text: # Copyright 2000 Andrew Dalke.
  # Copyright 2000-2002 Brad Chapman.
  # Copyright 2004-2005, 2010 by M de Hoon.
  # Copyright 2007-2020 by Peter Cock.
  # All rights reserved.
  #
  # This file is part of the Biopython distribution and governed by your
  # choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
  # Please see the LICENSE file that should have been included as part of this
  # package.
  """Provide objects to represent biological sequences with alphabets.
  
  See also the Seq_ wiki and the chapter in our tutorial:
   - `HTML Tutorial`_
   - `PDF Tutorial`_
  
  .. _Seq: http://biopython.org/wiki/Seq
  .. _`HTML Tutorial`: http://biopython.org/DIST/docs/tutorial/Tutorial.html
  .. _`PDF Tutorial`: http://biopython.org/DIST/docs/tutorial/Tutorial.pdf
  
  """
  
  import array
  import sys
  import warnings
  
  from Bio import BiopythonWarning
  from Bio import Alphabet
  from Bio.Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
  from Bio.Data.IUPACData import ambiguous_dna_letters as _ambiguous_dna_letters
  from Bio.Data.IUPACData import ambiguous_rna_letters as _ambiguous_rna_letters
  from Bio.Data import CodonTable
  
  
  def _maketrans(complement_mapping):
      """Make a python string translation table (PRIVATE).
  
      Arguments:
       - complement_mapping - a dictionary such as ambiguous_dna_complement
         and ambiguous_rna_complement from Data.IUPACData.
  
      Returns a translation table (a string of length 256) for use with the
      python string's translate method to use in a (reverse) complement.
  
      Compatible with lower case and upper case sequences.
  
      For internal use only.
      """
      before = "".join(complement_mapping.keys())
      after = "".join(complement_mapping.values())
      before += before.lower()
      after += after.lower()
      return str.maketrans(before, after)
  
  
  _dna_complement_table = _maketrans(ambiguous_dna_complement)
  _rna_complement_table = _maketrans(ambiguous_rna_complement)
  
  
  class Seq:
      """Read-only sequence object (essentially a string with an alphabet).
  
      Like normal python strings, our basic sequence object is immutable.
      This prevents you from doing my_seq[5] = "A" for example, but does allow
      Seq objects to be used as dictionary keys.
  
      The Seq object provides a number of string like methods (such as count,
      find, split and strip), which are alphabet aware where appropriate.
  
      In addition to the string like sequence, the Seq object has an alphabet
      property. This is an instance of an Alphabet class from Bio.Alphabet,
      for example generic DNA, or IUPAC DNA. This describes the type of molecule
      (e.g. RNA, DNA, protein) and may also indicate the expected symbols
      (letters).
  
      The Seq object also provides some biological methods, such as complement,
      reverse_complement, transcribe, back_transcribe and translate (which are
      not applicable to sequences with a protein alphabet).
      """
  
      def __init__(self, data, alphabet=Alphabet.generic_alphabet):
          """Create a Seq object.
  
          Arguments:
           - seq - Sequence, required (string)
           - alphabet - Optional argument, an Alphabet object from
             Bio.Alphabet
  
          You will typically use Bio.SeqIO to read in sequences from files as
          SeqRecord objects, whose sequence will be exposed as a Seq object via
          the seq property.
  
          However, will often want to create your own Seq objects directly:
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF")
          >>> my_seq
          Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF')
          >>> print(my_seq)
          MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
          """
          # Enforce string storage
          if not isinstance(data, str):
              raise TypeError(
                  "The sequence data given to a Seq object should "
                  "be a string (not another Seq object etc)"
              )
          self._data = data
          self.alphabet = alphabet  # Seq API requirement
  
      def __repr__(self):
          """Return (truncated) representation of the sequence for debugging."""
          if len(self) > 60:
              # Shows the last three letters as it is often useful to see if
              # there is a stop codon at the end of a sequence.
              # Note total length is 54+3+3=60
              return f"{self.__class__.__name__}('{str(self)[:54]}...{str(self)[-3:]}')"
          else:
              return f"{self.__class__.__name__}({self._data!r})"
  
      def __str__(self):
          """Return the full sequence as a python string, use str(my_seq).
  
          Note that Biopython 1.44 and earlier would give a truncated
          version of repr(my_seq) for str(my_seq).  If you are writing code
          which need to be backwards compatible with really old Biopython,
          you should continue to use my_seq.tostring() as follows::
  
              try:
                  # The old way, removed in Biopython 1.73
                  as_string = seq_obj.tostring()
              except AttributeError:
                  # The new way, needs Biopython 1.45 or later.
                  # Don't use this on Biopython 1.44 or older as truncates
                  as_string = str(seq_obj)
  
          """
          return self._data
  
      def __hash__(self):
          """Hash of the sequence as a string (ignoring alphabet) for comparison.
  
          See Seq object comparison documentation (method ``__eq__`` in
          particular) as this has changed in Biopython 1.65. Older versions
          would hash on object identity.
          """
          return hash(str(self))
  
      def __eq__(self, other):
          """Compare the sequence to another sequence or a string (README).
  
          Historically comparing Seq objects has done Python object comparison.
          After considerable discussion (keeping in mind constraints of the
          Python language, hashes and dictionary support), Biopython now uses
          simple string comparison (with a warning about the change).
  
          If you still need to support releases prior to Biopython 1.65, please
          just do explicit comparisons:
  
          >>> from Bio.Seq import Seq
          >>> seq1 = Seq("ACGT")
          >>> seq2 = Seq("ACGT")
          >>> id(seq1) == id(seq2)
          False
          >>> str(seq1) == str(seq2)
          True
  
          The new behaviour is to use string-like equality:
  
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import generic_dna
          >>> seq1 == seq2
          True
          >>> seq1 == "ACGT"
          True
          >>> seq1 == Seq("ACGT", generic_dna)
          True
  
          """
          return str(self) == str(other)
  
      def __lt__(self, other):
          """Implement the less-than operand."""
          if isinstance(other, (str, Seq, MutableSeq)):
              return str(self) < str(other)
          raise TypeError(
              f"'<' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __le__(self, other):
          """Implement the less-than or equal operand."""
          if isinstance(other, (str, Seq, MutableSeq)):
              return str(self) <= str(other)
          raise TypeError(
              f"'<=' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __gt__(self, other):
          """Implement the greater-than operand."""
          if isinstance(other, (str, Seq, MutableSeq)):
              return str(self) > str(other)
          raise TypeError(
              f"'>' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __ge__(self, other):
          """Implement the greater-than or equal operand."""
          if isinstance(other, (str, Seq, MutableSeq)):
              return str(self) >= str(other)
          raise TypeError(
              f"'>=' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __len__(self):
          """Return the length of the sequence, use len(my_seq)."""
          return len(self._data)  # Seq API requirement
  
      def __getitem__(self, index):  # Seq API requirement
          """Return a subsequence of single letter, use my_seq[index].
  
          >>> my_seq = Seq('ACTCGACGTCG')
          >>> my_seq[5]
          'A'
          """
          if isinstance(index, int):
              # Return a single letter as a string
              return self._data[index]
          else:
              # Return the (sub)sequence as another Seq object
              return Seq(self._data[index])
  
      def __add__(self, other):
          """Add another sequence or string to this sequence.
  
          If adding a string to a Seq, the alphabet is preserved:
  
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import generic_protein
          >>> Seq("MELKI", generic_protein) + "LV"
          Seq('MELKILV')
  
          When adding two Seq (like) objects, if they share the
          same alphabet it is preserved, but otherwise discarded.
          This means you can add RNA and DNA, or nucleotide and
          protein if you really want to. This is a change as of
          Biopython 1.78, this previously raised a TypeError:
  
          >>> from Bio.Alphabet import generic_dna, generic_rna
          >>> Seq("ACGT", generic_dna) + Seq("ACGU", generic_rna)
          Seq('ACGTACGU')
  
          >>> from Bio.Alphabet import generic_dna, generic_protein
          >>> Seq("ACGT", generic_dna) + Seq("MELKI", generic_protein)
          Seq('ACGTMELKI')
          """
          if hasattr(other, "alphabet"):
              if other.alphabet == self.alphabet:
                  # Perfect match, preserve the alphabet
                  return self.__class__(str(self) + str(other), self.alphabet)
              else:
                  # Discard the alphabet
                  return self.__class__(str(self) + str(other))
          elif isinstance(other, str):
              # other is a plain string - use the current alphabet
              return self.__class__(str(self) + other, self.alphabet)
  
          from Bio.SeqRecord import SeqRecord  # Lazy to avoid circular imports
  
          if isinstance(other, SeqRecord):
              # Get the SeqRecord's __radd__ to handle this
              return NotImplemented
          else:
              raise TypeError
  
      def __radd__(self, other):
          """Add a sequence on the left.
  
          If adding a string to a Seq, the alphabet is preserved:
  
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import generic_protein
          >>> "LV" + Seq("MELKI", generic_protein)
          Seq('LVMELKI')
  
          Adding two Seq (like) objects is handled via the __add__ method.
          """
          if hasattr(other, "alphabet"):
              if other.alphabet == self.alphabet:
                  # Perfect match, preserve the alphabet
                  return self.__class__(str(other) + str(self), self.alphabet)
              else:
                  # Discard the alphabet
                  return self.__class__(str(other) + str(self))
          elif isinstance(other, str):
              # other is a plain string - use the current alphabet
              return self.__class__(other + str(self), self.alphabet)
          else:
              raise TypeError
  
      def __mul__(self, other):
          """Multiply Seq by integer.
  
          >>> from Bio.Seq import Seq
          >>> Seq('ATG') * 2
          Seq('ATGATG')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(str(self) * other)
  
      def __rmul__(self, other):
          """Multiply integer by Seq.
  
          >>> from Bio.Seq import Seq
          >>> 2 * Seq('ATG')
          Seq('ATGATG')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(str(self) * other)
  
      def __imul__(self, other):
          """Multiply Seq in-place.
  
          Note although Seq is immutable, the in-place method is
          included to match the behaviour for regular Python strings.
  
          >>> from Bio.Seq import Seq
          >>> seq = Seq('ATG')
          >>> seq *= 2
          >>> seq
          Seq('ATGATG')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(str(self) * other)
  
      def tomutable(self):  # Needed?  Or use a function?
          """Return the full sequence as a MutableSeq object.
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL")
          >>> my_seq
          Seq('MKQHKAMIVALIVICITAVVAAL')
          >>> my_seq.tomutable()
          MutableSeq('MKQHKAMIVALIVICITAVVAAL')
          """
          return MutableSeq(str(self))
  
      def count(self, sub, start=0, end=sys.maxsize):
          """Return a non-overlapping count, like that of a python string.
  
