text: # Copyright 2000 by Jeffrey Chang, Brad Chapman.  All rights reserved.
  # Copyright 2006-2016 by Peter Cock.  All rights reserved.
  #
  # This code is part of the Biopython distribution and governed by its
  # license.  Please see the LICENSE file that should have been included
  # as part of this package.
  
  """Code to work with GenBank formatted files.
  
  Rather than using Bio.GenBank, you are now encouraged to use Bio.SeqIO with
  the "genbank" or "embl" format names to parse GenBank or EMBL files into
  SeqRecord and SeqFeature objects (see the Biopython tutorial for details).
  
  Using Bio.GenBank directly to parse GenBank files is only useful if you want
  to obtain GenBank-specific Record objects, which is a much closer
  representation to the raw file contents than the SeqRecord alternative from
  the FeatureParser (used in Bio.SeqIO).
  
  To use the Bio.GenBank parser, there are two helper functions:
  
      - read                  Parse a handle containing a single GenBank record
        as Bio.GenBank specific Record objects.
      - parse                 Iterate over a handle containing multiple GenBank
        records as Bio.GenBank specific Record objects.
  
  The following internal classes are not intended for direct use and may
  be deprecated in a future release.
  
  Classes:
  
      - Iterator              Iterate through a file of GenBank entries
      - ErrorFeatureParser    Catch errors caused during parsing.
      - FeatureParser         Parse GenBank data in SeqRecord and SeqFeature objects.
      - RecordParser          Parse GenBank data into a Record object.
  
  Exceptions:
  
      - ParserFailureError    Exception indicating a failure in the parser (ie.
        scanner or consumer)
      - LocationParserError   Exception indicating a problem with the spark based
        location parser.
  
  """
  from __future__ import print_function
  
  import re
  import sys  # for checking if Python 2
  
  # other Biopython stuff
  from Bio import SeqFeature
  
  # other Bio.GenBank stuff
  from .utils import FeatureValueCleaner
  from .Scanner import GenBankScanner
  
  
  # Constants used to parse GenBank header lines
  GENBANK_INDENT = 12
  GENBANK_SPACER = " " * GENBANK_INDENT
  
  # Constants for parsing GenBank feature lines
  FEATURE_KEY_INDENT = 5
  FEATURE_QUALIFIER_INDENT = 21
  FEATURE_KEY_SPACER = " " * FEATURE_KEY_INDENT
  FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT
  
  # Regular expressions for location parsing
  _solo_location = r"[<>]?\d+"
  _pair_location = r"[<>]?\d+\.\.[<>]?\d+"
  _between_location = r"\d+\^\d+"
  
  _within_position = r"\(\d+\.\d+\)"
  _re_within_position = re.compile(_within_position)
  _within_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)" \
                     % (_within_position, _within_position)
  assert _re_within_position.match("(3.9)")
  assert re.compile(_within_location).match("(3.9)..10")
  assert re.compile(_within_location).match("26..(30.33)")
  assert re.compile(_within_location).match("(13.19)..(20.28)")
  
  _oneof_position = r"one\-of\(\d+(,\d+)+\)"
  _re_oneof_position = re.compile(_oneof_position)
  _oneof_location = r"([<>]?\d+|%s)\.\.([<>]?\d+|%s)" \
                     % (_oneof_position, _oneof_position)
  assert _re_oneof_position.match("one-of(6,9)")
  assert re.compile(_oneof_location).match("one-of(6,9)..101")
  assert re.compile(_oneof_location).match("one-of(6,9)..one-of(101,104)")
  assert re.compile(_oneof_location).match("6..one-of(101,104)")
  
  assert not _re_oneof_position.match("one-of(3)")
  assert _re_oneof_position.match("one-of(3,6)")
  assert _re_oneof_position.match("one-of(3,6,9)")
  
  
  _simple_location = r"\d+\.\.\d+"
  _re_simple_location = re.compile(r"^%s$" % _simple_location)
  _re_simple_compound = re.compile(r"^(join|order|bond)\(%s(,%s)*\)$"
                                   % (_simple_location, _simple_location))
  _complex_location = r"([a-zA-Z][a-zA-Z0-9_\.\|]*[a-zA-Z0-9]?\:)?(%s|%s|%s|%s|%s)" \
                      % (_pair_location, _solo_location, _between_location,
                         _within_location, _oneof_location)
  _re_complex_location = re.compile(r"^%s$" % _complex_location)
  _possibly_complemented_complex_location = r"(%s|complement\(%s\))" \
                                            % (_complex_location, _complex_location)
  _re_complex_compound = re.compile(r"^(join|order|bond)\(%s(,%s)*\)$"
                                    % (_possibly_complemented_complex_location,
                                       _possibly_complemented_complex_location))
  
  
  assert _re_simple_location.match("104..160")
  assert not _re_simple_location.match("68451760..68452073^68452074")
  assert not _re_simple_location.match("<104..>160")
  assert not _re_simple_location.match("104")
  assert not _re_simple_location.match("<1")
  assert not _re_simple_location.match(">99999")
  assert not _re_simple_location.match("join(104..160,320..390,504..579)")
  assert not _re_simple_compound.match("bond(12,63)")
  assert _re_simple_compound.match("join(104..160,320..390,504..579)")
  assert _re_simple_compound.match("order(1..69,1308..1465)")
  assert not _re_simple_compound.match("order(1..69,1308..1465,1524)")
  assert not _re_simple_compound.match("join(<1..442,992..1228,1524..>1983)")
  assert not _re_simple_compound.match("join(<1..181,254..336,422..497,574..>590)")
  assert not _re_simple_compound.match("join(1475..1577,2841..2986,3074..3193,3314..3481,4126..>4215)")
  assert not _re_simple_compound.match("test(1..69,1308..1465)")
  assert not _re_simple_compound.match("complement(1..69)")
  assert not _re_simple_compound.match("(1..69)")
  assert _re_complex_location.match("(3.9)..10")
  assert _re_complex_location.match("26..(30.33)")
  assert _re_complex_location.match("(13.19)..(20.28)")
  assert _re_complex_location.match("41^42")  # between
  assert _re_complex_location.match("AL121804:41^42")
  assert _re_complex_location.match("AL121804:41..610")
  assert _re_complex_location.match("AL121804.2:41..610")
  assert _re_complex_location.match("AL358792.24.1.166931:3274..3461")  # lots of dots in external reference
  assert _re_complex_location.match("one-of(3,6)..101")
  assert _re_complex_compound.match("join(153490..154269,AL121804.2:41..610,AL121804.2:672..1487)")
  assert not _re_simple_compound.match("join(153490..154269,AL121804.2:41..610,AL121804.2:672..1487)")
  assert _re_complex_compound.match("join(complement(69611..69724),139856..140650)")
  assert _re_complex_compound.match("join(complement(AL354868.10.1.164018:80837..81016),complement(AL354868.10.1.164018:80539..80835))")
  
