text: # Copyright 2000-2002 Andrew Dalke.  All rights reserved.
  # Copyright 2002-2004 Brad Chapman.  All rights reserved.
  # Copyright 2006-2017 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.
  """Represent a Sequence Record, a sequence with annotation."""
  
  
  # NEEDS TO BE SYNCH WITH THE REST OF BIOPYTHON AND BIOPERL
  # In particular, the SeqRecord and BioSQL.BioSeq.DBSeqRecord classes
  # need to be in sync (this is the BioSQL "Database SeqRecord", see
  # also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
  
  _NO_SEQRECORD_COMPARISON = "SeqRecord comparison is deliberately not implemented. Explicitly compare the attributes of interest."
  
  
  class _RestrictedDict(dict):
      """Dict which only allows sequences of given length as values (PRIVATE).
  
      This simple subclass of the Python dictionary is used in the SeqRecord
      object for holding per-letter-annotations.  This class is intended to
      prevent simple errors by only allowing python sequences (e.g. lists,
      strings and tuples) to be stored, and only if their length matches that
      expected (the length of the SeqRecord's seq object).  It cannot however
      prevent the entries being edited in situ (for example appending entries
      to a list).
  
      >>> x = _RestrictedDict(5)
      >>> x["test"] = "hello"
      >>> x
      {'test': 'hello'}
  
      Adding entries which don't have the expected length are blocked:
  
      >>> x["test"] = "hello world"
      Traceback (most recent call last):
      ...
      TypeError: We only allow python sequences (lists, tuples or strings) of length 5.
  
      The expected length is stored as a private attribute,
  
      >>> x._length
      5
  
      In order that the SeqRecord (and other objects using this class) can be
      pickled, for example for use in the multiprocessing library, we need to
      be able to pickle the restricted dictionary objects.
  
      Using the default protocol, which is 0 on Python 2.x,
  
      >>> import pickle
      >>> y = pickle.loads(pickle.dumps(x))
      >>> y
      {'test': 'hello'}
      >>> y._length
      5
  
      Using the highest protocol, which is 2 on Python 2.x,
  
      >>> import pickle
      >>> z = pickle.loads(pickle.dumps(x, pickle.HIGHEST_PROTOCOL))
      >>> z
      {'test': 'hello'}
      >>> z._length
      5
      """
  
      def __init__(self, length):
          """Create an EMPTY restricted dictionary."""
          dict.__init__(self)
          self._length = int(length)
  
      def __setitem__(self, key, value):
          # The check hasattr(self, "_length") is to cope with pickle protocol 2
          # I couldn't seem to avoid this with __getstate__ and __setstate__
          if (
              not hasattr(value, "__len__")
              or not hasattr(value, "__getitem__")
              or (hasattr(self, "_length") and len(value) != self._length)
          ):
              raise TypeError(
                  "We only allow python sequences (lists, tuples or "
                  "strings) of length {0}.".format(self._length)
              )
          dict.__setitem__(self, key, value)
  
      def update(self, new_dict):
          # Force this to go via our strict __setitem__ method
          for (key, value) in new_dict.items():
              self[key] = value
  
  
  class SeqRecord:
      """A SeqRecord object holds a sequence and information about it.
  
      Main attributes:
       - id          - Identifier such as a locus tag (string)
       - seq         - The sequence itself (Seq object or similar)
  
      Additional attributes:
       - name        - Sequence name, e.g. gene name (string)
       - description - Additional text (string)
       - dbxrefs     - List of database cross references (list of strings)
       - features    - Any (sub)features defined (list of SeqFeature objects)
       - annotations - Further information about the whole sequence (dictionary).
         Most entries are strings, or lists of strings.
       - letter_annotations - Per letter/symbol annotation (restricted
         dictionary). This holds Python sequences (lists, strings
         or tuples) whose length matches that of the sequence.
         A typical use would be to hold a list of integers
         representing sequencing quality scores, or a string
         representing the secondary structure.
  
      You will typically use Bio.SeqIO to read in sequences from files as
      SeqRecord objects.  However, you may want to create your own SeqRecord
      objects directly (see the __init__ method for further details):
  
      >>> from Bio.Seq import Seq
      >>> from Bio.SeqRecord import SeqRecord
      >>> from Bio.Alphabet import IUPAC
      >>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
      ...                         IUPAC.protein),
      ...                    id="YP_025292.1", name="HokC",
      ...                    description="toxic membrane protein")
      >>> print(record)
      ID: YP_025292.1
      Name: HokC
      Description: toxic membrane protein
      Number of features: 0
      Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
  
      If you want to save SeqRecord objects to a sequence file, use Bio.SeqIO
      for this.  For the special case where you want the SeqRecord turned into
      a string in a particular file format there is a format method which uses
      Bio.SeqIO internally:
  
      >>> print(record.format("fasta"))
      >YP_025292.1 toxic membrane protein
      MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
      <BLANKLINE>
  
      You can also do things like slicing a SeqRecord, checking its length, etc
  
      >>> len(record)
      44
      >>> edited = record[:10] + record[11:]
      >>> print(edited.seq)
      MKQHKAMIVAIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
      >>> print(record.seq)
      MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
  
      """
  
      def __init__(
          self,
          seq,
          id="<unknown id>",
          name="<unknown name>",
          description="<unknown description>",
          dbxrefs=None,
          features=None,
          annotations=None,
          letter_annotations=None,
      ):
          """Create a SeqRecord.
  
          Arguments:
           - seq         - Sequence, required (Seq, MutableSeq or UnknownSeq)
           - id          - Sequence identifier, recommended (string)
           - name        - Sequence name, optional (string)
           - description - Sequence description, optional (string)
           - dbxrefs     - Database cross references, optional (list of strings)
           - features    - Any (sub)features, optional (list of SeqFeature objects)
           - annotations - Dictionary of annotations for the whole sequence
           - letter_annotations - Dictionary of per-letter-annotations, values
             should be strings, list or tuples of the same length as the full
             sequence.
  