          This behaves like the python string method of the same name,
          which does a non-overlapping count!
  
          For an overlapping search use the newer count_overlap() method.
  
          Returns an integer, the number of occurrences of substring
          argument sub in the (sub)sequence given by [start:end].
          Optional arguments start and end are interpreted as in slice
          notation.
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          e.g.
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("AAAATGA")
          >>> print(my_seq.count("A"))
          5
          >>> print(my_seq.count("ATG"))
          1
          >>> print(my_seq.count(Seq("AT")))
          1
          >>> print(my_seq.count("AT", 2, -1))
          1
  
          HOWEVER, please note because python strings and Seq objects (and
          MutableSeq objects) do a non-overlapping search, this may not give
          the answer you expect:
  
          >>> "AAAA".count("AA")
          2
          >>> print(Seq("AAAA").count("AA"))
          2
  
          An overlapping search, as implemented in .count_overlap(),
          would give the answer as three!
          """
          return str(self).count(str(sub), start, end)
  
      def count_overlap(self, sub, start=0, end=sys.maxsize):
          """Return an overlapping count.
  
          For a non-overlapping search use the count() method.
  
          Returns an integer, the number of occurrences of substring
          argument sub in the (sub)sequence given by [start:end].
          Optional arguments start and end are interpreted as in slice
          notation.
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          e.g.
  
          >>> from Bio.Seq import Seq
          >>> print(Seq("AAAA").count_overlap("AA"))
          3
          >>> print(Seq("ATATATATA").count_overlap("ATA"))
          4
          >>> print(Seq("ATATATATA").count_overlap("ATA", 3, -1))
          1
  
          Where substrings do not overlap, should behave the same as
          the count() method:
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("AAAATGA")
          >>> print(my_seq.count_overlap("A"))
          5
          >>> my_seq.count_overlap("A") == my_seq.count("A")
          True
          >>> print(my_seq.count_overlap("ATG"))
          1
          >>> my_seq.count_overlap("ATG") == my_seq.count("ATG")
          True
          >>> print(my_seq.count_overlap(Seq("AT")))
          1
          >>> my_seq.count_overlap(Seq("AT")) == my_seq.count(Seq("AT"))
          True
          >>> print(my_seq.count_overlap("AT", 2, -1))
          1
          >>> my_seq.count_overlap("AT", 2, -1) == my_seq.count("AT", 2, -1)
          True
  
          HOWEVER, do not use this method for such cases because the
          count() method is much for efficient.
          """
          sub_str = str(sub)
          self_str = str(self)
          overlap_count = 0
          while True:
              start = self_str.find(sub_str, start, end) + 1
              if start != 0:
                  overlap_count += 1
              else:
                  return overlap_count
  
      def __contains__(self, char):
          """Implement the 'in' keyword, like a python string.
  
          e.g.
  
          >>> from Bio.Seq import Seq
          >>> my_dna = Seq("ATATGAAATTTGAAAA")
          >>> "AAA" in my_dna
          True
          >>> Seq("AAA") in my_dna
          True
          """
          return str(char) in str(self)
  
      def find(self, sub, start=0, end=sys.maxsize):
          """Find method, like that of a python string.
  
          This behaves like the python string method of the same name.
  
          Returns an integer, the index of the first occurrence of substring
          argument sub in the (sub)sequence given by [start:end].
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          Returns -1 if the subsequence is NOT found.
  
          e.g. Locating the first typical start codon, AUG, in an RNA sequence:
  
          >>> from Bio.Seq import Seq
          >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
          >>> my_rna.find("AUG")
          3
          """
          return str(self).find(str(sub), start, end)
  
      def rfind(self, sub, start=0, end=sys.maxsize):
          """Find from right method, like that of a python string.
  
          This behaves like the python string method of the same name.
  
          Returns an integer, the index of the last (right most) occurrence of
          substring argument sub in the (sub)sequence given by [start:end].
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          Returns -1 if the subsequence is NOT found.
  
          e.g. Locating the last typical start codon, AUG, in an RNA sequence:
  
          >>> from Bio.Seq import Seq
          >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
          >>> my_rna.rfind("AUG")
          15
          """
          return str(self).rfind(str(sub), start, end)
  
      def index(self, sub, start=0, end=sys.maxsize):
          """Like find() but raise ValueError when the substring is not found.
  
          >>> from Bio.Seq import Seq
          >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
          >>> my_rna.find("T")
          -1
          >>> my_rna.index("T")
          Traceback (most recent call last):
                     ...
          ValueError: substring not found...
          """
          return str(self).index(str(sub), start, end)
  
      def rindex(self, sub, start=0, end=sys.maxsize):
          """Like rfind() but raise ValueError when the substring is not found."""
          return str(self).rindex(str(sub), start, end)
  
      def startswith(self, prefix, start=0, end=sys.maxsize):
          """Return True if the Seq starts with the given prefix, False otherwise.
  
          This behaves like the python string method of the same name.
  
          Return True if the sequence starts with the specified prefix
          (a string or another Seq object), False otherwise.
          With optional start, test sequence beginning at that position.
          With optional end, stop comparing sequence at that position.
          prefix can also be a tuple of strings to try.  e.g.
  
          >>> from Bio.Seq import Seq
          >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
          >>> my_rna.startswith("GUC")
          True
          >>> my_rna.startswith("AUG")
          False
          >>> my_rna.startswith("AUG", 3)
          True
          >>> my_rna.startswith(("UCC", "UCA", "UCG"), 1)
          True
          """
          if isinstance(prefix, tuple):
              prefix_strs = tuple(str(p) for p in prefix)
              return str(self).startswith(prefix_strs, start, end)
          else:
              return str(self).startswith(str(prefix), start, end)
  
      def endswith(self, suffix, start=0, end=sys.maxsize):
          """Return True if the Seq ends with the given suffix, False otherwise.
  
          This behaves like the python string method of the same name.
  
          Return True if the sequence ends with the specified suffix
          (a string or another Seq object), False otherwise.
          With optional start, test sequence beginning at that position.
          With optional end, stop comparing sequence at that position.
          suffix can also be a tuple of strings to try.  e.g.
  
          >>> from Bio.Seq import Seq
          >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
          >>> my_rna.endswith("UUG")
          True
          >>> my_rna.endswith("AUG")
          False
          >>> my_rna.endswith("AUG", 0, 18)
          True
          >>> my_rna.endswith(("UCC", "UCA", "UUG"))
          True
          """
          if isinstance(suffix, tuple):
              suffix_strs = tuple(str(p) for p in suffix)
              return str(self).endswith(suffix_strs, start, end)
          else:
              return str(self).endswith(str(suffix), start, end)
  
      def split(self, sep=None, maxsplit=-1):
          """Split method, like that of a python string.
  
          This behaves like the python string method of the same name.
  
          Return a list of the 'words' in the string (as Seq objects),
          using sep as the delimiter string.  If maxsplit is given, at
          most maxsplit splits are done.  If maxsplit is omitted, all
          splits are made.
  
          Following the python string method, sep will by default be any
          white space (tabs, spaces, newlines) but this is unlikely to
          apply to biological sequences.
  
          e.g.
  
          >>> from Bio.Seq import Seq
          >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG")
          >>> my_aa = my_rna.translate()
          >>> my_aa
          Seq('VMAIVMGR*KGAR*L')
          >>> for pep in my_aa.split("*"):
          ...     pep
          Seq('VMAIVMGR')
          Seq('KGAR')
          Seq('L')
          >>> for pep in my_aa.split("*", 1):
          ...     pep
          Seq('VMAIVMGR')
          Seq('KGAR*L')
  
          See also the rsplit method:
  
          >>> for pep in my_aa.rsplit("*", 1):
          ...     pep
          Seq('VMAIVMGR*KGAR')
          Seq('L')
          """
          return [Seq(part) for part in str(self).split(str(sep), maxsplit)]
  
      def rsplit(self, sep=None, maxsplit=-1):
          """Do a right split method, like that of a python string.
  
          This behaves like the python string method of the same name.
  
          Return a list of the 'words' in the string (as Seq objects),
          using sep as the delimiter string.  If maxsplit is given, at
          most maxsplit splits are done COUNTING FROM THE RIGHT.
          If maxsplit is omitted, all splits are made.
  
          Following the python string method, sep will by default be any
          white space (tabs, spaces, newlines) but this is unlikely to
          apply to biological sequences.
  
          e.g. print(my_seq.rsplit("*",1))
  
          See also the split method.
          """
          return [Seq(part) for part in str(self).rsplit(str(sep), maxsplit)]
  
      def strip(self, chars=None):
          """Return a new Seq object with leading and trailing ends stripped.
  
          This behaves like the python string method of the same name.
  
          Optional argument chars defines which characters to remove.  If
          omitted or None (default) then as for the python string method,
          this defaults to removing any white space.
  
          e.g. print(my_seq.strip("-"))
  
          See also the lstrip and rstrip methods.
          """
          return Seq(str(self).strip(str(chars)))
  
      def lstrip(self, chars=None):
          """Return a new Seq object with leading (left) end stripped.
  
          This behaves like the python string method of the same name.
  
          Optional argument chars defines which characters to remove.  If
          omitted or None (default) then as for the python string method,
          this defaults to removing any white space.
  
          e.g. print(my_seq.lstrip("-"))
  
          See also the strip and rstrip methods.
          """
          return Seq(str(self).lstrip(str(chars)))
  
      def rstrip(self, chars=None):
          """Return a new Seq object with trailing (right) end stripped.
  
          This behaves like the python string method of the same name.
  
          Optional argument chars defines which characters to remove.  If
          omitted or None (default) then as for the python string method,
          this defaults to removing any white space.
  
          e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail):
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA")
          >>> my_seq
          Seq('CGGTACGCTTATGTCACGTAGAAAAAA')
          >>> my_seq.rstrip("A")
          Seq('CGGTACGCTTATGTCACGTAG')
  
          See also the strip and lstrip methods.
          """
          return Seq(str(self).rstrip(str(chars)))
  
      def upper(self):
          """Return an upper case copy of the sequence.
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("VHLTPeeK*")
          >>> my_seq
          Seq('VHLTPeeK*')
          >>> my_seq.lower()
          Seq('vhltpeek*')
          >>> my_seq.upper()
          Seq('VHLTPEEK*')
          """
          return Seq(str(self).upper())
  
      def lower(self):
          """Return a lower case copy of the sequence.
  