  # Trans-spliced example from NC_016406, note underscore in reference name:
  assert _re_complex_location.match("NC_016402.1:6618..6676")
  assert _re_complex_location.match("181647..181905")
  assert _re_complex_compound.match("join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)")
  assert not _re_complex_location.match("join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)")
  assert not _re_simple_compound.match("join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)")
  assert not _re_complex_location.match("join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)")
  assert not _re_simple_location.match("join(complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905)")
  
  _solo_bond = re.compile("bond\(%s\)" % _solo_location)
  assert _solo_bond.match("bond(196)")
  assert _solo_bond.search("bond(196)")
  assert _solo_bond.search("join(bond(284),bond(305),bond(309),bond(305))")
  
  
  def _pos(pos_str, offset=0):
      """Build a Position object (PRIVATE).
  
      For an end position, leave offset as zero (default):
  
      >>> _pos("5")
      ExactPosition(5)
  
      For a start position, set offset to minus one (for Python counting):
  
      >>> _pos("5", -1)
      ExactPosition(4)
  
      This also covers fuzzy positions:
  
      >>> p = _pos("<5")
      >>> p
      BeforePosition(5)
      >>> print(p)
      <5
      >>> int(p)
      5
  
      >>> _pos(">5")
      AfterPosition(5)
  
      By default assumes an end position, so note the integer behaviour:
  
      >>> p = _pos("one-of(5,8,11)")
      >>> p
      OneOfPosition(11, choices=[ExactPosition(5), ExactPosition(8), ExactPosition(11)])
      >>> print(p)
      one-of(5,8,11)
      >>> int(p)
      11
  
      >>> _pos("(8.10)")
      WithinPosition(10, left=8, right=10)
  
      Fuzzy start positions:
  
      >>> p = _pos("<5", -1)
      >>> p
      BeforePosition(4)
      >>> print(p)
      <4
      >>> int(p)
      4
  
      Notice how the integer behaviour changes too!
  
      >>> p = _pos("one-of(5,8,11)", -1)
      >>> p
      OneOfPosition(4, choices=[ExactPosition(4), ExactPosition(7), ExactPosition(10)])
      >>> print(p)
      one-of(4,7,10)
      >>> int(p)
      4
  
      """
      if pos_str.startswith("<"):
          return SeqFeature.BeforePosition(int(pos_str[1:]) + offset)
      elif pos_str.startswith(">"):
          return SeqFeature.AfterPosition(int(pos_str[1:]) + offset)
      elif _re_within_position.match(pos_str):
          s, e = pos_str[1:-1].split(".")
          s = int(s) + offset
          e = int(e) + offset
          if offset == -1:
              default = s
          else:
              default = e
          return SeqFeature.WithinPosition(default, left=s, right=e)
      elif _re_oneof_position.match(pos_str):
          assert pos_str.startswith("one-of(")
          assert pos_str[-1] == ")"
          parts = [SeqFeature.ExactPosition(int(pos) + offset)
                   for pos in pos_str[7:-1].split(",")]
          if offset == -1:
              default = min(int(pos) for pos in parts)
          else:
              default = max(int(pos) for pos in parts)
          return SeqFeature.OneOfPosition(default, choices=parts)
      else:
          return SeqFeature.ExactPosition(int(pos_str) + offset)
  
  
  def _loc(loc_str, expected_seq_length, strand):
      """FeatureLocation from non-compound non-complement location (PRIVATE).
  
      Simple examples,
  
      >>> _loc("123..456", 1000, +1)
      FeatureLocation(ExactPosition(122), ExactPosition(456), strand=1)
      >>> _loc("<123..>456", 1000, strand = -1)
      FeatureLocation(BeforePosition(122), AfterPosition(456), strand=-1)
  
      A more complex location using within positions,
  
      >>> _loc("(9.10)..(20.25)", 1000, 1)
      FeatureLocation(WithinPosition(8, left=8, right=9), WithinPosition(25, left=20, right=25), strand=1)
  
      Notice how that will act as though it has overall start 8 and end 25.
  
      Zero length between feature,
  
      >>> _loc("123^124", 1000, 0)
      FeatureLocation(ExactPosition(123), ExactPosition(123), strand=0)
  
      The expected sequence length is needed for a special case, a between
      position at the start/end of a circular genome:
  
      >>> _loc("1000^1", 1000, 1)
      FeatureLocation(ExactPosition(1000), ExactPosition(1000), strand=1)
  
      Apart from this special case, between positions P^Q must have P+1==Q,
  
      >>> _loc("123^456", 1000, 1)
      Traceback (most recent call last):
         ...
      ValueError: Invalid between location '123^456'
  
      You can optionally provide a reference name:
  
      >>> _loc("AL391218.9:105173..108462", 2000000, 1)
      FeatureLocation(ExactPosition(105172), ExactPosition(108462), strand=1, ref='AL391218.9')
  
      """
      if ":" in loc_str:
          ref, loc_str = loc_str.split(":")
      else:
          ref = None
      try:
          s, e = loc_str.split("..")
      except ValueError:
          assert ".." not in loc_str
          if "^" in loc_str:
              # A between location like "67^68" (one based counting) is a
              # special case (note it has zero length). In python slice
              # notation this is 67:67, a zero length slice.  See Bug 2622
              # Further more, on a circular genome of length N you can have
              # a location N^1 meaning the junction at the origin. See Bug 3098.
              # NOTE - We can imagine between locations like "2^4", but this
              # is just "3".  Similarly, "2^5" is just "3..4"
              s, e = loc_str.split("^")
              if int(s) + 1 == int(e):
                  pos = _pos(s)
              elif int(s) == expected_seq_length and e == "1":
                  pos = _pos(s)
              else:
                  raise ValueError("Invalid between location %s" % repr(loc_str))
              return SeqFeature.FeatureLocation(pos, pos, strand, ref=ref)
          else:
              # e.g. "123"
              s = loc_str
              e = loc_str
      return SeqFeature.FeatureLocation(_pos(s, -1), _pos(e), strand, ref=ref)
  
  
  def _split_compound_loc(compound_loc):
      """Split a tricky compound location string (PRIVATE).
  