          You will typically use Bio.SeqIO to read in sequences from files as
          SeqRecord objects.  However, you may want to create your own SeqRecord
          objects directly.
  
          Note that while an id is optional, we strongly recommend you supply a
          unique id string for each record.  This is especially important
          if you wish to write your sequences to a file.
  
          If you don't have the actual sequence, but you do know its length,
          then using the UnknownSeq object from Bio.Seq is appropriate.
  
          You can create a 'blank' SeqRecord object, and then populate the
          attributes later.
          """
          if id is not None and not isinstance(id, str):
              # Lots of existing code uses id=None... this may be a bad idea.
              raise TypeError("id argument should be a string")
          if not isinstance(name, str):
              raise TypeError("name argument should be a string")
          if not isinstance(description, str):
              raise TypeError("description argument should be a string")
          self._seq = seq
          self.id = id
          self.name = name
          self.description = description
  
          # database cross references (for the whole sequence)
          if dbxrefs is None:
              dbxrefs = []
          elif not isinstance(dbxrefs, list):
              raise TypeError("dbxrefs argument should be a list (of strings)")
          self.dbxrefs = dbxrefs
  
          # annotations about the whole sequence
          if annotations is None:
              annotations = {}
          elif not isinstance(annotations, dict):
              raise TypeError("annotations argument should be a dict")
          self.annotations = annotations
  
          if letter_annotations is None:
              # annotations about each letter in the sequence
              if seq is None:
                  # Should we allow this and use a normal unrestricted dict?
                  self._per_letter_annotations = _RestrictedDict(length=0)
              else:
                  try:
                      self._per_letter_annotations = _RestrictedDict(length=len(seq))
                  except TypeError:
                      raise TypeError("seq argument should be a Seq object or similar")
          else:
              # This will be handled via the property set function, which will
              # turn this into a _RestrictedDict and thus ensure all the values
              # in the dict are the right length
              self.letter_annotations = letter_annotations
  
          # annotations about parts of the sequence
          if features is None:
              features = []
          elif not isinstance(features, list):
              raise TypeError(
                  "features argument should be a list (of SeqFeature objects)"
              )
          self.features = features
  
      # TODO - Just make this a read only property?
      def _set_per_letter_annotations(self, value):
          if not isinstance(value, dict):
              raise TypeError(
                  "The per-letter-annotations should be a (restricted) dictionary."
              )
          # Turn this into a restricted-dictionary (and check the entries)
          try:
              self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
          except AttributeError:
              # e.g. seq is None
              self._per_letter_annotations = _RestrictedDict(length=0)
          self._per_letter_annotations.update(value)
  
      letter_annotations = property(
          fget=lambda self: self._per_letter_annotations,
          fset=_set_per_letter_annotations,
          doc="""Dictionary of per-letter-annotation for the sequence.
  
          For example, this can hold quality scores used in FASTQ or QUAL files.
          Consider this example using Bio.SeqIO to read in an example Solexa
          variant FASTQ file as a SeqRecord:
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
          >>> print("%s %s" % (record.id, record.seq))
          slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
          >>> print(list(record.letter_annotations))
          ['solexa_quality']
          >>> print(record.letter_annotations["solexa_quality"])
          [40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, -1, -2, -3, -4, -5]
  
          The letter_annotations get sliced automatically if you slice the
          parent SeqRecord, for example taking the last ten bases:
  
          >>> sub_record = record[-10:]
          >>> print("%s %s" % (sub_record.id, sub_record.seq))
          slxa_0001_1_0001_01 ACGTNNNNNN
          >>> print(sub_record.letter_annotations["solexa_quality"])
          [4, 3, 2, 1, 0, -1, -2, -3, -4, -5]
  
          Any python sequence (i.e. list, tuple or string) can be recorded in
          the SeqRecord's letter_annotations dictionary as long as the length
          matches that of the SeqRecord's sequence.  e.g.
  
          >>> len(sub_record.letter_annotations)
          1
          >>> sub_record.letter_annotations["dummy"] = "abcdefghij"
          >>> len(sub_record.letter_annotations)
          2
  
          You can delete entries from the letter_annotations dictionary as usual:
  
          >>> del sub_record.letter_annotations["solexa_quality"]
          >>> sub_record.letter_annotations
          {'dummy': 'abcdefghij'}
  
          You can completely clear the dictionary easily as follows:
  
          >>> sub_record.letter_annotations = {}
          >>> sub_record.letter_annotations
          {}
  
          Note that if replacing the record's sequence with a sequence of a
          different length you must first clear the letter_annotations dict.
          """,
      )
  
      def _set_seq(self, value):
          # TODO - Add a deprecation warning that the seq should be write only?
          if self._per_letter_annotations:
              if len(self) != len(value):
                  # TODO - Make this a warning? Silently empty the dictionary?
                  raise ValueError("You must empty the letter annotations first!")
              else:
                  # Leave the existing per letter annotations unchanged:
                  self._seq = value
          else:
              self._seq = value
              # Reset the (empty) letter annotations dict with new length:
              try:
                  self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
              except AttributeError:
                  # e.g. seq is None
                  self._per_letter_annotations = _RestrictedDict(length=0)
  
      seq = property(
          fget=lambda self: self._seq,
          fset=_set_seq,
          doc="The sequence itself, as a Seq or MutableSeq object.",
      )
  
      def __getitem__(self, index):
          """Return a sub-sequence or an individual letter.
  