          >>> from Bio.Seq import Seq
          >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA")
          >>> my_seq
          Seq('CGGTACGCTTATGTCACGTAGAAAAAA')
          >>> my_seq.lower()
          Seq('cggtacgcttatgtcacgtagaaaaaa')
  
          See also the upper method.
          """
          return Seq(str(self).lower())
  
      def encode(self, encoding="utf-8", errors="strict"):
          """Return an encoded version of the sequence as a bytes object.
  
          The Seq object aims to match the interface of a Python string.
  
          This is essentially to save you doing str(my_seq).encode() when
          you need a bytes string, for example for computing a hash:
  
          >>> from Bio.Seq import Seq
          >>> Seq("ACGT").encode("ascii")
          b'ACGT'
          """
          return str(self).encode(encoding, errors)
  
      def complement(self):
          """Return the complement sequence by creating a new Seq object.
  
          This method is intended for use with DNA sequences:
  
          >>> from Bio.Seq import Seq
          >>> my_dna = Seq("CCCCCGATAG")
          >>> my_dna
          Seq('CCCCCGATAG')
          >>> my_dna.complement()
          Seq('GGGGGCTATC')
  
          You can of course used mixed case sequences,
  
          >>> from Bio.Seq import Seq
          >>> my_dna = Seq("CCCCCgatA-GD")
          >>> my_dna
          Seq('CCCCCgatA-GD')
          >>> my_dna.complement()
          Seq('GGGGGctaT-CH')
  
          Note in the above example, ambiguous character D denotes
          G, A or T so its complement is H (for C, T or A).
  
          Note that if the sequence contains neither T nor U, we
          assume it is DNA and map any A character to T:
  
          >>> Seq("CGA").complement()
          Seq('GCT')
          >>> Seq("CGAT").complement()
          Seq('GCTA')
  
          If you actually have RNA, this currently works but we
          may deprecate this later. We recommend using the new
          complement_rna method instead:
  
          >>> Seq("CGAU").complement()
          Seq('GCUA')
          >>> Seq("CGAU").complement_rna()
          Seq('GCUA')
  
          If the sequence contains both T and U, an exception is
          raised:
  
          >>> Seq("CGAUT").complement()
          Traceback (most recent call last):
             ...
          ValueError: Mixed RNA/DNA found
  
          Trying to complement a protein sequence gives a meaningless
          sequence:
  
          >>> from Bio.Alphabet import generic_protein
          >>> my_protein = Seq("MAIVMGR", generic_protein)
          >>> my_protein.complement()
          Seq('KTIBKCY')
  
          Here "M" was interpretted as the IUPAC ambiguity code for
          "A" or "C", with complement "K" for "T" or "G". Likewise
          "A" has complement "T". The letter "I" has no defined
          meaning under the IUPAC convention, and is unchanged.
          """
          if ("U" in self._data or "u" in self._data) and (
              "T" in self._data or "t" in self._data
          ):
              # TODO - Handle this cleanly?
              raise ValueError("Mixed RNA/DNA found")
          elif "U" in self._data or "u" in self._data:
              ttable = _rna_complement_table
          else:
              ttable = _dna_complement_table
          # Much faster on really long sequences than the previous loop based
          # one. Thanks to Michael Palmer, University of Waterloo.
          return Seq(str(self).translate(ttable))
  
      def reverse_complement(self):
          """Return the reverse complement sequence by creating a new Seq object.
  
          This method is intended for use with DNA sequences:
  
          >>> from Bio.Seq import Seq
          >>> my_dna = Seq("CCCCCGATAGNR")
          >>> my_dna
          Seq('CCCCCGATAGNR')
          >>> my_dna.reverse_complement()
          Seq('YNCTATCGGGGG')
  
          Note in the above example, since R = G or A, its complement
          is Y (which denotes C or T).
  
          You can of course used mixed case sequences,
  
          >>> from Bio.Alphabet import generic_dna
          >>> from Bio.Seq import Seq
          >>> my_dna = Seq("CCCCCgatA-G", generic_dna)
          >>> my_dna
          Seq('CCCCCgatA-G')
          >>> my_dna.reverse_complement()
          Seq('C-TatcGGGGG')
  
          As discussed for the complement method, if the sequence
          contains neither T nor U, is is assumed to be DNA and
          will map any letter A to T.
  
          If you are dealing with RNA you should use the new
          reverse_complement_rna method instead
  
          >>> Seq("CGA").reverse_complement()  # defaults to DNA
          Seq('TCG')
          >>> Seq("CGA").reverse_complement_rna()
          Seq('UCG')
  
          If the sequence contains both T and U, an exception is raised:
  
          >>> Seq("CGAUT").reverse_complement()
          Traceback (most recent call last):
             ...
          ValueError: Mixed RNA/DNA found
  
          Trying to reverse complement a protein sequence will give
          a meaningless sequence:
  
          >>> from Bio.Alphabet import generic_protein
          >>> from Bio.Seq import Seq
          >>> my_protein = Seq("MAIVMGR", generic_protein)
          >>> my_protein.reverse_complement()
          Seq('YCKBITK')
  
          Here "M" was interpretted as the IUPAC ambiguity code for
          "A" or "C", with complement "K" for "T" or "G" - and so on.
          """
          # Use -1 stride/step to reverse the complement
          return self.complement()[::-1]
  
      def complement_rna(self):
          """Complement of an RNA sequence.
  
          >>> Seq("CGA").complement()  # defaults to DNA
          Seq('GCT')
          >>> Seq("CGA").complement_rna()
          Seq('GCU')
  
          If the sequence contains both T and U, an exception is raised:
  
          >>> Seq("CGAUT").complement_rna()
          Traceback (most recent call last):
             ...
          ValueError: Mixed RNA/DNA found
  
          If the sequence contains T, an exception is raised:
  
          >>> Seq("ACGT").complement_rna()
          Traceback (most recent call last):
             ...
          ValueError: DNA found, RNA expected
          """
          if "T" in self._data or "t" in self._data:
              if "U" in self._data or "u" in self._data:
                  raise ValueError("Mixed RNA/DNA found")
              else:
                  raise ValueError("DNA found, RNA expected")
          return Seq(str(self).translate(_rna_complement_table))
  
      def reverse_complement_rna(self):
          """Reverse complement of an RNA sequence.
  
          >>> from Bio.Seq import Seq
          >>> Seq("ACG").reverse_complement_rna()
          Seq('CGU')
          """
          # Use -1 stride/step to reverse the complement
          return self.complement_rna()[::-1]
  
      def transcribe(self):
          """Return the RNA sequence from a DNA sequence by creating a new Seq object.
  
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import generic_dna
          >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG",
          ...                  generic_dna)
          >>> coding_dna
          Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG')
          >>> coding_dna.transcribe()
          Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG')
  
          Trying to transcribe an RNA sequence should have no effect.
          If you have a nucleotide sequence which might be DNA or RNA
          (or even a mixture), calling the transcribe method will ensure
          any T becomes U.
  
          Trying to transcribe a protein sequence will replace any
          T for Threonine with U for Selenocysteine, which has no
          biologically plausible rational. Older versions of Biopython
          would throw an exception.
  
          >>> from Bio.Alphabet import generic_protein
          >>> from Bio.Seq import Seq
          >>> my_protein = Seq("MAIVMGRT", generic_protein)
          >>> my_protein.transcribe()
          Seq('MAIVMGRU')
          """
          return Seq(str(self).replace("T", "U").replace("t", "u"))
  
      def back_transcribe(self):
          """Return the DNA sequence from an RNA sequence by creating a new Seq object.
  
          >>> from Bio.Alphabet import generic_rna
          >>> from Bio.Seq import Seq
          >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG",
          ...                     generic_rna)
          >>> messenger_rna
          Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG')
          >>> messenger_rna.back_transcribe()
          Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG')
  
          Trying to back-transcribe DNA has no effect, If you have a nucleotide
          sequence which might be DNA or RNA (or even a mixture), calling the
          back-transcribe method will ensure any T becomes U.
  
          Trying to back-transcribe a protein sequence will replace any U for
          Selenocysteine with T for Threonine, which is biologically meaningless.
          Older versions of Biopython would raise an exception here:
  
          >>> from Bio.Alphabet import generic_protein
          >>> from Bio.Seq import Seq
          >>> my_protein = Seq("MAIVMGRU", generic_protein)
          >>> my_protein.back_transcribe()
          Seq('MAIVMGRT')
          """
          return Seq(str(self).replace("U", "T").replace("u", "t"))
  
      def translate(
          self, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap="-"
      ):
          """Turn a nucleotide sequence into a protein sequence by creating a new Seq object.
  
          This method will translate DNA or RNA sequences, and those with a
          nucleotide or generic alphabet.  Trying to translate a protein
          sequence raises an exception.
  
          Arguments:
           - table - Which codon table to use?  This can be either a name
             (string), an NCBI identifier (integer), or a CodonTable
             object (useful for non-standard genetic codes).  This
             defaults to the "Standard" table.
           - stop_symbol - Single character string, what to use for
             terminators.  This defaults to the asterisk, "*".
           - to_stop - Boolean, defaults to False meaning do a full
             translation continuing on past any stop codons (translated as the
             specified stop_symbol).  If True, translation is terminated at
             the first in frame stop codon (and the stop_symbol is not
             appended to the returned protein sequence).
           - cds - Boolean, indicates this is a complete CDS.  If True,
             this checks the sequence starts with a valid alternative start
             codon (which will be translated as methionine, M), that the
             sequence length is a multiple of three, and that there is a
             single in frame stop codon at the end (this will be excluded
             from the protein sequence, regardless of the to_stop option).
             If these tests fail, an exception is raised.
           - gap - Single character string to denote symbol used for gaps.
             Defaults to the minus sign.
  
          e.g. Using the standard table:
  
          >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG")
          >>> coding_dna.translate()
          Seq('VAIVMGR*KGAR*')
          >>> coding_dna.translate(stop_symbol="@")
          Seq('VAIVMGR@KGAR@')
          >>> coding_dna.translate(to_stop=True)
          Seq('VAIVMGR')
  
          Now using NCBI table 2, where TGA is not a stop codon:
  
          >>> coding_dna.translate(table=2)
          Seq('VAIVMGRWKGAR*')
          >>> coding_dna.translate(table=2, to_stop=True)
          Seq('VAIVMGRWKGAR')
  
          In fact, GTG is an alternative start codon under NCBI table 2, meaning
          this sequence could be a complete CDS:
  
          >>> coding_dna.translate(table=2, cds=True)
          Seq('MAIVMGRWKGAR')
  
          It isn't a valid CDS under NCBI table 1, due to both the start codon
          and also the in frame stop codons:
  
          >>> coding_dna.translate(table=1, cds=True)
          Traceback (most recent call last):
              ...
          Bio.Data.CodonTable.TranslationError: First codon 'GTG' is not a start codon
  
          If the sequence has no in-frame stop codon, then the to_stop argument
          has no effect:
  
          >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC")
          >>> coding_dna2.translate()
          Seq('LAIVMGR')
          >>> coding_dna2.translate(to_stop=True)
          Seq('LAIVMGR')
  
          NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
          or a stop codon.  These are translated as "X".  Any invalid codon
          (e.g. "TA?" or "T-A") will throw a TranslationError.
  