      >>> list(_split_compound_loc("123..145"))
      ['123..145']
      >>> list(_split_compound_loc("123..145,200..209"))
      ['123..145', '200..209']
      >>> list(_split_compound_loc("one-of(200,203)..300"))
      ['one-of(200,203)..300']
      >>> list(_split_compound_loc("complement(123..145),200..209"))
      ['complement(123..145)', '200..209']
      >>> list(_split_compound_loc("123..145,one-of(200,203)..209"))
      ['123..145', 'one-of(200,203)..209']
      >>> list(_split_compound_loc("123..145,one-of(200,203)..one-of(209,211),300"))
      ['123..145', 'one-of(200,203)..one-of(209,211)', '300']
      >>> list(_split_compound_loc("123..145,complement(one-of(200,203)..one-of(209,211)),300"))
      ['123..145', 'complement(one-of(200,203)..one-of(209,211))', '300']
      >>> list(_split_compound_loc("123..145,200..one-of(209,211),300"))
      ['123..145', '200..one-of(209,211)', '300']
      >>> list(_split_compound_loc("123..145,200..one-of(209,211)"))
      ['123..145', '200..one-of(209,211)']
      >>> list(_split_compound_loc("complement(149815..150200),complement(293787..295573),NC_016402.1:6618..6676,181647..181905"))
      ['complement(149815..150200)', 'complement(293787..295573)', 'NC_016402.1:6618..6676', '181647..181905']
      """
      if "one-of(" in compound_loc:
          # Hard case
          while "," in compound_loc:
              assert compound_loc[0] != ","
              assert compound_loc[0:2] != ".."
              i = compound_loc.find(",")
              part = compound_loc[:i]
              compound_loc = compound_loc[i:]  # includes the comma
              while part.count("(") > part.count(")"):
                  assert "one-of(" in part, (part, compound_loc)
                  i = compound_loc.find(")")
                  part += compound_loc[:i + 1]
                  compound_loc = compound_loc[i + 1:]
              if compound_loc.startswith(".."):
                  i = compound_loc.find(",")
                  if i == -1:
                      part += compound_loc
                      compound_loc = ""
                  else:
                      part += compound_loc[:i]
                      compound_loc = compound_loc[i:]  # includes the comma
              while part.count("(") > part.count(")"):
                  assert part.count("one-of(") == 2
                  i = compound_loc.find(")")
                  part += compound_loc[:i + 1]
                  compound_loc = compound_loc[i + 1:]
              if compound_loc.startswith(","):
                  compound_loc = compound_loc[1:]
              assert part
              yield part
          if compound_loc:
              yield compound_loc
      else:
          # Easy case
          for part in compound_loc.split(","):
              yield part
  
  
  class Iterator(object):
      """Iterator interface to move over a file of GenBank entries one at a time (OBSOLETE).
  
      This class is likely to be deprecated in a future release of Biopython.
      Please use Bio.SeqIO.parse(..., format="gb") or Bio.GenBank.parse(...)
      for SeqRecord and GenBank specific Record objects respectively instead.
      """
      def __init__(self, handle, parser=None):
          """Initialize the iterator.
  
          Arguments:
  
              - handle - A handle with GenBank entries to iterate through.
              - parser - An optional parser to pass the entries through before
                returning them. If None, then the raw entry will be returned.
          """
          self.handle = handle
          self._parser = parser
  
      def __next__(self):
          """Return the next GenBank record from the handle.
  
          Will return None if we ran out of records.
          """
          if self._parser is None:
              lines = []
              while True:
                  line = self.handle.readline()
                  if not line:
                      return None  # Premature end of file?
                  lines.append(line)
                  if line.rstrip() == "//":
                      break
              return "".join(lines)
          try:
              return self._parser.parse(self.handle)
          except StopIteration:
              return None
  
      if sys.version_info[0] < 3:
          def next(self):
              """Python 2 style alias for Python 3 style __next__ method."""
              return self.__next__()
  
      def __iter__(self):
          return iter(self.__next__, None)
  
  
  class ParserFailureError(Exception):
      """Failure caused by some kind of problem in the parser.
      """
      pass
  
  
  class LocationParserError(Exception):
      """Could not Properly parse out a location from a GenBank file.
      """
      pass
  
  
  class FeatureParser(object):
      """Parse GenBank files into Seq + Feature objects (OBSOLETE).
  
      Direct use of this class is discouraged, and may be deprecated in
      a future release of Biopython.
  
      Please use Bio.SeqIO.parse(...) or Bio.SeqIO.read(...) instead.
      """
      def __init__(self, debug_level=0, use_fuzziness=1,
                   feature_cleaner=FeatureValueCleaner()):
          """Initialize a GenBank parser and Feature consumer.
  
          Arguments:
  
              - debug_level - An optional argument that species the amount of
                debugging information the parser should spit out. By default we have
                no debugging info (the fastest way to do things), but if you want
                you can set this as high as two and see exactly where a parse fails.
              - use_fuzziness - Specify whether or not to use fuzzy representations.
                The default is 1 (use fuzziness).
              - feature_cleaner - A class which will be used to clean out the
                values of features. This class must implement the function
                clean_value. GenBank.utils has a "standard" cleaner class, which
                is used by default.
          """
          self._scanner = GenBankScanner(debug_level)
          self.use_fuzziness = use_fuzziness
          self._cleaner = feature_cleaner
  
      def parse(self, handle):
          """Parse the specified handle.
          """
          _consumer = _FeatureConsumer(self.use_fuzziness,
                                       self._cleaner)
          self._scanner.feed(handle, _consumer)
          return _consumer.data
  
  
  class RecordParser(object):
      """Parse GenBank files into Record objects (OBSOLETE).
  
      Direct use of this class is discouraged, and may be deprecated in
      a future release of Biopython.
  
      Please use the Bio.GenBank.parse(...) or Bio.GenBank.read(...) functions
      instead.
      """
      def __init__(self, debug_level=0):
          """Initialize the parser.
  
          Arguments:
  
              - debug_level - An optional argument that species the amount of
                debugging information the parser should spit out. By default we have
                no debugging info (the fastest way to do things), but if you want
                you can set this as high as two and see exactly where a parse fails.
          """
          self._scanner = GenBankScanner(debug_level)
  
      def parse(self, handle):
          """Parse the specified handle into a GenBank record.
          """
          _consumer = _RecordConsumer()
  
          self._scanner.feed(handle, _consumer)
          return _consumer.data
  
  
  class _BaseGenBankConsumer(object):
      """Abstract GenBank consumer providing useful general functions (PRIVATE).
  