          Slicing, e.g. my_record[5:10], returns a new SeqRecord for
          that sub-sequence with some annotation preserved as follows:
  
          * The name, id and description are kept as-is.
          * Any per-letter-annotations are sliced to match the requested
            sub-sequence.
          * Unless a stride is used, all those features which fall fully
            within the subsequence are included (with their locations
            adjusted accordingly). If you want to preserve any truncated
            features (e.g. GenBank/EMBL source features), you must
            explicitly add them to the new SeqRecord yourself.
          * The annotations dictionary and the dbxrefs list are not used
            for the new SeqRecord, as in general they may not apply to the
            subsequence. If you want to preserve them, you must explicitly
            copy them to the new SeqRecord yourself.
  
          Using an integer index, e.g. my_record[5] is shorthand for
          extracting that letter from the sequence, my_record.seq[5].
  
          For example, consider this short protein and its secondary
          structure as encoded by the PDB (e.g. H for alpha helices),
          plus a simple feature for its histidine self phosphorylation
          site:
  
          >>> from Bio.Seq import Seq
          >>> from Bio.SeqRecord import SeqRecord
          >>> from Bio.SeqFeature import SeqFeature, FeatureLocation
          >>> from Bio.Alphabet import IUPAC
          >>> rec = SeqRecord(Seq("MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLAT"
          ...                     "EMMSEQDGYLAESINKDIEECNAIIEQFIDYLR",
          ...                     IUPAC.protein),
          ...                 id="1JOY", name="EnvZ",
          ...                 description="Homodimeric domain of EnvZ from E. coli")
          >>> rec.letter_annotations["secondary_structure"] = "  S  SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT  "
          >>> rec.features.append(SeqFeature(FeatureLocation(20, 21),
          ...                     type = "Site"))
  
          Now let's have a quick look at the full record,
  
          >>> print(rec)
          ID: 1JOY
          Name: EnvZ
          Description: Homodimeric domain of EnvZ from E. coli
          Number of features: 1
          Per letter annotation for: secondary_structure
          Seq('MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLATEMMSEQDGYLAESINKDIEE...YLR', IUPACProtein())
          >>> rec.letter_annotations["secondary_structure"]
          '  S  SSSSSSHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHTT  '
          >>> print(rec.features[0].location)
          [20:21]
  
          Now let's take a sub sequence, here chosen as the first (fractured)
          alpha helix which includes the histidine phosphorylation site:
  
          >>> sub = rec[11:41]
          >>> print(sub)
          ID: 1JOY
          Name: EnvZ
          Description: Homodimeric domain of EnvZ from E. coli
          Number of features: 1
          Per letter annotation for: secondary_structure
          Seq('RTLLMAGVSHDLRTPLTRIRLATEMMSEQD', IUPACProtein())
          >>> sub.letter_annotations["secondary_structure"]
          'HHHHHTTTHHHHHHHHHHHHHHHHHHHHHH'
          >>> print(sub.features[0].location)
          [9:10]
  
          You can also of course omit the start or end values, for
          example to get the first ten letters only:
  
          >>> print(rec[:10])
          ID: 1JOY
          Name: EnvZ
          Description: Homodimeric domain of EnvZ from E. coli
          Number of features: 0
          Per letter annotation for: secondary_structure
          Seq('MAAGVKQLAD', IUPACProtein())
  
          Or for the last ten letters:
  
          >>> print(rec[-10:])
          ID: 1JOY
          Name: EnvZ
          Description: Homodimeric domain of EnvZ from E. coli
          Number of features: 0
          Per letter annotation for: secondary_structure
          Seq('IIEQFIDYLR', IUPACProtein())
  
          If you omit both, then you get a copy of the original record (although
          lacking the annotations and dbxrefs):
  
          >>> print(rec[:])
          ID: 1JOY
          Name: EnvZ
          Description: Homodimeric domain of EnvZ from E. coli
          Number of features: 1
          Per letter annotation for: secondary_structure
          Seq('MAAGVKQLADDRTLLMAGVSHDLRTPLTRIRLATEMMSEQDGYLAESINKDIEE...YLR', IUPACProtein())
  
          Finally, indexing with a simple integer is shorthand for pulling out
          that letter from the sequence directly:
  
          >>> rec[5]
          'K'
          >>> rec.seq[5]
          'K'
          """
          if isinstance(index, int):
              # NOTE - The sequence level annotation like the id, name, etc
              # do not really apply to a single character.  However, should
              # we try and expose any per-letter-annotation here?  If so how?
              return self.seq[index]
          elif isinstance(index, slice):
              if self.seq is None:
                  raise ValueError("If the sequence is None, we cannot slice it.")
              parent_length = len(self)
              try:
                  from BioSQL.BioSeq import DBSeqRecord
  
                  biosql_available = True
              except ImportError:
                  biosql_available = False
  
              if biosql_available and isinstance(self, DBSeqRecord):
                  answer = SeqRecord(
                      self.seq[index],
                      id=self.id,
                      name=self.name,
                      description=self.description,
                  )
              else:
                  answer = self.__class__(
                      self.seq[index],
                      id=self.id,
                      name=self.name,
                      description=self.description,
                  )
              # TODO - The description may no longer apply.
              # It would be safer to change it to something
              # generic like "edited" or the default value.
  
              # Don't copy the annotation dict and dbxefs list,
              # they may not apply to a subsequence.
              # answer.annotations = dict(self.annotations.items())
              # answer.dbxrefs = self.dbxrefs[:]
              # TODO - Review this in light of adding SeqRecord objects?
  