          NOTE - This does NOT behave like the python string's translate
          method.  For that use str(my_seq).translate(...) instead.
          """
          if isinstance(table, str) and len(table) == 256:
              raise ValueError(
                  "The Seq object translate method DOES NOT take "
                  "a 256 character string mapping table like "
                  "the python string object's translate method. "
                  "Use str(my_seq).translate(...) instead."
              )
          try:
              table_id = int(table)
          except ValueError:
              # Assume its a table name
              # This will use the extended IUPAC protein alphabet with X etc.
              # The same table can be used for RNA or DNA (we use this for
              # translating strings).
              codon_table = CodonTable.ambiguous_generic_by_name[table]
          except (AttributeError, TypeError):
              # Assume its a CodonTable object
              if isinstance(table, CodonTable.CodonTable):
                  codon_table = table
              else:
                  raise ValueError("Bad table argument") from None
          else:
              # Assume its a table ID
              # This will use the extended IUPAC protein alphabet with X etc.
              # The same table can be used for RNA or DNA (we use this for
              # translating strings).
              codon_table = CodonTable.ambiguous_generic_by_id[table_id]
  
          return Seq(
              _translate_str(str(self), codon_table, stop_symbol, to_stop, cds, gap=gap)
          )
  
      def ungap(self, gap="-"):
          """Return a copy of the sequence without the gap character(s).
  
          The gap character now defaults to the minus sign, and can only
          be specified via the method argument. This is no longer possible
          via sequence's alphabet (as was possible up to Biopython 1.77):
  
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import generic_dna
          >>> my_dna = Seq("-ATA--TGAAAT-TTGAAAA", generic_dna)
          >>> my_dna
          Seq('-ATA--TGAAAT-TTGAAAA')
          >>> my_dna.ungap("-")
          Seq('ATATGAAATTTGAAAA')
          """
          if hasattr(self.alphabet, "gap_char"):
              raise NotImplementedError("We stopped supporting the Gapped class...")
          elif not gap:
              raise ValueError("Gap character required.")
          elif len(gap) != 1 or not isinstance(gap, str):
              raise ValueError(f"Unexpected gap character, {gap!r}")
          return Seq(str(self).replace(gap, ""))
  
      def join(self, other):
          """Return a merge of the sequences in other, spaced by the sequence from self.
  
          Accepts either a Seq or string (and iterates over the letters), or an
          iterable containing Seq or string objects. These arguments will be
          concatenated with the calling sequence as the spacer:
  
          >>> concatenated = Seq('NNNNN').join([Seq("AAA"), Seq("TTT"), Seq("PPP")])
          >>> concatenated
          Seq('AAANNNNNTTTNNNNNPPP')
  
          Joining the letters of a single sequence:
  
          >>> Seq('NNNNN').join(Seq("ACGT"))
          Seq('ANNNNNCNNNNNGNNNNNT')
          >>> Seq('NNNNN').join("ACGT")
          Seq('ANNNNNCNNNNNGNNNNNT')
          """
          if isinstance(other, (str, Seq, MutableSeq)):
              return self.__class__(str(self).join(str(other)))
  
          from Bio.SeqRecord import SeqRecord  # Lazy to avoid circular imports
  
          if isinstance(other, SeqRecord):
              raise TypeError("Iterable cannot be a SeqRecord")
  
          for c in other:
              if isinstance(c, SeqRecord):
                  raise TypeError("Iterable cannot contain SeqRecords")
              elif not isinstance(c, (str, Seq, MutableSeq)):
                  raise TypeError("Input must be an iterable of Seqs or Strings")
          return self.__class__(str(self).join([str(_) for _ in other]))
  
  
  class UnknownSeq(Seq):
      """Read-only sequence object of known length but unknown contents.
  
      If you have an unknown sequence, you can represent this with a normal
      Seq object, for example:
  
      >>> my_seq = Seq("N"*5)
      >>> my_seq
      Seq('NNNNN')
      >>> len(my_seq)
      5
      >>> print(my_seq)
      NNNNN
  
      However, this is rather wasteful of memory (especially for large
      sequences), which is where this class is most useful:
  
      >>> unk_five = UnknownSeq(5)
      >>> unk_five
      UnknownSeq(5, character='?')
      >>> len(unk_five)
      5
      >>> print(unk_five)
      ?????
  
      You can add unknown sequence together, provided their alphabets and
      characters are compatible, and get another memory saving UnknownSeq:
  
      >>> unk_four = UnknownSeq(4)
      >>> unk_four
      UnknownSeq(4, character='?')
      >>> unk_four + unk_five
      UnknownSeq(9, character='?')
  
      If the alphabet or characters don't match up, the addition gives an
      ordinary Seq object:
  
      >>> unk_nnnn = UnknownSeq(4, character="N")
      >>> unk_nnnn
      UnknownSeq(4, character='N')
      >>> unk_nnnn + unk_four
      Seq('NNNN????')
  
      Combining with a real Seq gives a new Seq object:
  
      >>> known_seq = Seq("ACGT")
      >>> unk_four + known_seq
      Seq('????ACGT')
      >>> known_seq + unk_four
      Seq('ACGT????')
      """
  
      def __init__(self, length, alphabet=Alphabet.generic_alphabet, character=None):
          """Create a new UnknownSeq object.
  
          If character is omitted, it is determined from the alphabet, "N" for
          nucleotides, "X" for proteins, and "?" otherwise.
          """
          self._length = int(length)
          if self._length < 0:
              # TODO - Block zero length UnknownSeq?  You can just use a Seq!
              raise ValueError("Length must not be negative.")
          self.alphabet = alphabet
          if character:
              if len(character) != 1:
                  raise ValueError("character argument should be a single letter string.")
              self._character = character
          else:
              base = Alphabet._get_base_alphabet(alphabet)
              # TODO? Check the case of the letters in the alphabet?
              # We may have to use "n" instead of "N" etc.
              if isinstance(base, Alphabet.NucleotideAlphabet):
                  self._character = "N"
              elif isinstance(base, Alphabet.ProteinAlphabet):
                  self._character = "X"
              else:
                  self._character = "?"
  
      def __len__(self):
          """Return the stated length of the unknown sequence."""
          return self._length
  
      def __str__(self):
          """Return the unknown sequence as full string of the given length."""
          return self._character * self._length
  
      def __repr__(self):
          """Return (truncated) representation of the sequence for debugging."""
          return f"UnknownSeq({self._length}, character={self._character!r})"
  
      def __add__(self, other):
          """Add another sequence or string to this sequence.
  
          Adding two UnknownSeq objects returns another UnknownSeq object
          provided the character is the same and the alphabets are compatible.
  
          >>> from Bio.Seq import UnknownSeq
          >>> from Bio.Alphabet import generic_protein
          >>> UnknownSeq(10, generic_protein) + UnknownSeq(5, generic_protein)
          UnknownSeq(15, character='X')
  
          If the characters differ, an UnknownSeq object cannot be used, so a
          Seq object is returned:
  
          >>> from Bio.Seq import UnknownSeq
          >>> from Bio.Alphabet import generic_protein
          >>> UnknownSeq(10, generic_protein) + UnknownSeq(5, generic_protein,
          ...                                              character="x")
          Seq('XXXXXXXXXXxxxxx')
  
          If adding a string to an UnknownSeq, a new Seq is returned with the
          same alphabet:
  
          >>> from Bio.Seq import UnknownSeq
          >>> from Bio.Alphabet import generic_protein
          >>> UnknownSeq(5, generic_protein) + "LV"
          Seq('XXXXXLV')
          """
          if isinstance(other, UnknownSeq) and other._character == self._character:
              return UnknownSeq(len(self) + len(other), self.alphabet, self._character)
          # Offload to the base class...
          return Seq(str(self), self.alphabet) + other
  
      def __radd__(self, other):
          """Add a sequence on the left."""
          # If other is an UnknownSeq, then __add__ would be called.
          # Offload to the base class...
          return other + Seq(str(self), self.alphabet)
  
      def __mul__(self, other):
          """Multiply UnknownSeq by integer.
  
          >>> from Bio.Seq import UnknownSeq
          >>> from Bio.Alphabet import generic_dna
          >>> UnknownSeq(3) * 2
          UnknownSeq(6, character='?')
          >>> UnknownSeq(3, generic_dna) * 2
          UnknownSeq(6, character='N')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(len(self) * other, character=self._character)
  
      def __rmul__(self, other):
          """Multiply integer by UnknownSeq.
  
          >>> from Bio.Seq import UnknownSeq
          >>> 2 * UnknownSeq(3)
          UnknownSeq(6, character='?')
          >>> 2 * UnknownSeq(3, character="N")
          UnknownSeq(6, character='N')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(len(self) * other, character=self._character)
  
      def __imul__(self, other):
          """Multiply UnknownSeq in-place.
  
          Note although UnknownSeq is immutable, the in-place method is
          included to match the behaviour for regular Python strings.
  
          >>> from Bio.Seq import UnknownSeq
          >>> seq = UnknownSeq(3, character="N")
          >>> seq *= 2
          >>> seq
          UnknownSeq(6, character='N')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(len(self) * other, character=self._character)
  
      def __getitem__(self, index):
          """Get a subsequence from the UnknownSeq object.
  
          >>> unk = UnknownSeq(8, character="N")
          >>> print(unk[:])
          NNNNNNNN
          >>> print(unk[5:3])
          <BLANKLINE>
          >>> print(unk[1:-1])
          NNNNNN
          >>> print(unk[1:-1:2])
          NNN
          """
          if isinstance(index, int):
              # TODO - Check the bounds without wasting memory
              return str(self)[index]
          old_length = self._length
          step = index.step
          if step is None or step == 1:
              # This calculates the length you'd get from ("N"*old_length)[index]
              start = index.start
              end = index.stop
              if start is None:
                  start = 0
              elif start < 0:
                  start = max(0, old_length + start)
              elif start > old_length:
                  start = old_length
              if end is None:
                  end = old_length
              elif end < 0:
                  end = max(0, old_length + end)
              elif end > old_length:
                  end = old_length
              new_length = max(0, end - start)
          elif step == 0:
              raise ValueError("slice step cannot be zero")
          else:
              # TODO - handle step efficiently
              new_length = len(("X" * old_length)[index])
          # assert new_length == len(("X"*old_length)[index]), \
          #       (index, start, end, step, old_length,
          #        new_length, len(("X"*old_length)[index]))
          return UnknownSeq(new_length, character=self._character)
  
      def count(self, sub, start=0, end=sys.maxsize):
          """Return a non-overlapping count, like that of a python string.
  