      This just helps to eliminate some duplication in things that most
      GenBank consumers want to do.
      """
      # Special keys in GenBank records that we should remove spaces from
      # For instance, \translation keys have values which are proteins and
      # should have spaces and newlines removed from them. This class
      # attribute gives us more control over specific formatting problems.
      remove_space_keys = ["translation"]
  
      def __init__(self):
          pass
  
      def _unhandled(self, data):
          pass
  
      def __getattr__(self, attr):
          return self._unhandled
  
      @staticmethod
      def _split_keywords(keyword_string):
          """Split a string of keywords into a nice clean list.
          """
          # process the keywords into a python list
          if keyword_string == "" or keyword_string == ".":
              keywords = ""
          elif keyword_string[-1] == '.':
              keywords = keyword_string[:-1]
          else:
              keywords = keyword_string
          keyword_list = keywords.split(';')
          clean_keyword_list = [x.strip() for x in keyword_list]
          return clean_keyword_list
  
      @staticmethod
      def _split_accessions(accession_string):
          """Split a string of accession numbers into a list.
          """
          # first replace all line feeds with spaces
          # Also, EMBL style accessions are split with ';'
          accession = accession_string.replace("\n", " ").replace(";", " ")
  
          return [x.strip() for x in accession.split() if x.strip()]
  
      @staticmethod
      def _split_taxonomy(taxonomy_string):
          """Split a string with taxonomy info into a list.
          """
          if not taxonomy_string or taxonomy_string == ".":
              # Missing data, no taxonomy
              return []
  
          if taxonomy_string[-1] == '.':
              tax_info = taxonomy_string[:-1]
          else:
              tax_info = taxonomy_string
          tax_list = tax_info.split(';')
          new_tax_list = []
          for tax_item in tax_list:
              new_items = tax_item.split("\n")
              new_tax_list.extend(new_items)
          while '' in new_tax_list:
              new_tax_list.remove('')
          clean_tax_list = [x.strip() for x in new_tax_list]
  
          return clean_tax_list
  
      @staticmethod
      def _clean_location(location_string):
          """Clean whitespace out of a location string.
  
          The location parser isn't a fan of whitespace, so we clean it out
          before feeding it into the parser.
          """
          # Originally this imported string.whitespace and did a replace
          # via a loop.  It's simpler to just split on whitespace and rejoin
          # the string - and this avoids importing string too.  See Bug 2684.
          return ''.join(location_string.split())
  
      @staticmethod
      def _remove_newlines(text):
          """Remove any newlines in the passed text, returning the new string.
          """
          # get rid of newlines in the qualifier value
          newlines = ["\n", "\r"]
          for ws in newlines:
              text = text.replace(ws, "")
  
          return text
  
      @staticmethod
      def _normalize_spaces(text):
          """Replace multiple spaces in the passed text with single spaces.
          """
          # get rid of excessive spaces
          return ' '.join(x for x in text.split(" ") if x)
  
      @staticmethod
      def _remove_spaces(text):
          """Remove all spaces from the passed text.
          """
          return text.replace(" ", "")
  
      @staticmethod
      def _convert_to_python_numbers(start, end):
          """Convert a start and end range to python notation.
  
          In GenBank, starts and ends are defined in "biological" coordinates,
          where 1 is the first base and [i, j] means to include both i and j.
  
          In python, 0 is the first base and [i, j] means to include i, but
          not j.
  
          So, to convert "biological" to python coordinates, we need to
          subtract 1 from the start, and leave the end and things should
          be converted happily.
          """
          new_start = start - 1
          new_end = end
  
          return new_start, new_end
  
  
  class _FeatureConsumer(_BaseGenBankConsumer):
      """Create a SeqRecord object with Features to return (PRIVATE).
  
      Attributes:
       - use_fuzziness - specify whether or not to parse with fuzziness in
         feature locations.
       - feature_cleaner - a class that will be used to provide specialized
         cleaning-up of feature values.
      """
      def __init__(self, use_fuzziness, feature_cleaner=None):
          from Bio.SeqRecord import SeqRecord
          _BaseGenBankConsumer.__init__(self)
          self.data = SeqRecord(None, id=None)
          self.data.id = None
          self.data.description = ""
  
          self._use_fuzziness = use_fuzziness
          self._feature_cleaner = feature_cleaner
  
          self._seq_type = ''
          self._seq_data = []
          self._cur_reference = None
          self._cur_feature = None
          self._expected_size = None
  
      def locus(self, locus_name):
          """Set the locus name is set as the name of the Sequence.
          """
          self.data.name = locus_name
  
      def size(self, content):
          """Record the sequence length."""
          self._expected_size = int(content)
  
      def residue_type(self, type):
          """Record the sequence type (SEMI-OBSOLETE).
  
          This reflects the fact that the topology (linear/circular) and
          molecule type (e.g. DNA vs RNA) were a single field in early
          files. Current GenBank/EMBL files have two fields.
          """
          self._seq_type = type.strip()
  
      def topology(self, topology):
          """Record the topology (linear or circular as strings)."""
          if topology:
              if topology not in ['linear', 'circular']:
                  raise ParserFailureError("Unexpected topology %r should be linear or circular" % topology)
              self.data.annotations['topology'] = topology
  
      def molecule_type(self, mol_type):
          """Record the molecule type (for round-trip etc)."""
          if mol_type:
              if "circular" in mol_type or 'linear' in mol_type:
                  raise ParserFailureError("Molecule type %r should not include topology" % mol_type)
              self.data.annotations['molecule_type'] = mol_type
  
      def data_file_division(self, division):
          self.data.annotations['data_file_division'] = division
  
      def date(self, submit_date):
          self.data.annotations['date'] = submit_date
  
      def definition(self, definition):
          """Set the definition as the description of the sequence.
          """
          if self.data.description:
              # Append to any existing description
              # e.g. EMBL files with two DE lines.
              self.data.description += " " + definition
          else:
              self.data.description = definition
  
      def accession(self, acc_num):
          """Set the accession number as the id of the sequence.
  
          If we have multiple accession numbers, the first one passed is
          used.
          """
          new_acc_nums = self._split_accessions(acc_num)
  
          # Also record them ALL in the annotations
          try:
              # On the off chance there was more than one accession line:
              for acc in new_acc_nums:
                  # Prevent repeat entries
                  if acc not in self.data.annotations['accessions']:
                      self.data.annotations['accessions'].append(acc)
          except KeyError:
              self.data.annotations['accessions'] = new_acc_nums
  