              # TODO - Cope with strides by generating ambiguous locations?
              start, stop, step = index.indices(parent_length)
              if step == 1:
                  # Select relevant features, add them with shifted locations
                  # assert str(self.seq)[index] == str(self.seq)[start:stop]
                  for f in self.features:
                      if f.ref or f.ref_db:
                          # TODO - Implement this (with lots of tests)?
                          import warnings
  
                          warnings.warn(
                              "When slicing SeqRecord objects, any "
                              "SeqFeature referencing other sequences (e.g. "
                              "from segmented GenBank records) are ignored."
                          )
                          continue
                      if (
                          start <= f.location.nofuzzy_start
                          and f.location.nofuzzy_end <= stop
                      ):
                          answer.features.append(f._shift(-start))
  
              # Slice all the values to match the sliced sequence
              # (this should also work with strides, even negative strides):
              for key, value in self.letter_annotations.items():
                  answer._per_letter_annotations[key] = value[index]
  
              return answer
          raise ValueError("Invalid index")
  
      def __iter__(self):
          """Iterate over the letters in the sequence.
  
          For example, using Bio.SeqIO to read in a protein FASTA file:
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Fasta/loveliesbleeding.pro", "fasta")
          >>> for amino in record:
          ...     print(amino)
          ...     if amino == "L": break
          X
          A
          G
          L
          >>> print(record.seq[3])
          L
  
          This is just a shortcut for iterating over the sequence directly:
  
          >>> for amino in record.seq:
          ...     print(amino)
          ...     if amino == "L": break
          X
          A
          G
          L
          >>> print(record.seq[3])
          L
  
          Note that this does not facilitate iteration together with any
          per-letter-annotation.  However, you can achieve that using the
          python zip function on the record (or its sequence) and the relevant
          per-letter-annotation:
  
          >>> from Bio import SeqIO
          >>> rec = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
          >>> print("%s %s" % (rec.id, rec.seq))
          slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
          >>> print(list(rec.letter_annotations))
          ['solexa_quality']
          >>> for nuc, qual in zip(rec, rec.letter_annotations["solexa_quality"]):
          ...     if qual > 35:
          ...         print("%s %i" % (nuc, qual))
          A 40
          C 39
          G 38
          T 37
          A 36
  
          You may agree that using zip(rec.seq, ...) is more explicit than using
          zip(rec, ...) as shown above.
          """
          return iter(self.seq)
  
      def __contains__(self, char):
          """Implement the 'in' keyword, searches the sequence.
  
          e.g.
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Fasta/sweetpea.nu", "fasta")
          >>> "GAATTC" in record
          False
          >>> "AAA" in record
          True
  
          This essentially acts as a proxy for using "in" on the sequence:
  
          >>> "GAATTC" in record.seq
          False
          >>> "AAA" in record.seq
          True
  
          Note that you can also use Seq objects as the query,
  
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import generic_dna
          >>> Seq("AAA") in record
          True
          >>> Seq("AAA", generic_dna) in record
          True
  
          See also the Seq object's __contains__ method.
          """
          return char in self.seq
  
      def __str__(self):
          """Return a human readable summary of the record and its annotation (string).
  
          The python built in function str works by calling the object's ___str__
          method.  e.g.
  
          >>> from Bio.Seq import Seq
          >>> from Bio.SeqRecord import SeqRecord
          >>> from Bio.Alphabet import IUPAC
          >>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
          ...                         IUPAC.protein),
          ...                    id="YP_025292.1", name="HokC",
          ...                    description="toxic membrane protein, small")
          >>> print(str(record))
          ID: YP_025292.1
          Name: HokC
          Description: toxic membrane protein, small
          Number of features: 0
          Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
  
          In this example you don't actually need to call str explicity, as the
          print command does this automatically:
  
          >>> print(record)
          ID: YP_025292.1
          Name: HokC
          Description: toxic membrane protein, small
          Number of features: 0
          Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein())
  
          Note that long sequences are shown truncated.
          """
          lines = []
          if self.id:
              lines.append("ID: {0}".format(self.id))
          if self.name:
              lines.append("Name: {0}".format(self.name))
          if self.description:
              lines.append("Description: {0}".format(self.description))
          if self.dbxrefs:
              lines.append("Database cross-references: " + ", ".join(self.dbxrefs))
          lines.append("Number of features: {0}".format(len(self.features)))
          for a in self.annotations:
              lines.append("/{0}={1}".format(a, str(self.annotations[a])))
          if self.letter_annotations:
              lines.append(
                  "Per letter annotation for: " + ", ".join(self.letter_annotations)
              )
          # Don't want to include the entire sequence,
          # and showing the alphabet is useful:
          lines.append(repr(self.seq))
          return "\n".join(lines)
  
      def __repr__(self):
          """Return a concise summary of the record for debugging (string).
  
          The python built in function repr works by calling the object's ___repr__
          method.  e.g.
  
          >>> from Bio.Seq import Seq
          >>> from Bio.SeqRecord import SeqRecord
          >>> from Bio.Alphabet import generic_protein
          >>> rec = SeqRecord(Seq("MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT"
          ...                    +"GEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQ"
          ...                    +"SGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQ"
          ...                    +"PQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF",
          ...                    generic_protein),
          ...                 id="NP_418483.1", name="b4059",
          ...                 description="ssDNA-binding protein",
          ...                 dbxrefs=["ASAP:13298", "GI:16131885", "GeneID:948570"])
          >>> print(repr(rec))
          SeqRecord(seq=Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE...IPF', ProteinAlphabet()), id='NP_418483.1', name='b4059', description='ssDNA-binding protein', dbxrefs=['ASAP:13298', 'GI:16131885', 'GeneID:948570'])
  
          At the python prompt you can also use this shorthand:
  
          >>> rec
          SeqRecord(seq=Seq('MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTE...IPF', ProteinAlphabet()), id='NP_418483.1', name='b4059', description='ssDNA-binding protein', dbxrefs=['ASAP:13298', 'GI:16131885', 'GeneID:948570'])
  
          Note that long sequences are shown truncated. Also note that any
          annotations, letter_annotations and features are not shown (as they
          would lead to a very long string).
          """
          return "{0}(seq={1!r}, id={2!r}, name={3!r}, description={4!r}, dbxrefs={5!r})".format(
              self.__class__.__name__,
              self.seq,
              self.id,
              self.name,
              self.description,
              self.dbxrefs,
          )
  
      def format(self, format):
          r"""Return the record as a string in the specified file format.
  