          This behaves like the python string (and Seq object) method of the
          same name, which does a non-overlapping count!
  
          For an overlapping search use the newer count_overlap() method.
  
          Returns an integer, the number of occurrences of substring
          argument sub in the (sub)sequence given by [start:end].
          Optional arguments start and end are interpreted as in slice
          notation.
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          >>> "NNNN".count("N")
          4
          >>> Seq("NNNN").count("N")
          4
          >>> UnknownSeq(4, character="N").count("N")
          4
          >>> UnknownSeq(4, character="N").count("A")
          0
          >>> UnknownSeq(4, character="N").count("AA")
          0
  
          HOWEVER, please note because that python strings and Seq objects (and
          MutableSeq objects) do a non-overlapping search, this may not give
          the answer you expect:
  
          >>> UnknownSeq(4, character="N").count("NN")
          2
          >>> UnknownSeq(4, character="N").count("NNN")
          1
          """
          sub_str = str(sub)
          len_self, len_sub_str = self._length, len(sub_str)
          # Handling case where substring not in self
          if set(sub_str) != set(self._character):
              return 0
          # Setting None to the default arguments
          if start is None:
              start = 0
          if end is None:
              end = sys.maxsize
          # Truncating start and end to max of self._length and min of -self._length
          start = max(min(start, len_self), -len_self)
          end = max(min(end, len_self), -len_self)
          # Convert start and ends to positive indexes
          if start < 0:
              start += len_self
          if end < 0:
              end += len_self
          # Handle case where end <= start (no negative step argument here)
          # and case where len_sub_str is larger than the search space
          if end <= start or (end - start) < len_sub_str:
              return 0
          # 'Normal' calculation
          return (end - start) // len_sub_str
  
      def count_overlap(self, sub, start=0, end=sys.maxsize):
          """Return an overlapping count.
  
          For a non-overlapping search use the count() method.
  
          Returns an integer, the number of occurrences of substring
          argument sub in the (sub)sequence given by [start:end].
          Optional arguments start and end are interpreted as in slice
          notation.
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          e.g.
  
          >>> from Bio.Seq import UnknownSeq
          >>> UnknownSeq(4, character="N").count_overlap("NN")
          3
          >>> UnknownSeq(4, character="N").count_overlap("NNN")
          2
  
          Where substrings do not overlap, should behave the same as
          the count() method:
  
          >>> UnknownSeq(4, character="N").count_overlap("N")
          4
          >>> UnknownSeq(4, character="N").count_overlap("N") == UnknownSeq(4, character="N").count("N")
          True
          >>> UnknownSeq(4, character="N").count_overlap("A")
          0
          >>> UnknownSeq(4, character="N").count_overlap("A") == UnknownSeq(4, character="N").count("A")
          True
          >>> UnknownSeq(4, character="N").count_overlap("AA")
          0
          >>> UnknownSeq(4, character="N").count_overlap("AA") == UnknownSeq(4, character="N").count("AA")
          True
          """
          sub_str = str(sub)
          len_self, len_sub_str = self._length, len(sub_str)
          # Handling case where substring not in self
          if set(sub_str) != set(self._character):
              return 0
          # Setting None to the default arguments
          if start is None:
              start = 0
          if end is None:
              end = sys.maxsize
          # Truncating start and end to max of self._length and min of -self._length
          start = max(min(start, len_self), -len_self)
          end = max(min(end, len_self), -len_self)
          # Convert start and ends to positive indexes
          if start < 0:
              start += len_self
          if end < 0:
              end += len_self
          # Handle case where end <= start (no negative step argument here)
          # and case where len_sub_str is larger than the search space
          if end <= start or (end - start) < len_sub_str:
              return 0
          # 'Normal' calculation
          return end - start - len_sub_str + 1
  
      def complement(self):
          """Return the complement of an unknown nucleotide equals itself.
  
          >>> my_nuc = UnknownSeq(8)
          >>> my_nuc
          UnknownSeq(8, character='?')
          >>> print(my_nuc)
          ????????
          >>> my_nuc.complement()
          UnknownSeq(8, character='?')
          >>> print(my_nuc.complement())
          ????????
          """
          return self
  
      def complement_rna(self):
          """Return the complement assuming it is RNA."""
          return self.complement()
  
      def reverse_complement(self):
          """Return the reverse complement of an unknown sequence.
  
          The reverse complement of an unknown nucleotide equals itself:
  
          >>> from Bio.Seq import UnknownSeq
          >>> from Bio.Alphabet import generic_dna
          >>> example = UnknownSeq(6, generic_dna)
          >>> print(example)
          NNNNNN
          >>> print(example.reverse_complement())
          NNNNNN
          """
          return self
  
      def reverse_complement_rna(self):
          """Return the reverse complement assuming it is RNA."""
          return self.reverse_complement()
  
      def transcribe(self):
          """Return an unknown RNA sequence from an unknown DNA sequence.
  
          >>> my_dna = UnknownSeq(10, character="N")
          >>> my_dna
          UnknownSeq(10, character='N')
          >>> print(my_dna)
          NNNNNNNNNN
          >>> my_rna = my_dna.transcribe()
          >>> my_rna
          UnknownSeq(10, character='N')
          >>> print(my_rna)
          NNNNNNNNNN
          """
          s = Seq(self._character).transcribe()
          return UnknownSeq(self._length, character=str(s))
  
      def back_transcribe(self):
          """Return an unknown DNA sequence from an unknown RNA sequence.
  
          >>> my_rna = UnknownSeq(20, character="N")
          >>> my_rna
          UnknownSeq(20, character='N')
          >>> print(my_rna)
          NNNNNNNNNNNNNNNNNNNN
          >>> my_dna = my_rna.back_transcribe()
          >>> my_dna
          UnknownSeq(20, character='N')
          >>> print(my_dna)
          NNNNNNNNNNNNNNNNNNNN
          """
          s = Seq(self._character).back_transcribe()
          return UnknownSeq(self._length, character=str(s))
  
      def upper(self):
          """Return an upper case copy of the sequence.
  
          >>> from Bio.Seq import UnknownSeq
          >>> my_seq = UnknownSeq(20, character="n")
          >>> my_seq
          UnknownSeq(20, character='n')
          >>> print(my_seq)
          nnnnnnnnnnnnnnnnnnnn
          >>> my_seq.upper()
          UnknownSeq(20, character='N')
          >>> print(my_seq.upper())
          NNNNNNNNNNNNNNNNNNNN
  
          See also the lower method.
          """
          return UnknownSeq(self._length, character=self._character.upper())
  
      def lower(self):
          """Return a lower case copy of the sequence.
  
          >>> from Bio.Seq import UnknownSeq
          >>> my_seq = UnknownSeq(20, character="X")
          >>> my_seq
          UnknownSeq(20, character='X')
          >>> print(my_seq)
          XXXXXXXXXXXXXXXXXXXX
          >>> my_seq.lower()
          UnknownSeq(20, character='x')
          >>> print(my_seq.lower())
          xxxxxxxxxxxxxxxxxxxx
  
          See also the upper method.
          """
          return UnknownSeq(self._length, character=self._character.lower())
  
      def translate(
          self, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap="-"
      ):
          """Translate an unknown nucleotide sequence into an unknown protein.
  
          e.g.
  
          >>> my_seq = UnknownSeq(9, character="N")
          >>> print(my_seq)
          NNNNNNNNN
          >>> my_protein = my_seq.translate()
          >>> my_protein
          UnknownSeq(3, character='X')
          >>> print(my_protein)
          XXX
  
          In comparison, using a normal Seq object:
  
          >>> my_seq = Seq("NNNNNNNNN")
          >>> print(my_seq)
          NNNNNNNNN
          >>> my_protein = my_seq.translate()
          >>> my_protein
          Seq('XXX')
          >>> print(my_protein)
          XXX
  
          """
          return UnknownSeq(self._length // 3, Alphabet.generic_protein, "X")
  
      def ungap(self, gap="-"):
          """Return a copy of the sequence without the gap character(s).
  
          The gap character now defaults to the minus sign, and can only
          be specified via the method argument. This is no longer possible
          via sequence's alphabet (as was possible up to Biopython 1.77):
  
          >>> from Bio.Alphabet import generic_dna
          >>> from Bio.Seq import UnknownSeq
          >>> my_dna = UnknownSeq(20, alphabet=generic_dna)
          >>> my_dna
          UnknownSeq(20, character='N')
          >>> my_dna.ungap()  # using default
          UnknownSeq(20, character='N')
          >>> my_dna.ungap("-")
          UnknownSeq(20, character='N')
  
          If the UnknownSeq is using the gap character, then an empty Seq is
          returned:
  
          >>> my_gap = UnknownSeq(20, generic_dna, character="-")
          >>> my_gap
          UnknownSeq(20, character='-')
          >>> my_gap.ungap()  # using default
          Seq('')
          >>> my_gap.ungap("-")
          Seq('')
          """
          # Offload the argument validation
          s = Seq(self._character, self.alphabet).ungap(gap)
          if s:
              return UnknownSeq(self._length, s.alphabet, self._character)
          else:
              return Seq("", s.alphabet)
  
      def join(self, other):
          """Return a merge of the sequences in other, spaced by the sequence from self.
  
          Accepts either a Seq or string (and iterates over the letters), or an
          iterable containing Seq or string objects. These arguments will be
          concatenated with the calling sequence as the spacer:
  
          >>> concatenated = UnknownSeq(5).join([Seq("AAA"), Seq("TTT"), Seq("PPP")])
          >>> concatenated
          Seq('AAA?????TTT?????PPP')
  
          If all the inputs are also UnknownSeq using the same character, then it
          returns a new UnknownSeq:
  
          >>> UnknownSeq(5).join([UnknownSeq(3), UnknownSeq(3), UnknownSeq(3)])
          UnknownSeq(19, character='?')
  
          Examples taking a single sequence and joining the letters:
  
          >>> UnknownSeq(3).join("ACGT")
          Seq('A???C???G???T')
          >>> UnknownSeq(3).join(UnknownSeq(4))
          UnknownSeq(13, character='?')
  
