/wmetric.py
# def count_seq_chars(seq, alphabet):
# def freq_seq_chars(counts):
# def freq_seqs_chars(seq_records, alphabet):
#     def __init__(self, seq_records, matrix):
#     def pairwise_distance(self, seqnum1, seqnum2):
# 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/utils/data/subsmat.py
# class SubsMat:
#     def __init__(self, name, data, alphabet_list):
# def get_alphabet_list(name):
# def get(name):
# def list_subsmats():
# def main():
# 
# Path: alfpy/version.py



import argparse
import sys
from alfpy import wmetric
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.utils.data import subsmat
from alfpy.version import __version__
    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    group.add_argument('--matrix', '-m', choices=l,
                       help='choose from: {} [DEFAULT: %(default)s]'.format(
                           ", ".join(l)), metavar='',
                       default="blosum62")

    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()
    try:

# Path: alfpy/wmetric.py
# def count_seq_chars(seq, alphabet):
# def freq_seq_chars(counts):
# def freq_seqs_chars(seq_records, alphabet):
#     def __init__(self, seq_records, matrix):
#     def pairwise_distance(self, seqnum1, seqnum2):
# 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/utils/data/subsmat.py
# class SubsMat:
#     def __init__(self, name, data, alphabet_list):
# def get_alphabet_list(name):
# def get(name):
# def list_subsmats():
# def main():
# 
# Path: alfpy/version.py



# Path: bin/calc_wmetric.py
import argparse
import sys
from alfpy import wmetric
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.utils.data import subsmat
from alfpy.version import __version__

    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    group.add_argument('--matrix', '-m', choices=l,
                       help='choose from: {} [DEFAULT: %(default)s]'.format(
                           ", ".join(l)), metavar='',
                       default="blosum62")

    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()
    try:

        args.matrix = subsmat.get(args.matrix)