          The format should be a lower case string supported as an output
          format by Bio.SeqIO, which is used to turn the SeqRecord into a
          string.  e.g.
  
          >>> from Bio.Seq import Seq
          >>> from Bio.SeqRecord import SeqRecord
          >>> from Bio.Alphabet import IUPAC
          >>> record = SeqRecord(Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF",
          ...                         IUPAC.protein),
          ...                    id="YP_025292.1", name="HokC",
          ...                    description="toxic membrane protein")
          >>> record.format("fasta")
          '>YP_025292.1 toxic membrane protein\nMKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF\n'
          >>> print(record.format("fasta"))
          >YP_025292.1 toxic membrane protein
          MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF
          <BLANKLINE>
  
          The python print command automatically appends a new line, meaning
          in this example a blank line is shown.  If you look at the string
          representation you can see there is a trailing new line (shown as
          slash n) which is important when writing to a file or if
          concatenating multiple sequence strings together.
  
          Note that this method will NOT work on every possible file format
          supported by Bio.SeqIO (e.g. some are for multiple sequences only,
          and binary formats are not supported).
          """
          # See also the __format__ added for Python 2.6 / 3.0, PEP 3101
          # See also the Bio.Align.Generic.Alignment class and its format()
          return self.__format__(format)
  
      def __format__(self, format_spec):
          """Return the record as a string in the specified file format.
  
          This method supports the python format() function added in
          Python 2.6/3.0.  The format_spec should be a lower case string
          supported by Bio.SeqIO as an output file format. See also the
          SeqRecord's format() method.
  
          Under Python 3 binary formats raise a ValueError, while on
          Python 2 this will work with a deprecation warning.
          """
          if not format_spec:
              # Follow python convention and default to using __str__
              return str(self)
          from Bio import SeqIO
  
          # Easy case, can call string-building function directly
          if format_spec in SeqIO._FormatToString:
              return SeqIO._FormatToString[format_spec](self)
  
          if format_spec in SeqIO._BinaryFormats:
              import sys
  
              if sys.version_info[0] < 3:
                  import warnings
                  from Bio import BiopythonDeprecationWarning
  
                  warnings.warn(
                      "Binary format %s cannot be used with SeqRecord format method on Python 3"
                      % format_spec,
                      BiopythonDeprecationWarning,
                  )
                  # Continue - Python 2 StringIO will work...
              else:
                  raise ValueError(
                      "Binary format %s cannot be used with SeqRecord format method"
                      % format_spec
                  )
  
          # Harder case, make a temp handle instead
          from io import StringIO
  
          handle = StringIO()
          SeqIO.write(self, handle, format_spec)
          return handle.getvalue()
  
      def __len__(self):
          """Return the length of the sequence.
  
          For example, using Bio.SeqIO to read in a FASTA nucleotide file:
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Fasta/sweetpea.nu", "fasta")
          >>> len(record)
          309
          >>> len(record.seq)
          309
          """
          return len(self.seq)
  
      def __lt__(self, other):
          """Define the less-than operand (not implemented)."""
          raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
  
      def __le___(self, other):
          """Define the less-than-or-equal-to operand (not implemented)."""
          raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
  
      def __eq__(self, other):
          """Define the equal-to operand (not implemented)."""
          raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
  
      def __ne__(self, other):
          """Define the not-equal-to operand (not implemented)."""
          raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
  
      def __gt__(self, other):
          """Define the greater-than operand (not implemented)."""
          raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
  
      def __ge__(self, other):
          """Define the greater-than-or-equal-to operand (not implemented)."""
          raise NotImplementedError(_NO_SEQRECORD_COMPARISON)
  
      # Make SeqRecord unhashable explicit, required for Python 2.
      # See github issue 929 for related discussion.
      __hash__ = None
  
      def __bool__(self):
          """Boolean value of an instance of this class (True).
  
          This behaviour is for backwards compatibility, since until the
          __len__ method was added, a SeqRecord always evaluated as True.
  
          Note that in comparison, a Seq object will evaluate to False if it
          has a zero length sequence.
  
          WARNING: The SeqRecord may in future evaluate to False when its
          sequence is of zero length (in order to better match the Seq
          object behaviour)!
          """
          return True
  
      def __add__(self, other):
          """Add another sequence or string to this sequence.
  
          The other sequence can be a SeqRecord object, a Seq object (or
          similar, e.g. a MutableSeq) or a plain Python string. If you add
          a plain string or a Seq (like) object, the new SeqRecord will simply
          have this appended to the existing data. However, any per letter
          annotation will be lost:
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
          >>> print("%s %s" % (record.id, record.seq))
          slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
          >>> print(list(record.letter_annotations))
          ['solexa_quality']
  
          >>> new = record + "ACT"
          >>> print("%s %s" % (new.id, new.seq))
          slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNNACT
          >>> print(list(new.letter_annotations))
          []
  
          The new record will attempt to combine the annotation, but for any
          ambiguities (e.g. different names) it defaults to omitting that
          annotation.
  
