# Path: alfpy/fcgr.py
# def fcgr_vector(dnaseq, word_size):
# def create_vectors(seq_records, word_size):
#     def __init__(self, vector, disttype='euclid_norm'):
# def main():
# class Distance(distance.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 fcgr
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.version import __version__
                       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()
    if args.word_size < 1:
        parser.error('--word_size must be >= 1')
    return args


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

    seq_records = seqrecords.read_fasta(args.fasta)

    vector = fcgr.create_vectors(seq_records, args.word_size)

# Path: alfpy/fcgr.py
# def fcgr_vector(dnaseq, word_size):
# def create_vectors(seq_records, word_size):
#     def __init__(self, vector, disttype='euclid_norm'):
# def main():
# class Distance(distance.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_fcgr.py
import argparse
import sys
from alfpy import fcgr
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.version import __version__

                       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()
    if args.word_size < 1:
        parser.error('--word_size must be >= 1')
    return args


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

    seq_records = seqrecords.read_fasta(args.fasta)

    vector = fcgr.create_vectors(seq_records, args.word_size)

    dist = fcgr.Distance(vector)