          # if we haven't set the id information yet, add the first acc num
          if not self.data.id:
              if len(new_acc_nums) > 0:
                  # self.data.id = new_acc_nums[0]
                  # Use the FIRST accession as the ID, not the first on this line!
                  self.data.id = self.data.annotations['accessions'][0]
  
      def wgs(self, content):
          self.data.annotations['wgs'] = content.split('-')
  
      def add_wgs_scafld(self, content):
          self.data.annotations.setdefault('wgs_scafld', []).append(content.split('-'))
  
      def nid(self, content):
          self.data.annotations['nid'] = content
  
      def pid(self, content):
          self.data.annotations['pid'] = content
  
      def version(self, version_id):
          # Want to use the versioned accession as the record.id
          # This comes from the VERSION line in GenBank files, or the
          # obsolete SV line in EMBL.  For the new EMBL files we need
          # both the version suffix from the ID line and the accession
          # from the AC line.
          if version_id.count(".") == 1 and version_id.split(".")[1].isdigit():
              self.accession(version_id.split(".")[0])
              self.version_suffix(version_id.split(".")[1])
          elif version_id:
              # For backwards compatibility...
              self.data.id = version_id
  
      def project(self, content):
          """Handle the information from the PROJECT line as a list of projects.
  
          e.g.::
  
              PROJECT     GenomeProject:28471
  
          or::
  
              PROJECT     GenomeProject:13543  GenomeProject:99999
  
          This is stored as dbxrefs in the SeqRecord to be consistent with the
          projected switch of this line to DBLINK in future GenBank versions.
          Note the NCBI plan to replace "GenomeProject:28471" with the shorter
          "Project:28471" as part of this transition.
          """
          content = content.replace("GenomeProject:", "Project:")
          self.data.dbxrefs.extend(p for p in content.split() if p)
  
      def dblink(self, content):
          """Store DBLINK cross references as dbxrefs in our record object.
  
          This line type is expected to replace the PROJECT line in 2009. e.g.
  
          During transition::
  
              PROJECT     GenomeProject:28471
              DBLINK      Project:28471
                          Trace Assembly Archive:123456
  
          Once the project line is dropped::
  
              DBLINK      Project:28471
                          Trace Assembly Archive:123456
  
          Note GenomeProject -> Project.
  
          We'll have to see some real examples to be sure, but based on the
          above example we can expect one reference per line.
  
          Note that at some point the NCBI have included an extra space, e.g.::
  
              DBLINK      Project: 28471
  
          """
          # During the transition period with both PROJECT and DBLINK lines,
          # we don't want to add the same cross reference twice.
          while ": " in content:
              content = content.replace(": ", ":")
          if content.strip() not in self.data.dbxrefs:
              self.data.dbxrefs.append(content.strip())
  
      def version_suffix(self, version):
          """Set the version to overwrite the id.
  
          Since the version provides the same information as the accession
          number, plus some extra info, we set this as the id if we have
          a version.
          """
          # e.g. GenBank line:
          # VERSION     U49845.1  GI:1293613
          # or the obsolete EMBL line:
          # SV   U49845.1
          # Scanner calls consumer.version("U49845.1")
          # which then calls consumer.version_suffix(1)
          #
          # e.g. EMBL new line:
          # ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
          # Scanner calls consumer.version_suffix(1)
          assert version.isdigit()
          self.data.annotations['sequence_version'] = int(version)
  
      def db_source(self, content):
          self.data.annotations['db_source'] = content.rstrip()
  
      def gi(self, content):
          self.data.annotations['gi'] = content
  
      def keywords(self, content):
          if 'keywords' in self.data.annotations:
              # Multi-line keywords, append to list
              # Note EMBL states "A keyword is never split between lines."
              self.data.annotations['keywords'].extend(self._split_keywords(content))
          else:
              self.data.annotations['keywords'] = self._split_keywords(content)
  
      def segment(self, content):
          self.data.annotations['segment'] = content
  
      def source(self, content):
          # Note that some software (e.g. VectorNTI) may produce an empty
          # source (rather than using a dot/period as might be expected).
          if content == "":
              source_info = ""
          elif content[-1] == '.':
              source_info = content[:-1]
          else:
              source_info = content
          self.data.annotations['source'] = source_info
  
      def organism(self, content):
          self.data.annotations['organism'] = content
  
      def taxonomy(self, content):
          """Records (another line of) the taxonomy lineage.
          """
          lineage = self._split_taxonomy(content)
          try:
              self.data.annotations['taxonomy'].extend(lineage)
          except KeyError:
              self.data.annotations['taxonomy'] = lineage
  
      def reference_num(self, content):
          """Signal the beginning of a new reference object.
          """
          # if we have a current reference that hasn't been added to
          # the list of references, add it.
          if self._cur_reference is not None:
              self.data.annotations['references'].append(self._cur_reference)
          else:
              self.data.annotations['references'] = []
  
          self._cur_reference = SeqFeature.Reference()
  
      def reference_bases(self, content):
          """Attempt to determine the sequence region the reference entails.
  
          Possible types of information we may have to deal with:
  
          (bases 1 to 86436)
          (sites)
          (bases 1 to 105654; 110423 to 111122)
          1  (residues 1 to 182)
          """
          # first remove the parentheses
          assert content.endswith(")"), content
          ref_base_info = content[1:-1]
  
          all_locations = []
          # parse if we've got 'bases' and 'to'
          if 'bases' in ref_base_info and 'to' in ref_base_info:
              # get rid of the beginning 'bases'
              ref_base_info = ref_base_info[5:]
              locations = self._split_reference_locations(ref_base_info)
              all_locations.extend(locations)
          elif 'residues' in ref_base_info and 'to' in ref_base_info:
              residues_start = ref_base_info.find("residues")
              # get only the information after "residues"
              ref_base_info = ref_base_info[(residues_start + len("residues ")):]
              locations = self._split_reference_locations(ref_base_info)
              all_locations.extend(locations)
  
          # make sure if we are not finding information then we have
          # the string 'sites' or the string 'bases'
          elif (ref_base_info == 'sites' or
                ref_base_info.strip() == 'bases'):
              pass
          # otherwise raise an error
          else:
              raise ValueError("Could not parse base info %s in record %s" %
                               (ref_base_info, self.data.id))
  
          self._cur_reference.location = all_locations
  
      def _split_reference_locations(self, location_string):
          """Get reference locations out of a string of reference information
  
          The passed string should be of the form::
  