          >>> from Bio import SeqIO
          >>> with open("GenBank/pBAD30.gb") as handle:
          ...     plasmid = SeqIO.read(handle, "gb")
          >>> print("%s %i" % (plasmid.id, len(plasmid)))
          pBAD30 4923
  
          Now let's cut the plasmid into two pieces, and join them back up the
          other way round (i.e. shift the starting point on this plasmid, have
          a look at the annotated features in the original file to see why this
          particular split point might make sense):
  
          >>> left = plasmid[:3765]
          >>> right = plasmid[3765:]
          >>> new = right + left
          >>> print("%s %i" % (new.id, len(new)))
          pBAD30 4923
          >>> str(new.seq) == str(right.seq + left.seq)
          True
          >>> len(new.features) == len(left.features) + len(right.features)
          True
  
          When we add the left and right SeqRecord objects, their annotation
          is all consistent, so it is all conserved in the new SeqRecord:
  
          >>> new.id == left.id == right.id == plasmid.id
          True
          >>> new.name == left.name == right.name == plasmid.name
          True
          >>> new.description == plasmid.description
          True
          >>> new.annotations == left.annotations == right.annotations
          True
          >>> new.letter_annotations == plasmid.letter_annotations
          True
          >>> new.dbxrefs == left.dbxrefs == right.dbxrefs
          True
  
          However, we should point out that when we sliced the SeqRecord,
          any annotations dictionary or dbxrefs list entries were lost.
          You can explicitly copy them like this:
  
          >>> new.annotations = plasmid.annotations.copy()
          >>> new.dbxrefs = plasmid.dbxrefs[:]
          """
          if not isinstance(other, SeqRecord):
              # Assume it is a string or a Seq.
              # Note can't transfer any per-letter-annotations
              return SeqRecord(
                  self.seq + other,
                  id=self.id,
                  name=self.name,
                  description=self.description,
                  features=self.features[:],
                  annotations=self.annotations.copy(),
                  dbxrefs=self.dbxrefs[:],
              )
          # Adding two SeqRecord objects... must merge annotation.
          answer = SeqRecord(
              self.seq + other.seq, features=self.features[:], dbxrefs=self.dbxrefs[:]
          )
          # Will take all the features and all the db cross refs,
          length = len(self)
          for f in other.features:
              answer.features.append(f._shift(length))
          del length
          for ref in other.dbxrefs:
              if ref not in answer.dbxrefs:
                  answer.dbxrefs.append(ref)
          # Take common id/name/description/annotation
          if self.id == other.id:
              answer.id = self.id
          if self.name == other.name:
              answer.name = self.name
          if self.description == other.description:
              answer.description = self.description
          for k, v in self.annotations.items():
              if k in other.annotations and other.annotations[k] == v:
                  answer.annotations[k] = v
          # Can append matching per-letter-annotation
          for k, v in self.letter_annotations.items():
              if k in other.letter_annotations:
                  answer.letter_annotations[k] = v + other.letter_annotations[k]
          return answer
  
      def __radd__(self, other):
          """Add another sequence or string to this sequence (from the left).
  
          This method handles adding a Seq object (or similar, e.g. MutableSeq)
          or a plain Python string (on the left) to a SeqRecord (on the right).
          See the __add__ method for more details, but for example:
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
          >>> print("%s %s" % (record.id, record.seq))
          slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
          >>> print(list(record.letter_annotations))
          ['solexa_quality']
  
          >>> new = "ACT" + record
          >>> print("%s %s" % (new.id, new.seq))
          slxa_0001_1_0001_01 ACTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
          >>> print(list(new.letter_annotations))
          []
          """
          if isinstance(other, SeqRecord):
              raise RuntimeError(
                  "This should have happened via the __add__ of "
                  "the other SeqRecord being added!"
              )
          # Assume it is a string or a Seq.
          # Note can't transfer any per-letter-annotations
          offset = len(other)
          return SeqRecord(
              other + self.seq,
              id=self.id,
              name=self.name,
              description=self.description,
              features=[f._shift(offset) for f in self.features],
              annotations=self.annotations.copy(),
              dbxrefs=self.dbxrefs[:],
          )
  
      def upper(self):
          """Return a copy of the record with an upper case sequence.
  
          All the annotation is preserved unchanged. e.g.
  
          >>> from Bio.Alphabet import generic_dna
          >>> from Bio.Seq import Seq
          >>> from Bio.SeqRecord import SeqRecord
          >>> record = SeqRecord(Seq("acgtACGT", generic_dna), id="Test",
          ...                    description = "Made up for this example")
          >>> record.letter_annotations["phred_quality"] = [1, 2, 3, 4, 5, 6, 7, 8]
          >>> print(record.upper().format("fastq"))
          @Test Made up for this example
          ACGTACGT
          +
          "#$%&'()
          <BLANKLINE>
  
          Naturally, there is a matching lower method:
  
          >>> print(record.lower().format("fastq"))
          @Test Made up for this example
          acgtacgt
          +
          "#$%&'()
          <BLANKLINE>
          """
          return SeqRecord(
              self.seq.upper(),
              id=self.id,
              name=self.name,
              description=self.description,
              dbxrefs=self.dbxrefs[:],
              features=self.features[:],
              annotations=self.annotations.copy(),
              letter_annotations=self.letter_annotations.copy(),
          )
  
      def lower(self):
          """Return a copy of the record with a lower case sequence.
  
          All the annotation is preserved unchanged. e.g.
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Fasta/aster.pro", "fasta")
          >>> print(record.format("fasta"))
          >gi|3298468|dbj|BAA31520.1| SAMIPF
          GGHVNPAVTFGAFVGGNITLLRGIVYIIAQLLGSTVACLLLKFVTNDMAVGVFSLSAGVG
          VTNALVFEIVMTFGLVYTVYATAIDPKKGSLGTIAPIAIGFIVGANI
          <BLANKLINE>
          >>> print(record.lower().format("fasta"))
          >gi|3298468|dbj|BAA31520.1| SAMIPF
          gghvnpavtfgafvggnitllrgivyiiaqllgstvaclllkfvtndmavgvfslsagvg
          vtnalvfeivmtfglvytvyataidpkkgslgtiapiaigfivgani
          <BLANKLINE>
  
          To take a more annotation rich example,
  
          >>> from Bio import SeqIO
          >>> old = SeqIO.read("EMBL/TRBG361.embl", "embl")
          >>> len(old.features)
          3
          >>> new = old.lower()
          >>> len(old.features) == len(new.features)
          True
          >>> old.annotations["organism"] == new.annotations["organism"]
          True
          >>> old.dbxrefs == new.dbxrefs
          True
          """
          return SeqRecord(
              self.seq.lower(),
              id=self.id,
              name=self.name,
              description=self.description,
              dbxrefs=self.dbxrefs[:],
              features=self.features[:],
              annotations=self.annotations.copy(),
              letter_annotations=self.letter_annotations.copy(),
          )
  
      def reverse_complement(
          self,
          id=False,
          name=False,
          description=False,
          features=True,
          annotations=False,
          letter_annotations=True,
          dbxrefs=False,
      ):
          """Return new SeqRecord with reverse complement sequence.
  
