# Path: alfpy/word_pattern.py
# class Pattern:
#     def __init__(self, pat_list, occr_list, pos_list=None):
#     def _alfree_format(self):
#     def _teiresias_format(self):
#     def format(self, formattype=None):
#     def reduce_alphabet(self, alphabet_dict):
#     def merge_revcomp(self):
#         def revcomp(s):
#     def __repr__(self):
#     def __str__(self):
# def _create_wordpattern(seq_list, k):
# def _create_wordpattern_positions(seq_list, k):
# def create(seq_list, word_size=1, wordpos=False):
# def create_from_fasta(handle, word_size=1, wordpos=False):
# def create_from_bigfasta(filename, k=1):
# def run_teiresias(input_filename, w=2, l=2, k=2, output_filename=None):
# def read(handle):
# def main():
# 
# 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_pattern
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', '-w', required=True, type=int,
                       metavar="k", help='word size (>=1)')

    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    group.add_argument('--word_position', '-p', action="store_true",
                       help='''report word positions in output''')
    group.add_argument('--out', '-o', help="output pattern filename",
                       metavar="FILE")

    t = '  Teiresias options'
    d = '  more info @ https://cm.jefferson.edu/data-tools-downloads/'
    d += 'teiresias-code/\n'
    group = parser.add_argument_group(t, d)
    group.add_argument('--teiresias', '-t', action="store_true",
                       help='''Teiresias program creates word patterns.
                       [by default: disabled]''',
                       )
    group.add_argument('--l', '-l', type=int,
                       help='minimum number of literals and/or brackets')
    group.add_argument('--k', '-k', type=int,
                       help='minimum support that any word can have')

    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',

# Path: alfpy/word_pattern.py
# class Pattern:
#     def __init__(self, pat_list, occr_list, pos_list=None):
#     def _alfree_format(self):
#     def _teiresias_format(self):
#     def format(self, formattype=None):
#     def reduce_alphabet(self, alphabet_dict):
#     def merge_revcomp(self):
#         def revcomp(s):
#     def __repr__(self):
#     def __str__(self):
# def _create_wordpattern(seq_list, k):
# def _create_wordpattern_positions(seq_list, k):
# def create(seq_list, word_size=1, wordpos=False):
# def create_from_fasta(handle, word_size=1, wordpos=False):
# def create_from_bigfasta(filename, k=1):
# def run_teiresias(input_filename, w=2, l=2, k=2, output_filename=None):
# def read(handle):
# def main():
# 
# 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/create_wordpattern.py
import argparse
import sys
from alfpy import word_pattern
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', '-w', required=True, type=int,
                       metavar="k", help='word size (>=1)')

    group = parser.add_argument_group('OPTIONAL ARGUMENTS')
    group.add_argument('--word_position', '-p', action="store_true",
                       help='''report word positions in output''')
    group.add_argument('--out', '-o', help="output pattern filename",
                       metavar="FILE")

    t = '  Teiresias options'
    d = '  more info @ https://cm.jefferson.edu/data-tools-downloads/'
    d += 'teiresias-code/\n'
    group = parser.add_argument_group(t, d)
    group.add_argument('--teiresias', '-t', action="store_true",
                       help='''Teiresias program creates word patterns.
                       [by default: disabled]''',
                       )
    group.add_argument('--l', '-l', type=int,
                       help='minimum number of literals and/or brackets')
    group.add_argument('--k', '-k', type=int,
                       help='minimum support that any word can have')

    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__))