              1 to 20; 20 to 100
  
          This splits the information out and returns a list of location objects
          based on the reference locations.
          """
          # split possibly multiple locations using the ';'
          all_base_info = location_string.split(';')
  
          new_locations = []
          for base_info in all_base_info:
              start, end = base_info.split('to')
              new_start, new_end = \
                  self._convert_to_python_numbers(int(start.strip()),
                                                  int(end.strip()))
              this_location = SeqFeature.FeatureLocation(new_start, new_end)
              new_locations.append(this_location)
          return new_locations
  
      def authors(self, content):
          if self._cur_reference.authors:
              self._cur_reference.authors += ' ' + content
          else:
              self._cur_reference.authors = content
  
      def consrtm(self, content):
          if self._cur_reference.consrtm:
              self._cur_reference.consrtm += ' ' + content
          else:
              self._cur_reference.consrtm = content
  
      def title(self, content):
          if self._cur_reference is None:
              import warnings
              from Bio import BiopythonParserWarning
              warnings.warn("GenBank TITLE line without REFERENCE line.",
                            BiopythonParserWarning)
          elif self._cur_reference.title:
              self._cur_reference.title += ' ' + content
          else:
              self._cur_reference.title = content
  
      def journal(self, content):
          if self._cur_reference.journal:
              self._cur_reference.journal += ' ' + content
          else:
              self._cur_reference.journal = content
  
      def medline_id(self, content):
          self._cur_reference.medline_id = content
  
      def pubmed_id(self, content):
          self._cur_reference.pubmed_id = content
  
      def remark(self, content):
          """Deal with a reference comment."""
          if self._cur_reference.comment:
              self._cur_reference.comment += ' ' + content
          else:
              self._cur_reference.comment = content
  
      def comment(self, content):
          try:
              self.data.annotations['comment'] += "\n" + "\n".join(content)
          except KeyError:
              self.data.annotations['comment'] = "\n".join(content)
  
      def structured_comment(self, content):
          self.data.annotations['structured_comment'] = content
  
      def features_line(self, content):
          """Get ready for the feature table when we reach the FEATURE line.
          """
          self.start_feature_table()
  
      def start_feature_table(self):
          """Indicate we've got to the start of the feature table.
          """
          # make sure we've added on our last reference object
          if self._cur_reference is not None:
              self.data.annotations['references'].append(self._cur_reference)
              self._cur_reference = None
  
      def feature_key(self, content):
          # start a new feature
          self._cur_feature = SeqFeature.SeqFeature()
          self._cur_feature.type = content
          self.data.features.append(self._cur_feature)
  
      def location(self, content):
          """Parse out location information from the location string.
  
          This uses simple Python code with some regular expressions to do the
          parsing, and then translates the results into appropriate objects.
          """
          # clean up newlines and other whitespace inside the location before
          # parsing - locations should have no whitespace whatsoever
          location_line = self._clean_location(content)
  
          # Older records have junk like replace(266,"c") in the
          # location line. Newer records just replace this with
          # the number 266 and have the information in a more reasonable
          # place. So we'll just grab out the number and feed this to the
          # parser. We shouldn't really be losing any info this way.
          if 'replace' in location_line:
              comma_pos = location_line.find(',')
              location_line = location_line[8:comma_pos]
  
          cur_feature = self._cur_feature
  
          # Handle top level complement here for speed
          if location_line.startswith("complement("):
              assert location_line.endswith(")")
              location_line = location_line[11:-1]
              strand = -1
          elif "PROTEIN" in self._seq_type.upper():
              strand = None
          else:
              # Assume nucleotide otherwise feature strand for
              # GenBank files with bad LOCUS lines set to None
              strand = 1
  
          # Special case handling of the most common cases for speed
          if _re_simple_location.match(location_line):
              # e.g. "123..456"
              s, e = location_line.split("..")
              cur_feature.location = SeqFeature.FeatureLocation(int(s) - 1,
                                                                int(e),
                                                                strand)
              return
  
          if ",)" in location_line:
              import warnings
              from Bio import BiopythonParserWarning
              warnings.warn("Dropping trailing comma in malformed feature location",
                            BiopythonParserWarning)
              location_line = location_line.replace(",)", ")")
  
          if _solo_bond.search(location_line):
              # e.g. bond(196)
              # e.g. join(bond(284),bond(305),bond(309),bond(305))
              import warnings
              from Bio import BiopythonParserWarning
              warnings.warn("Dropping bond qualifier in feature location", BiopythonParserWarning)
              # There ought to be a better way to do this...
              for x in _solo_bond.finditer(location_line):
                  x = x.group()
                  location_line = location_line.replace(x, x[5:-1])
  
          if _re_simple_compound.match(location_line):
              # e.g. join(<123..456,480..>500)
              i = location_line.find("(")
              # cur_feature.location_operator = location_line[:i]
              # we can split on the comma because these are simple locations
              locs = []
              for part in location_line[i + 1:-1].split(","):
                  s, e = part.split("..")
                  locs.append(SeqFeature.FeatureLocation(int(s) - 1,
                                                         int(e),
                                                         strand))
              if len(locs) < 2:
                  # The CompoundLocation will raise a ValueError here!
                  import warnings
                  from Bio import BiopythonParserWarning
                  warnings.warn("Should have at least 2 parts for compound location",
                                BiopythonParserWarning)
                  cur_feature.location = None
                  return
              if strand == -1:
                  cur_feature.location = SeqFeature.CompoundLocation(locs[::-1],
                                                                     operator=location_line[:i])
              else:
                  cur_feature.location = SeqFeature.CompoundLocation(locs,
                                                                     operator=location_line[:i])
              return
  
          # Handle the general case with more complex regular expressions
          if _re_complex_location.match(location_line):
              # e.g. "AL121804.2:41..610"
              cur_feature.location = _loc(location_line, self._expected_size, strand)
              return
  
          if _re_complex_compound.match(location_line):
              i = location_line.find("(")
              # cur_feature.location_operator = location_line[:i]
              # Can't split on the comma because of positions like one-of(1,2,3)
              locs = []
              for part in _split_compound_loc(location_line[i + 1:-1]):
                  if part.startswith("complement("):
                      assert part[-1] == ")"
                      part = part[11:-1]
                      assert strand != -1, "Double complement?"
                      part_strand = -1
                  else:
                      part_strand = strand
                  try:
                      loc = _loc(part, self._expected_size, part_strand)
                  except ValueError as err:
                      print(location_line)
                      print(part)
                      raise err
                  locs.append(loc)
              # Historically a join on the reverse strand has been represented
              # in Biopython with both the parent SeqFeature and its children
              # (the exons for a CDS) all given a strand of -1.  Likewise, for
              # a join feature on the forward strand they all have strand +1.
              # However, we must also consider evil mixed strand examples like
              # this, join(complement(69611..69724),139856..140087,140625..140650)
              if strand == -1:
                  # Whole thing was wrapped in complement(...)
                  for l in locs:
                      assert l.strand == -1
                  # Reverse the backwards order used in GenBank files
                  # with complement(join(...))
                  cur_feature.location = SeqFeature.CompoundLocation(locs[::-1],
                                                                     operator=location_line[:i])
              else:
                  cur_feature.location = SeqFeature.CompoundLocation(locs,
                                                                     operator=location_line[:i])
              return
          # Not recognised
          if "order" in location_line and "join" in location_line:
              # See Bug 3197
              msg = 'Combinations of "join" and "order" within the same ' + \
                    'location (nested operators) are illegal:\n' + location_line
              raise LocationParserError(msg)
          # This used to be an error....
          cur_feature.location = None
          import warnings
          from Bio import BiopythonParserWarning
          warnings.warn(BiopythonParserWarning("Couldn't parse feature location: %r"
                                               % location_line))
  
      def feature_qualifier(self, key, value):
          """When we get a qualifier key and its value.
  