          By default the new record does NOT preserve the sequence identifier,
          name, description, general annotation or database cross-references -
          these are unlikely to apply to the reversed sequence.
  
          You can specify the returned record's id, name and description as
          strings, or True to keep that of the parent, or False for a default.
  
          You can specify the returned record's features with a list of
          SeqFeature objects, or True to keep that of the parent, or False to
          omit them. The default is to keep the original features (with the
          strand and locations adjusted).
  
          You can also specify both the returned record's annotations and
          letter_annotations as dictionaries, True to keep that of the parent,
          or False to omit them. The default is to keep the original
          annotations (with the letter annotations reversed).
  
          To show what happens to the pre-letter annotations, consider an
          example Solexa variant FASTQ file with a single entry, which we'll
          read in as a SeqRecord:
  
          >>> from Bio import SeqIO
          >>> record = SeqIO.read("Quality/solexa_faked.fastq", "fastq-solexa")
          >>> print("%s %s" % (record.id, record.seq))
          slxa_0001_1_0001_01 ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTNNNNNN
          >>> print(list(record.letter_annotations))
          ['solexa_quality']
          >>> print(record.letter_annotations["solexa_quality"])
          [40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0, -1, -2, -3, -4, -5]
  
          Now take the reverse complement, here we explicitly give a new
          identifier (the old identifier with a suffix):
  
          >>> rc_record = record.reverse_complement(id=record.id + "_rc")
          >>> print("%s %s" % (rc_record.id, rc_record.seq))
          slxa_0001_1_0001_01_rc NNNNNNACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT
  
          Notice that the per-letter-annotations have also been reversed,
          although this may not be appropriate for all cases.
  
          >>> print(rc_record.letter_annotations["solexa_quality"])
          [-5, -4, -3, -2, -1, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]
  
          Now for the features, we need a different example. Parsing a GenBank
          file is probably the easiest way to get an nice example with features
          in it...
  
          >>> from Bio import SeqIO
          >>> with open("GenBank/pBAD30.gb") as handle:
          ...     plasmid = SeqIO.read(handle, "gb")
          >>> print("%s %i" % (plasmid.id, len(plasmid)))
          pBAD30 4923
          >>> plasmid.seq
          Seq('GCTAGCGGAGTGTATACTGGCTTACTATGTTGGCACTGATGAGGGTGTCAGTGA...ATG', IUPACAmbiguousDNA())
          >>> len(plasmid.features)
          13
  
          Now, let's take the reverse complement of this whole plasmid:
  
          >>> rc_plasmid = plasmid.reverse_complement(id=plasmid.id+"_rc")
          >>> print("%s %i" % (rc_plasmid.id, len(rc_plasmid)))
          pBAD30_rc 4923
          >>> rc_plasmid.seq
          Seq('CATGGGCAAATATTATACGCAAGGCGACAAGGTGCTGATGCCGCTGGCGATTCA...AGC', IUPACAmbiguousDNA())
          >>> len(rc_plasmid.features)
          13
  
          Let's compare the first CDS feature - it has gone from being the
          second feature (index 1) to the second last feature (index -2), its
          strand has changed, and the location switched round.
  
          >>> print(plasmid.features[1])
          type: CDS
          location: [1081:1960](-)
          qualifiers:
              Key: label, Value: ['araC']
              Key: note, Value: ['araC regulator of the arabinose BAD promoter']
              Key: vntifkey, Value: ['4']
          <BLANKLINE>
          >>> print(rc_plasmid.features[-2])
          type: CDS
          location: [2963:3842](+)
          qualifiers:
              Key: label, Value: ['araC']
              Key: note, Value: ['araC regulator of the arabinose BAD promoter']
              Key: vntifkey, Value: ['4']
          <BLANKLINE>
  
          You can check this new location, based on the length of the plasmid:
  
          >>> len(plasmid) - 1081
          3842
          >>> len(plasmid) - 1960
          2963
  
          Note that if the SeqFeature annotation includes any strand specific
          information (e.g. base changes for a SNP), this information is not
          amended, and would need correction after the reverse complement.
  
          Note trying to reverse complement a protein SeqRecord raises an
          exception:
  
          >>> from Bio.SeqRecord import SeqRecord
          >>> from Bio.Seq import Seq
          >>> from Bio.Alphabet import IUPAC
          >>> protein_rec = SeqRecord(Seq("MAIVMGR", IUPAC.protein), id="Test")
          >>> protein_rec.reverse_complement()
          Traceback (most recent call last):
             ...
          ValueError: Proteins do not have complements!
  
