# 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():


from alfpy.utils import seqrecords
    from .utils import seqrecords
    from .utils.data import seqcontent
    import subprocess
        import uuid
        import os
        k (int) : word size
        wordpos (bool) : record (True) or ignore (False) the word positions

    Returns:
        instance of Pattern

    Examples:
        >>> seqs = ['ATGC', 'CGCG', 'GCAT']
        >>> p = create(seqs, 1)
        >>> print(p)
        4   3   G 0:1 1:2 2:1
        4   3   C 0:1 1:2 2:1
        2   2   T 0:1 2:1
        2   2   A 0:1 2:1

        >>> p = create(seqs, 1, True)
        >>> print(p)
        4   3   G 0 2 1 1 1 3 2 0
        4   3   C 0 3 1 0 1 2 2 1
        2   2   T 0 1 2 3
        2   2   A 0 0 2 2

    """
    if wordpos:
        return _create_wordpattern_positions(seq_list, word_size)
    return _create_wordpattern(seq_list, word_size)


def create_from_fasta(handle, word_size=1, wordpos=False):
    """Create word patterns (Pattern object) from a FASTA file"""

# 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/word_pattern.py
from alfpy.utils import seqrecords
    from .utils import seqrecords
    from .utils.data import seqcontent
    import subprocess
        import uuid
        import os

        k (int) : word size
        wordpos (bool) : record (True) or ignore (False) the word positions

    Returns:
        instance of Pattern

    Examples:
        >>> seqs = ['ATGC', 'CGCG', 'GCAT']
        >>> p = create(seqs, 1)
        >>> print(p)
        4   3   G 0:1 1:2 2:1
        4   3   C 0:1 1:2 2:1
        2   2   T 0:1 2:1
        2   2   A 0:1 2:1

        >>> p = create(seqs, 1, True)
        >>> print(p)
        4   3   G 0 2 1 1 1 3 2 0
        4   3   C 0 3 1 0 1 2 2 1
        2   2   T 0 1 2 3
        2   2   A 0 0 2 2

    """
    if wordpos:
        return _create_wordpattern_positions(seq_list, word_size)
    return _create_wordpattern(seq_list, word_size)


def create_from_fasta(handle, word_size=1, wordpos=False):
    """Create word patterns (Pattern object) from a FASTA file"""

    seq_records = seqrecords.read_fasta(handle)