          Will only return an UnknownSeq object if all of the objects to be joined are
          also UnknownSeqs with the same character as the spacer, similar to how the
          addition of an UnknownSeq and another UnknownSeq would work.
          """
          from Bio.SeqRecord import SeqRecord  # Lazy to avoid circular imports
  
          if isinstance(other, (str, Seq, MutableSeq)):
              if isinstance(other, UnknownSeq) and self._character == other._character:
                  # Special case, can return an UnknownSeq
                  return self.__class__(
                      len(other) + len(self) * (len(other) - 1), character=self._character
                  )
              return Seq(str(self).join(str(other)))
          if isinstance(other, SeqRecord):
              raise TypeError("Iterable cannot be a SeqRecord")
  
          for c in other:
              if isinstance(c, SeqRecord):
                  raise TypeError("Iterable cannot contain SeqRecords")
              elif not isinstance(c, (str, Seq, MutableSeq)):
                  raise TypeError("Input must be an iterable of Seqs or Strings")
          temp_data = str(self).join([str(_) for _ in other])
          if temp_data.count(self._character) == len(temp_data):
              # Can return an UnknownSeq
              return self.__class__(len(temp_data), character=self._character)
          return Seq(temp_data)
  
  
  class MutableSeq:
      """An editable sequence object (with an alphabet).
  
      Unlike normal python strings and our basic sequence object (the Seq class)
      which are immutable, the MutableSeq lets you edit the sequence in place.
      However, this means you cannot use a MutableSeq object as a dictionary key.
  
      >>> from Bio.Seq import MutableSeq
      >>> from Bio.Alphabet import generic_dna
      >>> my_seq = MutableSeq("ACTCGTCGTCG", generic_dna)
      >>> my_seq
      MutableSeq('ACTCGTCGTCG')
      >>> my_seq[5]
      'T'
      >>> my_seq[5] = "A"
      >>> my_seq
      MutableSeq('ACTCGACGTCG')
      >>> my_seq[5]
      'A'
      >>> my_seq[5:8] = "NNN"
      >>> my_seq
      MutableSeq('ACTCGNNNTCG')
      >>> len(my_seq)
      11
  
      Note that the MutableSeq object does not support as many string-like
      or biological methods as the Seq object.
      """
  
      def __init__(self, data, alphabet=Alphabet.generic_alphabet):
          """Initialize the class."""
          if isinstance(data, str):  # TODO - What about unicode?
              self.data = array.array("u", data)
          elif isinstance(data, (Seq, int, float)):
              raise TypeError(
                  "The sequence data given to a MutableSeq object "
                  "should be a string or an array (not a Seq object etc)"
              )
          else:
              self.data = data  # assumes the input is an array
          self.alphabet = alphabet
  
      def __repr__(self):
          """Return (truncated) representation of the sequence for debugging."""
          if len(self) > 60:
              # Shows the last three letters as it is often useful to see if
              # there is a stop codon at the end of a sequence.
              # Note total length is 54+3+3=60
              return f"{self.__class__.__name__}('{str(self[:54])}...{str(self[-3:])}')"
          else:
              return f"{self.__class__.__name__}('{str(self)}')"
  
      def __str__(self):
          """Return the full sequence as a python string.
  
          Note that Biopython 1.44 and earlier would give a truncated
          version of repr(my_seq) for str(my_seq).  If you are writing code
          which needs to be backwards compatible with old Biopython, you
          should continue to use my_seq.tostring() rather than str(my_seq).
          """
          # See test_GAQueens.py for an historic usage of a non-string alphabet!
          return "".join(self.data)
  
      def __eq__(self, other):
          """Compare the sequence to another sequence or a string.
  
          Historically comparing DNA to RNA, or Nucleotide to Protein would
          raise an exception. This was later downgraded to a warning, but since
          Biopython 1.78 the alphabet is ignored for comparisons.
  
          If you need to support older Biopython versions, please just do
          explicit comparisons:
  
          >>> seq1 = MutableSeq("ACGT")
          >>> seq2 = MutableSeq("ACGT")
          >>> id(seq1) == id(seq2)
          False
          >>> str(seq1) == str(seq2)
          True
  
          Biopython now does:
  
          >>> seq1 == seq2
          True
          >>> seq1 == Seq("ACGT")
          True
          >>> seq1 == "ACGT"
          True
  
          """
          if isinstance(other, MutableSeq):
              return self.data == other.data
          return str(self) == str(other)
  
      def __lt__(self, other):
          """Implement the less-than operand."""
          if isinstance(other, MutableSeq):
              return self.data < other.data
          if isinstance(other, (str, Seq, UnknownSeq)):
              return str(self) < str(other)
          raise TypeError(
              f"'<' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __le__(self, other):
          """Implement the less-than or equal operand."""
          if isinstance(other, MutableSeq):
              return self.data <= other.data
          if isinstance(other, (str, Seq, UnknownSeq)):
              return str(self) <= str(other)
          raise TypeError(
              f"'<=' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __gt__(self, other):
          """Implement the greater-than operand."""
          if isinstance(other, MutableSeq):
              return self.data > other.data
          if isinstance(other, (str, Seq, UnknownSeq)):
              return str(self) > str(other)
          raise TypeError(
              f"'>' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __ge__(self, other):
          """Implement the greater-than or equal operand."""
          if isinstance(other, MutableSeq):
              return self.data >= other.data
          if isinstance(other, (str, Seq, UnknownSeq)):
              return str(self) >= str(other)
          raise TypeError(
              f"'>=' not supported between instances of '{type(self).__name__}'"
              f" and '{type(other).__name__}'"
          )
  
      def __len__(self):
          """Return the length of the sequence, use len(my_seq)."""
          return len(self.data)
  
      def __getitem__(self, index):
          """Return a subsequence of single letter, use my_seq[index].
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq[5]
          'A'
          """
          if isinstance(index, int):
              # Return a single letter as a string
              return self.data[index]
          else:
              # Return the (sub)sequence as another Seq object
              return MutableSeq(self.data[index], self.alphabet)
  
      def __setitem__(self, index, value):
          """Set a subsequence of single letter via value parameter.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq[0] = 'T'
          >>> my_seq
          MutableSeq('TCTCGACGTCG')
          """
          if isinstance(index, int):
              # Replacing a single letter with a new string
              self.data[index] = value
          else:
              # Replacing a sub-sequence
              if isinstance(value, MutableSeq):
                  self.data[index] = value.data
              elif isinstance(value, type(self.data)):
                  self.data[index] = value
              else:
                  self.data[index] = array.array("u", str(value))
  
      def __delitem__(self, index):
          """Delete a subsequence of single letter.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> del my_seq[0]
          >>> my_seq
          MutableSeq('CTCGACGTCG')
          """
          # Could be deleting a single letter, or a slice
          del self.data[index]
  
      def __add__(self, other):
          """Add another sequence or string to this sequence.
  
          Returns a new MutableSeq object.
          """
          a = self.alphabet
          if hasattr(other, "alphabet"):
              if a != other.alphabet:
                  # Drop alphabet unless agree
                  a = Alphabet.generic_alphabet
              if isinstance(other, MutableSeq):
                  # See test_GAQueens.py for an historic usage of a non-string
                  # alphabet!  Adding the arrays should support this.
                  return self.__class__(self.data + other.data, a)
              else:
                  return self.__class__(str(self) + str(other), a)
          elif isinstance(other, str):
              # other is a plain string - use the current alphabet
              return self.__class__(str(self) + str(other), a)
          else:
              raise TypeError
  
      def __radd__(self, other):
          """Add a sequence on the left.
  
          >>> from Bio.Seq import MutableSeq
          >>> from Bio.Alphabet import generic_protein
          >>> "LV" + MutableSeq("MELKI", generic_protein)
          MutableSeq('LVMELKI')
          """
          a = self.alphabet
          if hasattr(other, "alphabet"):
              if a != other.alphabet:
                  a = Alphabet.generic_alphabet
              if isinstance(other, MutableSeq):
                  # See test_GAQueens.py for an historic usage of a non-string
                  # alphabet!  Adding the arrays should support this.
                  return self.__class__(other.data + self.data, a)
              else:
                  return self.__class__(str(other) + str(self), a)
          elif isinstance(other, str):
              # other is a plain string - use the current alphabet
              return self.__class__(str(other) + str(self), self.alphabet)
          else:
              raise TypeError
  
      def __mul__(self, other):
          """Multiply MutableSeq by integer.
  
          Note this is not in-place and returns a new object,
          matching native Python list multiplication.
  
          >>> from Bio.Seq import MutableSeq
          >>> from Bio.Alphabet import generic_dna
          >>> MutableSeq('ATG') * 2
          MutableSeq('ATGATG')
          >>> MutableSeq('ATG', generic_dna) * 2
          MutableSeq('ATGATG')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(self.data * other)
  
      def __rmul__(self, other):
          """Multiply integer by MutableSeq.
  
          Note this is not in-place and returns a new object,
          matching native Python list multiplication.
  
          >>> from Bio.Seq import MutableSeq
          >>> from Bio.Alphabet import generic_dna
          >>> 2 * MutableSeq('ATG')
          MutableSeq('ATGATG')
          >>> 2 * MutableSeq('ATG', generic_dna)
          MutableSeq('ATGATG')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(self.data * other)
  
      def __imul__(self, other):
          """Multiply MutableSeq in-place.
  
          >>> from Bio.Seq import MutableSeq
          >>> from Bio.Alphabet import generic_dna
          >>> seq = MutableSeq('ATG', generic_dna)
          >>> seq *= 2
          >>> seq
          MutableSeq('ATGATG')
          """
          if not isinstance(other, int):
              raise TypeError(f"can't multiply {self.__class__.__name__} by non-int type")
          return self.__class__(self.data * other)
  
      def append(self, c):
          """Add a subsequence to the mutable sequence object.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq.append('A')
          >>> my_seq
          MutableSeq('ACTCGACGTCGA')
  
          No return value.
          """
          self.data.append(c)
  
      def insert(self, i, c):
          """Add a subsequence to the mutable sequence object at a given index.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq.insert(0,'A')
          >>> my_seq
          MutableSeq('AACTCGACGTCG')
          >>> my_seq.insert(8,'G')
          >>> my_seq
          MutableSeq('AACTCGACGGTCG')
  
          No return value.
          """
          self.data.insert(i, c)
  
      def pop(self, i=(-1)):
          """Remove a subsequence of a single letter at given index.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq.pop()
          'G'
          >>> my_seq
          MutableSeq('ACTCGACGTC')
          >>> my_seq.pop()
          'C'
          >>> my_seq
          MutableSeq('ACTCGACGT')
  
          Returns the last character of the sequence.
          """
          c = self.data[i]
          del self.data[i]
          return c
  
      def remove(self, item):
          """Remove a subsequence of a single letter from mutable sequence.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq.remove('C')
          >>> my_seq
          MutableSeq('ATCGACGTCG')
          >>> my_seq.remove('A')
          >>> my_seq
          MutableSeq('TCGACGTCG')
  
          No return value.
          """
          for i in range(len(self.data)):
              if self.data[i] == item:
                  del self.data[i]
                  return
          raise ValueError("MutableSeq.remove(x): x not in list")
  
      def count(self, sub, start=0, end=sys.maxsize):
          """Return a non-overlapping count, like that of a python string.
  