          Can receive None, since you can have valueless keys such as /pseudo
          """
          # Hack to try to preserve historical behaviour of /pseudo etc
          if value is None:
              # if the key doesn't exist yet, add an empty string
              if key not in self._cur_feature.qualifiers:
                  self._cur_feature.qualifiers[key] = [""]
                  return
              # otherwise just skip this key
              return
  
          value = value.replace('"', '')
          if self._feature_cleaner is not None:
              value = self._feature_cleaner.clean_value(key, value)
  
          # if the qualifier name exists, append the value
          if key in self._cur_feature.qualifiers:
              self._cur_feature.qualifiers[key].append(value)
          # otherwise start a new list of the key with its values
          else:
              self._cur_feature.qualifiers[key] = [value]
  
      def feature_qualifier_name(self, content_list):
          """Use feature_qualifier instead (OBSOLETE)."""
          raise NotImplementedError("Use the feature_qualifier method instead.")
  
      def feature_qualifier_description(self, content):
          """Use feature_qualifier instead (OBSOLETE)."""
          raise NotImplementedError("Use the feature_qualifier method instead.")
  
      def contig_location(self, content):
          """Deal with CONTIG information."""
          # Historically this was stored as a SeqFeature object, but it was
          # stored under record.annotations["contig"] and not under
          # record.features with the other SeqFeature objects.
          #
          # The CONTIG location line can include additional tokens like
          # Gap(), Gap(100) or Gap(unk100) which are not used in the feature
          # location lines, so storing it using SeqFeature based location
          # objects is difficult.
          #
          # We now store this a string, which means for BioSQL we are now in
          # much better agreement with how BioPerl records the CONTIG line
          # in the database.
          #
          # NOTE - This code assumes the scanner will return all the CONTIG
          # lines already combined into one long string!
          self.data.annotations["contig"] = content
  
      def origin_name(self, content):
          pass
  
      def base_count(self, content):
          pass
  
      def base_number(self, content):
          pass
  
      def sequence(self, content):
          """Add up sequence information as we get it.
  
          To try and make things speedier, this puts all of the strings
          into a list of strings, and then uses string.join later to put
          them together. Supposedly, this is a big time savings
          """
          assert ' ' not in content
          self._seq_data.append(content.upper())
  
      def record_end(self, content):
          """Clean up when we've finished the record.
          """
          from Bio import Alphabet
          from Bio.Alphabet import IUPAC
          from Bio.Seq import Seq, UnknownSeq
  
          # Try and append the version number to the accession for the full id
          if not self.data.id:
              assert 'accessions' not in self.data.annotations, \
                     self.data.annotations['accessions']
              self.data.id = self.data.name  # Good fall back?
          elif self.data.id.count('.') == 0:
              try:
                  self.data.id += '.%i' % self.data.annotations['sequence_version']
              except KeyError:
                  pass
  
          # add the sequence information
          # first, determine the alphabet
          # we default to an generic alphabet if we don't have a
          # seq type or have strange sequence information.
          seq_alphabet = Alphabet.generic_alphabet
  
          # now set the sequence
          sequence = "".join(self._seq_data)
  
          if self._expected_size is not None \
                  and len(sequence) != 0 \
                  and self._expected_size != len(sequence):
              import warnings
              from Bio import BiopythonParserWarning
              warnings.warn("Expected sequence length %i, found %i (%s)."
                            % (self._expected_size, len(sequence), self.data.id),
                            BiopythonParserWarning)
  
          if self._seq_type:
              # mRNA is really also DNA, since it is actually cDNA
              if 'DNA' in self._seq_type.upper() or 'MRNA' in self._seq_type.upper():
                  seq_alphabet = IUPAC.ambiguous_dna
              # are there ever really RNA sequences in GenBank?
              elif 'RNA' in self._seq_type.upper():
                  # Even for data which was from RNA, the sequence string
                  # is usually given as DNA (T not U).  Bug 2408
                  if "T" in sequence and "U" not in sequence:
                      seq_alphabet = IUPAC.ambiguous_dna
                  else:
                      seq_alphabet = IUPAC.ambiguous_rna
              elif 'PROTEIN' in self._seq_type.upper() \
                      or self._seq_type == "PRT":  # PRT is used in EMBL-bank for patents
                  seq_alphabet = IUPAC.protein  # or extended protein?
              # work around ugly GenBank records which have circular or
              # linear but no indication of sequence type
              elif self._seq_type in ["circular", "linear", "unspecified"]:
                  pass
              # we have a bug if we get here
              else:
                  raise ValueError("Could not determine alphabet for seq_type %s"
                                   % self._seq_type)
  
          if not sequence and self.__expected_size:
              self.data.seq = UnknownSeq(self._expected_size, seq_alphabet)
          else:
              self.data.seq = Seq(sequence, seq_alphabet)
  
  
  class _RecordConsumer(_BaseGenBankConsumer):
      """Create a GenBank Record object from scanner generated information (PRIVATE).
      """
      def __init__(self):
          _BaseGenBankConsumer.__init__(self)
          from . import Record
          self.data = Record.Record()
  
          self._seq_data = []
          self._cur_reference = None
          self._cur_feature = None
          self._cur_qualifier = None
  
      def wgs(self, content):
          self.data.wgs = content.split('-')
  
      def add_wgs_scafld(self, content):
          self.data.wgs_scafld.append(content.split('-'))
  
      def locus(self, content):
          self.data.locus = content
  
      def size(self, content):
          self.data.size = content
  
      def residue_type(self, content):
          # Be lenient about parsing, but technically lowercase residue types are malformed.
          if 'dna' in content or 'rna' in content:
              import warnings
              from Bio import BiopythonParserWarning
              warnings.warn("Invalid seq_type (%s): DNA/RNA should be uppercase." % content,
                            BiopythonParserWarning)
          self.data.residue_type = content
  
      def data_file_division(self, content):
          self.data.data_file_division = content
  
      def date(self, content):
          self.data.date = content
  
      def definition(self, content):
          self.data.definition = content
  
      def accession(self, content):
          for acc in self._split_accessions(content):
              if acc not in self.data.accession:
                  self.data.accession.append(acc)
  