          Also note you can reverse complement a SeqRecord using a MutableSeq:
  
          >>> from Bio.SeqRecord import SeqRecord
          >>> from Bio.Seq import MutableSeq
          >>> from Bio.Alphabet import generic_dna
          >>> rec = SeqRecord(MutableSeq("ACGT", generic_dna), id="Test")
          >>> rec.seq[0] = "T"
          >>> print("%s %s" % (rec.id, rec.seq))
          Test TCGT
          >>> rc = rec.reverse_complement(id=True)
          >>> print("%s %s" % (rc.id, rc.seq))
          Test ACGA
          """
          from Bio.Seq import MutableSeq  # Lazy to avoid circular imports
  
          if isinstance(self.seq, MutableSeq):
              # Currently the MutableSeq reverse complement is in situ
              answer = SeqRecord(self.seq.toseq().reverse_complement())
          else:
              answer = SeqRecord(self.seq.reverse_complement())
          if isinstance(id, str):
              answer.id = id
          elif id:
              answer.id = self.id
          if isinstance(name, str):
              answer.name = name
          elif name:
              answer.name = self.name
          if isinstance(description, str):
              answer.description = description
          elif description:
              answer.description = self.description
          if isinstance(dbxrefs, list):
              answer.dbxrefs = dbxrefs
          elif dbxrefs:
              # Copy the old dbxrefs
              answer.dbxrefs = self.dbxrefs[:]
          if isinstance(features, list):
              answer.features = features
          elif features:
              # Copy the old features, adjusting location and string
              length = len(answer)
              answer.features = [f._flip(length) for f in self.features]
              # The old list should have been sorted by start location,
              # reversing it will leave it sorted by what is now the end position,
              # so we need to resort in case of overlapping features.
              # NOTE - In the common case of gene before CDS (and similar) with
              # the exact same locations, this will still maintain gene before CDS
              answer.features.sort(key=lambda x: x.location.start.position)
          if isinstance(annotations, dict):
              answer.annotations = annotations
          elif annotations:
              # Copy the old annotations,
              answer.annotations = self.annotations.copy()
          if isinstance(letter_annotations, dict):
              answer.letter_annotations = letter_annotations
          elif letter_annotations:
              # Copy the old per letter annotations, reversing them
              for key, value in self.letter_annotations.items():
                  answer._per_letter_annotations[key] = value[::-1]
          return answer
  
      def translate(
          self,
          # Seq translation arguments:
          table="Standard",
          stop_symbol="*",
          to_stop=False,
          cds=False,
          gap=None,
          # SeqRecord annotation arguments:
          id=False,
          name=False,
          description=False,
          features=False,
          annotations=False,
          letter_annotations=False,
          dbxrefs=False,
      ):
          """Return new SeqRecord with translated sequence.
  
          This calls the record's .seq.translate() method (which describes
          the translation related arguments, like table for the genetic code),
  
          By default the new record does NOT preserve the sequence identifier,
          name, description, general annotation or database cross-references -
          these are unlikely to apply to the translated sequence.
  
          You can specify the returned record's id, name and description as
          strings, or True to keep that of the parent, or False for a default.
  
          You can specify the returned record's features with a list of
          SeqFeature objects, or False (default) to omit them.
  
          You can also specify both the returned record's annotations and
          letter_annotations as dictionaries, True to keep that of the parent
          (annotations only), or False (default) to omit them.
  
          e.g. Loading a FASTA gene and translating it,
  
          >>> from Bio import SeqIO
          >>> gene_record = SeqIO.read("Fasta/sweetpea.nu", "fasta")
          >>> print(gene_record.format("fasta"))
          >gi|3176602|gb|U78617.1|LOU78617 Lathyrus odoratus phytochrome A (PHYA) gene, partial cds
          CAGGCTGCGCGGTTTCTATTTATGAAGAACAAGGTCCGTATGATAGTTGATTGTCATGCA
          AAACATGTGAAGGTTCTTCAAGACGAAAAACTCCCATTTGATTTGACTCTGTGCGGTTCG
          ACCTTAAGAGCTCCACATAGTTGCCATTTGCAGTACATGGCTAACATGGATTCAATTGCT
          TCATTGGTTATGGCAGTGGTCGTCAATGACAGCGATGAAGATGGAGATAGCCGTGACGCA
          GTTCTACCACAAAAGAAAAAGAGACTTTGGGGTTTGGTAGTTTGTCATAACACTACTCCG
          AGGTTTGTT
          <BLANKLINE>
  
          And now translating the record, specifying the new ID and description:
  
          >>> protein_record = gene_record.translate(table=11,
          ...                                        id="phya",
          ...                                        description="translation")
          >>> print(protein_record.format("fasta"))
          >phya translation
          QAARFLFMKNKVRMIVDCHAKHVKVLQDEKLPFDLTLCGSTLRAPHSCHLQYMANMDSIA
          SLVMAVVVNDSDEDGDSRDAVLPQKKKRLWGLVVCHNTTPRFV
          <BLANKLINE>
  
          """
          answer = SeqRecord(
              self.seq.translate(
                  table=table, stop_symbol=stop_symbol, to_stop=to_stop, cds=cds, gap=gap
              )
          )
          if isinstance(id, str):
              answer.id = id
          elif id:
              answer.id = self.id
          if isinstance(name, str):
              answer.name = name
          elif name:
              answer.name = self.name
          if isinstance(description, str):
              answer.description = description
          elif description:
              answer.description = self.description
          if isinstance(dbxrefs, list):
              answer.dbxrefs = dbxrefs
          elif dbxrefs:
              # Copy the old dbxrefs
              answer.dbxrefs = self.dbxrefs[:]
          if isinstance(features, list):
              answer.features = features
          elif features:
              # Does not make sense to copy old features as locations wrong
              raise TypeError("Unexpected features argument %r" % features)
          if isinstance(annotations, dict):
              answer.annotations = annotations
          elif annotations:
              # Copy the old annotations
              answer.annotations = self.annotations.copy()
          if isinstance(letter_annotations, dict):
              answer.letter_annotations = letter_annotations
          elif letter_annotations:
              # Does not make sense to copy these as length now wrong
              raise TypeError(
                  "Unexpected letter_annotations argument %r" % letter_annotations
              )
          return answer
  
  
  if __name__ == "__main__":
      from Bio._utils import run_doctest
  
      run_doctest()
  