          This behaves like the python string method of the same name,
          which does a non-overlapping count!
  
          For an overlapping search use the newer count_overlap() method.
  
          Returns an integer, the number of occurrences of substring
          argument sub in the (sub)sequence given by [start:end].
          Optional arguments start and end are interpreted as in slice
          notation.
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          e.g.
  
          >>> from Bio.Seq import MutableSeq
          >>> my_mseq = MutableSeq("AAAATGA")
          >>> print(my_mseq.count("A"))
          5
          >>> print(my_mseq.count("ATG"))
          1
          >>> print(my_mseq.count(Seq("AT")))
          1
          >>> print(my_mseq.count("AT", 2, -1))
          1
  
          HOWEVER, please note because that python strings, Seq objects and
          MutableSeq objects do a non-overlapping search, this may not give
          the answer you expect:
  
          >>> "AAAA".count("AA")
          2
          >>> print(MutableSeq("AAAA").count("AA"))
          2
  
          An overlapping search would give the answer as three!
          """
          try:
              # TODO - Should we check the alphabet?
              search = str(sub)
          except AttributeError:
              search = sub
  
          if not isinstance(search, str):
              raise TypeError("expected a string, Seq or MutableSeq")
  
          if len(search) == 1:
              # Try and be efficient and work directly from the array.
              count = 0
              for c in self.data[start:end]:
                  if c == search:
                      count += 1
              return count
          else:
              # TODO - Can we do this more efficiently?
              return str(self).count(search, start, end)
  
      def count_overlap(self, sub, start=0, end=sys.maxsize):
          """Return an overlapping count.
  
          For a non-overlapping search use the count() method.
  
          Returns an integer, the number of occurrences of substring
          argument sub in the (sub)sequence given by [start:end].
          Optional arguments start and end are interpreted as in slice
          notation.
  
          Arguments:
           - sub - a string or another Seq object to look for
           - start - optional integer, slice start
           - end - optional integer, slice end
  
          e.g.
  
          >>> from Bio.Seq import MutableSeq
          >>> print(MutableSeq("AAAA").count_overlap("AA"))
          3
          >>> print(MutableSeq("ATATATATA").count_overlap("ATA"))
          4
          >>> print(MutableSeq("ATATATATA").count_overlap("ATA", 3, -1))
          1
  
          Where substrings do not overlap, should behave the same as
          the count() method:
  
          >>> from Bio.Seq import MutableSeq
          >>> my_mseq = MutableSeq("AAAATGA")
          >>> print(my_mseq.count_overlap("A"))
          5
          >>> my_mseq.count_overlap("A") == my_mseq.count("A")
          True
          >>> print(my_mseq.count_overlap("ATG"))
          1
          >>> my_mseq.count_overlap("ATG") == my_mseq.count("ATG")
          True
          >>> print(my_mseq.count_overlap(Seq("AT")))
          1
          >>> my_mseq.count_overlap(Seq("AT")) == my_mseq.count(Seq("AT"))
          True
          >>> print(my_mseq.count_overlap("AT", 2, -1))
          1
          >>> my_mseq.count_overlap("AT", 2, -1) == my_mseq.count("AT", 2, -1)
          True
  
          HOWEVER, do not use this method for such cases because the
          count() method is much for efficient.
          """
          # The implementation is currently identical to that of
          # Seq.count_overlap() apart from the definition of sub_str
          sub_str = str(sub)
          self_str = str(self)
          overlap_count = 0
          while True:
              start = self_str.find(sub_str, start, end) + 1
              if start != 0:
                  overlap_count += 1
              else:
                  return overlap_count
  
      def index(self, item):
          """Return first occurrence position of a single entry (i.e. letter).
  
          >>> my_seq = MutableSeq("ACTCGACGTCG")
          >>> my_seq.index("A")
          0
          >>> my_seq.index("T")
          2
          >>> my_seq.index(Seq("T"))
          2
  
          Note unlike a Biopython Seq object, or Python string, multi-letter
          subsequences are not supported.  Instead this acts like an array or
          a list of the entries. There is therefore no ``.rindex()`` method.
          """
          # TODO?: return self.data.index(i)
          for i in range(len(self.data)):
              if self.data[i] == item:
                  return i
          raise ValueError("MutableSeq.index(x): x not in list")
  
      def reverse(self):
          """Modify the mutable sequence to reverse itself.
  
          No return value.
          """
          self.data.reverse()
  
      def complement(self):
          """Modify the mutable sequence to take on its complement.
  
          No return value.
  
          If the sequence contains neither T nor U, DNA is assumed
          and any A will be mapped to T.
  
          If the sequence contains both T and U, an exception is raised.
          """
          if "U" in self.data and "T" in self.data:
              raise ValueError("Mixed RNA/DNA found")
          elif "U" in self.data:
              d = ambiguous_rna_complement
          else:
              d = ambiguous_dna_complement
          mixed = d.copy()  # We're going to edit this to be mixed case!
          mixed.update((x.lower(), y.lower()) for x, y in d.items())
          self.data = [mixed[_] for _ in self.data]
          self.data = array.array("u", self.data)
  
      def reverse_complement(self):
          """Modify the mutable sequence to take on its reverse complement.
  
          No return value.
          """
          self.complement()
          self.data.reverse()
  
      def extend(self, other):
          """Add a sequence to the original mutable sequence object.
  
          >>> my_seq = MutableSeq('ACTCGACGTCG')
          >>> my_seq.extend('A')
          >>> my_seq
          MutableSeq('ACTCGACGTCGA')
          >>> my_seq.extend('TTT')
          >>> my_seq
          MutableSeq('ACTCGACGTCGATTT')
  
          No return value.
          """
          if isinstance(other, MutableSeq):
              for c in other.data:
                  self.data.append(c)
          else:
              for c in other:
                  self.data.append(c)
  
      def toseq(self):
          """Return the full sequence as a new immutable Seq object.
  
          >>> from Bio.Seq import Seq
          >>> my_mseq = MutableSeq("MKQHKAMIVALIVICITAVVAAL")
          >>> my_mseq
          MutableSeq('MKQHKAMIVALIVICITAVVAAL')
          >>> my_mseq.toseq()
          Seq('MKQHKAMIVALIVICITAVVAAL')
          """
          return Seq("".join(self.data))
  
      def join(self, other):
          """Return a merge of the sequences in other, spaced by the sequence from self.
  
          Accepts all Seq objects and Strings as objects to be concatenated with the spacer
  
          >>> concatenated = MutableSeq('NNNNN').join([Seq("AAA"), Seq("TTT"), Seq("PPP")])
          >>> concatenated
          Seq('AAANNNNNTTTNNNNNPPP')
  
          Throws error if other is not an iterable and if objects inside of the iterable
          are not Seq or String objects
          """
          # returns Seq object instead of MutableSeq
          return self.toseq().join(other)
  
  
  # The transcribe, backward_transcribe, and translate functions are
  # user-friendly versions of the corresponding functions in Bio.Transcribe
  # and Bio.Translate. The functions work both on Seq objects, and on strings.
  
  
  def transcribe(dna):
      """Transcribe a DNA sequence into RNA.
  
      If given a string, returns a new string object.
  
      Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.
  
      e.g.
  
      >>> transcribe("ACTGN")
      'ACUGN'
      """
      if isinstance(dna, Seq):
          return dna.transcribe()
      elif isinstance(dna, MutableSeq):
          return dna.toseq().transcribe()
      else:
          return dna.replace("T", "U").replace("t", "u")
  
  
  def back_transcribe(rna):
      """Return the RNA sequence back-transcribed into DNA.
  
      If given a string, returns a new string object.
  
      Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet.
  
      e.g.
  
      >>> back_transcribe("ACUGN")
      'ACTGN'
      """
      if isinstance(rna, Seq):
          return rna.back_transcribe()
      elif isinstance(rna, MutableSeq):
          return rna.toseq().back_transcribe()
      else:
          return rna.replace("U", "T").replace("u", "t")
  
  
  def _translate_str(
      sequence, table, stop_symbol="*", to_stop=False, cds=False, pos_stop="X", gap=None
  ):
      """Translate nucleotide string into a protein string (PRIVATE).
  
      Arguments:
       - sequence - a string
       - table - a CodonTable object (NOT a table name or id number)
       - stop_symbol - a single character string, what to use for terminators.
       - to_stop - boolean, should translation terminate at the first
         in frame stop codon?  If there is no in-frame stop codon
         then translation continues to the end.
       - pos_stop - a single character string for a possible stop codon
         (e.g. TAN or NNN)
       - cds - Boolean, indicates this is a complete CDS.  If True, this
         checks the sequence starts with a valid alternative start
         codon (which will be translated as methionine, M), that the
         sequence length is a multiple of three, and that there is a
         single in frame stop codon at the end (this will be excluded
         from the protein sequence, regardless of the to_stop option).
         If these tests fail, an exception is raised.
       - gap - Single character string to denote symbol used for gaps.
         Defaults to None.
  
      Returns a string.
  
      e.g.
  
      >>> from Bio.Data import CodonTable
      >>> table = CodonTable.ambiguous_dna_by_id[1]
      >>> _translate_str("AAA", table)
      'K'
      >>> _translate_str("TAR", table)
      '*'
      >>> _translate_str("TAN", table)
      'X'
      >>> _translate_str("TAN", table, pos_stop="@")
      '@'
      >>> _translate_str("TA?", table)
      Traceback (most recent call last):
         ...
      Bio.Data.CodonTable.TranslationError: Codon 'TA?' is invalid
  
      In a change to older versions of Biopython, partial codons are now
      always regarded as an error (previously only checked if cds=True)
      and will trigger a warning (likely to become an exception in a
      future release).
  
      If **cds=True**, the start and stop codons are checked, and the start
      codon will be translated at methionine. The sequence must be an
      while number of codons.
  