      def nid(self, content):
          self.data.nid = content
  
      def pid(self, content):
          self.data.pid = content
  
      def version(self, content):
          self.data.version = content
  
      def db_source(self, content):
          self.data.db_source = content.rstrip()
  
      def gi(self, content):
          self.data.gi = content
  
      def keywords(self, content):
          self.data.keywords = self._split_keywords(content)
  
      def project(self, content):
          self.data.projects.extend(p for p in content.split() if p)
  
      def dblink(self, content):
          self.data.dblinks.append(content)
  
      def segment(self, content):
          self.data.segment = content
  
      def source(self, content):
          self.data.source = content
  
      def organism(self, content):
          self.data.organism = content
  
      def taxonomy(self, content):
          self.data.taxonomy = self._split_taxonomy(content)
  
      def reference_num(self, content):
          """Grab the reference number and signal the start of a new reference.
          """
          # check if we have a reference to add
          if self._cur_reference is not None:
              self.data.references.append(self._cur_reference)
  
          from . import Record
          self._cur_reference = Record.Reference()
          self._cur_reference.number = content
  
      def reference_bases(self, content):
          self._cur_reference.bases = content
  
      def authors(self, content):
          self._cur_reference.authors = content
  
      def consrtm(self, content):
          self._cur_reference.consrtm = content
  
      def title(self, content):
          if self._cur_reference is None:
              import warnings
              from Bio import BiopythonParserWarning
              warnings.warn("GenBank TITLE line without REFERENCE line.",
                            BiopythonParserWarning)
              return
          self._cur_reference.title = content
  
      def journal(self, content):
          self._cur_reference.journal = content
  
      def medline_id(self, content):
          self._cur_reference.medline_id = content
  
      def pubmed_id(self, content):
          self._cur_reference.pubmed_id = content
  
      def remark(self, content):
          self._cur_reference.remark = content
  
      def comment(self, content):
          self.data.comment += "\n".join(content)
  
      def structured_comment(self, content):
          self.data.structured_comment = content
  
      def primary_ref_line(self, content):
          """Data for the PRIMARY line"""
          self.data.primary.append(content)
  
      def primary(self, content):
          pass
  
      def features_line(self, content):
          """Get ready for the feature table when we reach the FEATURE line.
          """
          self.start_feature_table()
  
      def start_feature_table(self):
          """Signal the start of the feature table.
          """
          # we need to add on the last reference
          if self._cur_reference is not None:
              self.data.references.append(self._cur_reference)
  
      def feature_key(self, content):
          """Grab the key of the feature and signal the start of a new feature.
          """
          # first add on feature information if we've got any
          self._add_feature()
  
          from . import Record
          self._cur_feature = Record.Feature()
          self._cur_feature.key = content
  
      def _add_feature(self):
          """Utility function to add a feature to the Record.
  
          This does all of the appropriate checking to make sure we haven't
          left any info behind, and that we are only adding info if it
          exists.
          """
          if self._cur_feature is not None:
              # if we have a left over qualifier, add it to the qualifiers
              # on the current feature
              if self._cur_qualifier is not None:
                  self._cur_feature.qualifiers.append(self._cur_qualifier)
  
              self._cur_qualifier = None
              self.data.features.append(self._cur_feature)
  
      def location(self, content):
          self._cur_feature.location = self._clean_location(content)
  
      def feature_qualifier(self, key, value):
          self.feature_qualifier_name([key])
          if value is not None:
              self.feature_qualifier_description(value)
  
      def feature_qualifier_name(self, content_list):
          """Deal with qualifier names
  
          We receive a list of keys, since you can have valueless keys such as
          /pseudo which would be passed in with the next key (since no other
          tags separate them in the file)
          """
          from . import Record
          for content in content_list:
              # the record parser keeps the /s -- add them if we don't have 'em
              if not content.startswith("/"):
                  content = "/%s" % content
              # add on a qualifier if we've got one
              if self._cur_qualifier is not None:
                  self._cur_feature.qualifiers.append(self._cur_qualifier)
  
              self._cur_qualifier = Record.Qualifier()
              self._cur_qualifier.key = content
  
      def feature_qualifier_description(self, content):
          # if we have info then the qualifier key should have a ='s
          if '=' not in self._cur_qualifier.key:
              self._cur_qualifier.key = "%s=" % self._cur_qualifier.key
          cur_content = self._remove_newlines(content)
          # remove all spaces from the value if it is a type where spaces
          # are not important
          for remove_space_key in self.__class__.remove_space_keys:
              if remove_space_key in self._cur_qualifier.key:
                  cur_content = self._remove_spaces(cur_content)
          self._cur_qualifier.value = self._normalize_spaces(cur_content)
  
      def base_count(self, content):
          self.data.base_counts = content
  
      def origin_name(self, content):
          self.data.origin = content
  
      def contig_location(self, content):
          """Signal that we have contig information to add to the record.
          """
          self.data.contig = self._clean_location(content)
  
      def sequence(self, content):
          """Add sequence information to a list of sequence strings.
  
          This removes spaces in the data and uppercases the sequence, and
          then adds it to a list of sequences. Later on we'll join this
          list together to make the final sequence. This is faster than
          adding on the new string every time.
          """
          assert ' ' not in content
          self._seq_data.append(content.upper())
  
      def record_end(self, content):
          """Signal the end of the record and do any necessary clean-up.
          """
          # add together all of the sequence parts to create the
          # final sequence string
          self.data.sequence = "".join(self._seq_data)
          # add on the last feature
          self._add_feature()
  
  
  def parse(handle):
      """Iterate over GenBank formatted entries as Record objects.
  
      >>> from Bio import GenBank
      >>> with open("GenBank/NC_000932.gb") as handle:
      ...     for record in GenBank.parse(handle):
      ...         print(record.accession)
      ['NC_000932']
  
      To get SeqRecord objects use Bio.SeqIO.parse(..., format="gb")
      instead.
      """
      return iter(Iterator(handle, RecordParser()))
  
  
  def read(handle):
      """Read a handle containing a single GenBank entry as a Record object.
  
      >>> from Bio import GenBank
      >>> with open("GenBank/NC_000932.gb") as handle:
      ...     record = GenBank.read(handle)
      ...     print(record.accession)
      ['NC_000932']
  
      To get a SeqRecord object use Bio.SeqIO.read(..., format="gb")
      instead.
      """
      iterator = parse(handle)
      try:
          first = next(iterator)
      except StopIteration:
          first = None
      if first is None:
          raise ValueError("No records found in handle")
      try:
          second = next(iterator)
      except StopIteration:
          second = None
      if second is not None:
          raise ValueError("More than one record found in handle")
      return first
  
  
  if __name__ == "__main__":
      from Bio._utils import run_doctest
      run_doctest()
  