# Path: alfpy/word_sets_distance.py
# def _getwords(seq, word_size):
#     def __init__(self, seq_records, word_size, disttype='jaccard'):
#     def pwdist_jaccard(self, seq1idx, seq2idx):
#     def pwdist_dice(self, seq1idx, seq2idx):
#     def pwdist_hamming(self, seq1idx, seq2idx):
# 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 word_sets_distance
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.version import __version__
    group = parser.add_argument_group('REQUIRED ARGUMENTS')
    group.add_argument('--fasta', '-f',
                       help='input FASTA sequence filename', required=True,
                       type=argparse.FileType('r'), metavar="FILE")
    group.add_argument('--word_size', '-s', metavar="N", required=True,
                       help='word size for creating word patterns',
                       type=int)

    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    distlist = ['dice', 'hamming', 'jaccard']
    group.add_argument('--distance', '-d', choices=distlist,
                       help='choose from: {} [DEFAULT: %(default)s]'.format(
                           ", ".join(distlist)),
                       metavar='', default="dice")

    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()

# Path: alfpy/word_sets_distance.py
# def _getwords(seq, word_size):
#     def __init__(self, seq_records, word_size, disttype='jaccard'):
#     def pwdist_jaccard(self, seq1idx, seq2idx):
#     def pwdist_dice(self, seq1idx, seq2idx):
#     def pwdist_hamming(self, seq1idx, seq2idx):
# 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_word_sets.py
import argparse
import sys
from alfpy import word_sets_distance
from alfpy.utils import distmatrix
from alfpy.utils import seqrecords
from alfpy.version import __version__

    group = parser.add_argument_group('REQUIRED ARGUMENTS')
    group.add_argument('--fasta', '-f',
                       help='input FASTA sequence filename', required=True,
                       type=argparse.FileType('r'), metavar="FILE")
    group.add_argument('--word_size', '-s', metavar="N", required=True,
                       help='word size for creating word patterns',
                       type=int)

    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    distlist = ['dice', 'hamming', 'jaccard']
    group.add_argument('--distance', '-d', choices=distlist,
                       help='choose from: {} [DEFAULT: %(default)s]'.format(
                           ", ".join(distlist)),
                       metavar='', default="dice")

    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()