      >>> _translate_str("ATGCCCTAG", table, cds=True)
      'MP'
      >>> _translate_str("AAACCCTAG", table, cds=True)
      Traceback (most recent call last):
         ...
      Bio.Data.CodonTable.TranslationError: First codon 'AAA' is not a start codon
      >>> _translate_str("ATGCCCTAGCCCTAG", table, cds=True)
      Traceback (most recent call last):
         ...
      Bio.Data.CodonTable.TranslationError: Extra in frame stop codon found.
      """
      sequence = sequence.upper()
      amino_acids = []
      forward_table = table.forward_table
      stop_codons = table.stop_codons
      if table.nucleotide_alphabet.letters is not None:
          valid_letters = set(table.nucleotide_alphabet.letters.upper())
      else:
          # Assume the worst case, ambiguous DNA or RNA:
          valid_letters = set(
              _ambiguous_dna_letters.upper() + _ambiguous_rna_letters.upper()
          )
      n = len(sequence)
  
      # Check for tables with 'ambiguous' (dual-coding) stop codons:
      dual_coding = [c for c in stop_codons if c in forward_table]
      if dual_coding:
          c = dual_coding[0]
          if to_stop:
              raise ValueError(
                  "You cannot use 'to_stop=True' with this table as it contains"
                  f" {len(dual_coding)} codon(s) which can be both  STOP and an"
                  f" amino acid (e.g. '{c}' -> '{forward_table[c]}' or STOP)."
              )
          warnings.warn(
              f"This table contains {len(dual_coding)} codon(s) which code(s) for"
              f" both STOP and an amino acid (e.g. '{c}' -> '{forward_table[c]}'"
              " or STOP). Such codons will be translated as amino acid.",
              BiopythonWarning,
          )
  
      if cds:
          if str(sequence[:3]).upper() not in table.start_codons:
              raise CodonTable.TranslationError(
                  f"First codon '{sequence[:3]}' is not a start codon"
              )
          if n % 3 != 0:
              raise CodonTable.TranslationError(
                  f"Sequence length {n} is not a multiple of three"
              )
          if str(sequence[-3:]).upper() not in stop_codons:
              raise CodonTable.TranslationError(
                  f"Final codon '{sequence[-3:]}' is not a stop codon"
              )
          # Don't translate the stop symbol, and manually translate the M
          sequence = sequence[3:-3]
          n -= 6
          amino_acids = ["M"]
      elif n % 3 != 0:
          warnings.warn(
              "Partial codon, len(sequence) not a multiple of three. "
              "Explicitly trim the sequence or add trailing N before "
              "translation. This may become an error in future.",
              BiopythonWarning,
          )
      if gap is not None:
          if not isinstance(gap, str):
              raise TypeError("Gap character should be a single character string.")
          elif len(gap) > 1:
              raise ValueError("Gap character should be a single character string.")
  
      for i in range(0, n - n % 3, 3):
          codon = sequence[i : i + 3]
          try:
              amino_acids.append(forward_table[codon])
          except (KeyError, CodonTable.TranslationError):
              if codon in table.stop_codons:
                  if cds:
                      raise CodonTable.TranslationError(
                          "Extra in frame stop codon found."
                      ) from None
                  if to_stop:
                      break
                  amino_acids.append(stop_symbol)
              elif valid_letters.issuperset(set(codon)):
                  # Possible stop codon (e.g. NNN or TAN)
                  amino_acids.append(pos_stop)
              elif gap is not None and codon == gap * 3:
                  # Gapped translation
                  amino_acids.append(gap)
              else:
                  raise CodonTable.TranslationError(
                      f"Codon '{codon}' is invalid"
                  ) from None
      return "".join(amino_acids)
  
  
  def translate(
      sequence, table="Standard", stop_symbol="*", to_stop=False, cds=False, gap=None
  ):
      """Translate a nucleotide sequence into amino acids.
  
      If given a string, returns a new string object. Given a Seq or
      MutableSeq, returns a Seq object with a protein alphabet.
  
      Arguments:
       - table - Which codon table to use?  This can be either a name
         (string), an NCBI identifier (integer), or a CodonTable object
         (useful for non-standard genetic codes).  Defaults to the "Standard"
         table.
       - stop_symbol - Single character string, what to use for any
         terminators, defaults to the asterisk, "*".
       - to_stop - Boolean, defaults to False meaning do a full
         translation continuing on past any stop codons
         (translated as the specified stop_symbol).  If
         True, translation is terminated at the first in
         frame stop codon (and the stop_symbol is not
         appended to the returned protein sequence).
       - cds - Boolean, indicates this is a complete CDS.  If True, this
         checks the sequence starts with a valid alternative start
         codon (which will be translated as methionine, M), that the
         sequence length is a multiple of three, and that there is a
         single in frame stop codon at the end (this will be excluded
         from the protein sequence, regardless of the to_stop option).
         If these tests fail, an exception is raised.
       - gap - Single character string to denote symbol used for gaps.
         Defaults to None.
  
      A simple string example using the default (standard) genetic code:
  
      >>> coding_dna = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG"
      >>> translate(coding_dna)
      'VAIVMGR*KGAR*'
      >>> translate(coding_dna, stop_symbol="@")
      'VAIVMGR@KGAR@'
      >>> translate(coding_dna, to_stop=True)
      'VAIVMGR'
  
      Now using NCBI table 2, where TGA is not a stop codon:
  
      >>> translate(coding_dna, table=2)
      'VAIVMGRWKGAR*'
      >>> translate(coding_dna, table=2, to_stop=True)
      'VAIVMGRWKGAR'
  
      In fact this example uses an alternative start codon valid under NCBI
      table 2, GTG, which means this example is a complete valid CDS which
      when translated should really start with methionine (not valine):
  
      >>> translate(coding_dna, table=2, cds=True)
      'MAIVMGRWKGAR'
  
      Note that if the sequence has no in-frame stop codon, then the to_stop
      argument has no effect:
  
      >>> coding_dna2 = "GTGGCCATTGTAATGGGCCGC"
      >>> translate(coding_dna2)
      'VAIVMGR'
      >>> translate(coding_dna2, to_stop=True)
      'VAIVMGR'
  
      NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid
      or a stop codon.  These are translated as "X".  Any invalid codon
      (e.g. "TA?" or "T-A") will throw a TranslationError.
  
      It will however translate either DNA or RNA.
  
      NOTE - Since version 1.71 Biopython contains codon tables with 'ambiguous
      stop codons'. These are stop codons with unambiguous sequence but which
      have a context dependent coding as STOP or as amino acid. With these tables
      'to_stop' must be False (otherwise a ValueError is raised). The dual
      coding codons will always be translated as amino acid, except for
      'cds=True', where the last codon will be translated as STOP.
  
      >>> coding_dna3 = "ATGGCACGGAAGTGA"
      >>> translate(coding_dna3)
      'MARK*'
  
      >>> translate(coding_dna3, table=27)  # Table 27: TGA -> STOP or W
      'MARKW'
  
      It will however raise a BiopythonWarning (not shown).
  
      >>> translate(coding_dna3, table=27, cds=True)
      'MARK'
  
      >>> translate(coding_dna3, table=27, to_stop=True)
      Traceback (most recent call last):
         ...
      ValueError: You cannot use 'to_stop=True' with this table ...
      """
      if isinstance(sequence, Seq):
          return sequence.translate(table, stop_symbol, to_stop, cds)
      elif isinstance(sequence, MutableSeq):
          # Return a Seq object
          return sequence.toseq().translate(table, stop_symbol, to_stop, cds)
      else:
          # Assume its a string, return a string
          try:
              codon_table = CodonTable.ambiguous_generic_by_id[int(table)]
          except ValueError:
              codon_table = CodonTable.ambiguous_generic_by_name[table]
          except (AttributeError, TypeError):
              if isinstance(table, CodonTable.CodonTable):
                  codon_table = table
              else:
                  raise ValueError("Bad table argument") from None
          return _translate_str(sequence, codon_table, stop_symbol, to_stop, cds, gap=gap)
  
  
  def reverse_complement(sequence):
      """Return the reverse complement sequence of a nucleotide string.
  
      If given a string, returns a new string object.
      Given a Seq or a MutableSeq, returns a new Seq object with the same
      alphabet.
  
      Supports unambiguous and ambiguous nucleotide sequences.
  
      e.g.
  
      >>> reverse_complement("ACTG-NH")
      'DN-CAGT'
  
      If neither T nor U is present, DNA is assumed and A is mapped to T:
  
      >>> reverse_complement("A")
      'T'
      """
      return complement(sequence)[::-1]
  
  
  def complement(sequence):
      """Return the complement sequence of a DNA string.
  
      If given a string, returns a new string object.
  
      Given a Seq or a MutableSeq, returns a new Seq object with the same
      alphabet.
  
      Supports unambiguous and ambiguous nucleotide sequences.
  
      e.g.
  
      >>> complement("ACTG-NH")
      'TGAC-ND'
  
      If neither T nor U is present, DNA is assumed and A is mapped to T:
  
      >>> complement("A")
      'T'
  
      However, this may not be supported in future. Please use the
      complement_rna function if you have RNA.
      """
      if isinstance(sequence, Seq):
          # Return a Seq
          return sequence.complement()
      elif isinstance(sequence, MutableSeq):
          # Return a Seq
          # Don't use the MutableSeq reverse_complement method as it is
          # 'in place'.
          return sequence.toseq().complement()
  
      # Assume its a string.
      # In order to avoid some code duplication, the old code would turn the
      # string into a Seq, use the reverse_complement method, and convert back
      # to a string.
      # This worked, but is over five times slower on short sequences!
      if ("U" in sequence or "u" in sequence) and ("T" in sequence or "t" in sequence):
          raise ValueError("Mixed RNA/DNA found")
      elif "U" in sequence or "u" in sequence:
          # TODO - warning or exception in future?
          ttable = _rna_complement_table
      else:
          ttable = _dna_complement_table
      return sequence.translate(ttable)
  
  
  def complement_rna(sequence):
      """Return the complement sequence of an RNA string.
  
      >>> complement("ACG")  # assumed DNA
      'TGC'
      >>> complement_rna("ACG")
      'UGC'
  
      If the sequence contains a T, and error is raised.
      """
      if isinstance(sequence, Seq):
          # Return a Seq
          return sequence.complement_rna()
      elif isinstance(sequence, MutableSeq):
          # Return a Seq
          return sequence.toseq().complement_rna()
      if "T" in sequence or "t" in sequence:
          if "U" in sequence or "u" in sequence:
              raise ValueError("Mixed RNA/DNA found")
          else:
              raise ValueError("DNA found, expect RNA")
      return sequence.translate(_rna_complement_table)
  
  
  def _test():
      """Run the Bio.Seq module's doctests (PRIVATE)."""
      print("Running doctests...")
      import doctest
  
      doctest.testmod(optionflags=doctest.IGNORE_EXCEPTION_DETAIL)
      print("Done")
  
  
  if __name__ == "__main__":
      _test()
  